Potassium in PDB 2dcn: Crystal Structure of 2-Keto-3-Deoxygluconate Kinase From Sulfolobus Tokodaii Complexed with 2-Keto-6-Phosphogluconate (Alpha-Furanose Form)
Enzymatic activity of Crystal Structure of 2-Keto-3-Deoxygluconate Kinase From Sulfolobus Tokodaii Complexed with 2-Keto-6-Phosphogluconate (Alpha-Furanose Form)
All present enzymatic activity of Crystal Structure of 2-Keto-3-Deoxygluconate Kinase From Sulfolobus Tokodaii Complexed with 2-Keto-6-Phosphogluconate (Alpha-Furanose Form):
2.7.1.45;
Protein crystallography data
The structure of Crystal Structure of 2-Keto-3-Deoxygluconate Kinase From Sulfolobus Tokodaii Complexed with 2-Keto-6-Phosphogluconate (Alpha-Furanose Form), PDB code: 2dcn
was solved by
S.Okazaki,
H.Onda,
A.Suzuki,
S.Kuramitsu,
R.Masui,
T.Yamane,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
46.37 /
2.25
|
|
Space group
|
P 1 21 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
84.638,
150.229,
154.757,
90.00,
93.73,
90.00
|
|
R / Rfree (%)
|
17.5 /
22.8
|
Other elements in 2dcn:
The structure of Crystal Structure of 2-Keto-3-Deoxygluconate Kinase From Sulfolobus Tokodaii Complexed with 2-Keto-6-Phosphogluconate (Alpha-Furanose Form) also contains other interesting chemical elements:
Potassium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
12;
Binding sites:
The binding sites of Potassium atom in the Crystal Structure of 2-Keto-3-Deoxygluconate Kinase From Sulfolobus Tokodaii Complexed with 2-Keto-6-Phosphogluconate (Alpha-Furanose Form)
(pdb code 2dcn). This binding sites where shown within
5.0 Angstroms radius around Potassium atom.
In total 12 binding sites of Potassium where determined in the
Crystal Structure of 2-Keto-3-Deoxygluconate Kinase From Sulfolobus Tokodaii Complexed with 2-Keto-6-Phosphogluconate (Alpha-Furanose Form), PDB code: 2dcn:
Jump to Potassium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Potassium binding site 1 out
of 12 in 2dcn
Go back to
Potassium Binding Sites List in 2dcn
Potassium binding site 1 out
of 12 in the Crystal Structure of 2-Keto-3-Deoxygluconate Kinase From Sulfolobus Tokodaii Complexed with 2-Keto-6-Phosphogluconate (Alpha-Furanose Form)
 Mono view
 Stereo pair view
|
|
A full contact list of Potassium with other atoms in the K binding
site number 1 of Crystal Structure of 2-Keto-3-Deoxygluconate Kinase From Sulfolobus Tokodaii Complexed with 2-Keto-6-Phosphogluconate (Alpha-Furanose Form) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K5001
b:21.4
occ:1.00
|
O
|
A:ASN286
|
2.8
|
18.6
|
1.0
|
|
O
|
A:ILE289
|
2.8
|
19.4
|
1.0
|
|
O
|
A:THR252
|
2.8
|
22.3
|
1.0
|
|
O
|
A:ASP250
|
2.9
|
20.1
|
1.0
|
|
O
|
A:GLY291
|
3.0
|
20.3
|
1.0
|
|
O
|
A:HOH5048
|
3.0
|
19.8
|
1.0
|
|
ND2
|
A:ASN286
|
3.2
|
17.1
|
1.0
|
|
C
|
A:ASN286
|
3.7
|
18.7
|
1.0
|
|
C
|
A:GLY291
|
3.8
|
19.9
|
1.0
|
|
C
|
A:ILE289
|
4.0
|
19.2
|
1.0
|
|
C
|
A:THR252
|
4.0
|
22.2
|
1.0
|
|
C
|
A:ASP250
|
4.0
|
20.7
|
1.0
|
|
CG
|
A:ASN286
|
4.1
|
19.6
|
1.0
|
|
N
|
A:GLY291
|
4.2
|
18.3
|
1.0
|
|
CB
|
A:ASP250
|
4.3
|
20.6
|
1.0
|
|
CA
|
A:ASP292
|
4.4
|
19.9
|
1.0
|
|
N
|
A:ASP292
|
4.4
|
20.1
|
1.0
|
|
N
|
A:VAL287
|
4.4
|
18.1
|
1.0
|
|
CA
|
A:VAL287
|
4.5
|
17.6
|
1.0
|
|
OD2
|
A:ASP250
|
4.5
|
20.1
|
1.0
|
|
N
|
A:THR252
|
4.5
|
21.6
|
1.0
|
|
CG2
|
A:ILE289
|
4.5
|
21.4
|
1.0
|
|
O
|
A:HOH5012
|
4.6
|
16.3
|
1.0
|
|
CG
|
A:ASP250
|
4.6
|
20.5
|
1.0
|
|
CA
|
A:ASN286
|
4.6
|
19.3
|
1.0
|
|
C
|
A:VAL251
|
4.6
|
21.3
|
1.0
|
|
CA
|
A:GLY291
|
4.7
|
19.2
|
1.0
|
|
CB
|
A:ASN286
|
4.7
|
19.5
|
1.0
|
|
OD1
|
A:ASP292
|
4.7
|
18.6
|
1.0
|
|
N
|
A:ILE289
|
4.7
|
19.3
|
1.0
|
|
C
|
A:ARG290
|
4.7
|
18.4
|
1.0
|
|
CA
|
A:ASP250
|
4.7
|
20.5
|
1.0
|
|
CA
|
A:THR252
|
4.8
|
21.9
|
1.0
|
|
OD1
|
A:ASN286
|
4.8
|
21.5
|
1.0
|
|
CA
|
A:ARG290
|
4.8
|
18.4
|
1.0
|
|
N
|
A:ARG290
|
4.8
|
18.8
|
1.0
|
|
CA
|
A:ILE289
|
4.9
|
19.9
|
1.0
|
|
C
|
A:VAL287
|
4.9
|
17.3
|
1.0
|
|
O
|
A:VAL251
|
4.9
|
21.7
|
1.0
|
|
N
|
A:VAL251
|
4.9
|
20.9
|
1.0
|
|
N
|
A:GLY253
|
5.0
|
22.4
|
1.0
|
|
Potassium binding site 2 out
of 12 in 2dcn
Go back to
Potassium Binding Sites List in 2dcn
Potassium binding site 2 out
of 12 in the Crystal Structure of 2-Keto-3-Deoxygluconate Kinase From Sulfolobus Tokodaii Complexed with 2-Keto-6-Phosphogluconate (Alpha-Furanose Form)
 Mono view
 Stereo pair view
|
|
A full contact list of Potassium with other atoms in the K binding
site number 2 of Crystal Structure of 2-Keto-3-Deoxygluconate Kinase From Sulfolobus Tokodaii Complexed with 2-Keto-6-Phosphogluconate (Alpha-Furanose Form) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:K5002
b:19.9
occ:1.00
|
O
|
B:ASN286
|
2.7
|
17.2
|
1.0
|
|
O
|
B:ILE289
|
2.8
|
20.3
|
1.0
|
|
O
|
B:ASP250
|
2.8
|
18.4
|
1.0
|
|
O
|
B:THR252
|
2.9
|
22.3
|
1.0
|
|
O
|
B:GLY291
|
3.1
|
18.6
|
1.0
|
|
O
|
B:HOH5061
|
3.1
|
26.6
|
1.0
|
|
ND2
|
B:ASN286
|
3.1
|
14.1
|
1.0
|
|
C
|
B:ASN286
|
3.7
|
17.3
|
1.0
|
|
C
|
B:GLY291
|
3.9
|
19.0
|
1.0
|
|
C
|
B:ILE289
|
3.9
|
19.6
|
1.0
|
|
C
|
B:ASP250
|
3.9
|
19.2
|
1.0
|
|
CG
|
B:ASN286
|
4.0
|
18.6
|
1.0
|
|
C
|
B:THR252
|
4.0
|
22.1
|
1.0
|
|
N
|
B:GLY291
|
4.1
|
19.3
|
1.0
|
|
CB
|
B:ASP250
|
4.3
|
18.3
|
1.0
|
|
CA
|
B:ASP292
|
4.4
|
18.1
|
1.0
|
|
OD2
|
B:ASP250
|
4.4
|
16.5
|
1.0
|
|
N
|
B:THR252
|
4.4
|
21.4
|
1.0
|
|
N
|
B:VAL287
|
4.5
|
17.7
|
1.0
|
|
CA
|
B:VAL287
|
4.5
|
18.0
|
1.0
|
|
CG
|
B:ASP250
|
4.5
|
17.8
|
1.0
|
|
N
|
B:ASP292
|
4.5
|
19.0
|
1.0
|
|
CA
|
B:ASN286
|
4.5
|
17.1
|
1.0
|
|
O
|
B:HOH5013
|
4.6
|
16.6
|
1.0
|
|
C
|
B:VAL251
|
4.6
|
20.8
|
1.0
|
|
CB
|
B:ASN286
|
4.6
|
16.4
|
1.0
|
|
CA
|
B:GLY291
|
4.7
|
18.9
|
1.0
|
|
C
|
B:ARG290
|
4.7
|
19.0
|
1.0
|
|
CA
|
B:ASP250
|
4.7
|
19.0
|
1.0
|
|
OD1
|
B:ASN286
|
4.7
|
23.1
|
1.0
|
|
CG1
|
B:ILE289
|
4.7
|
20.9
|
1.0
|
|
CA
|
B:THR252
|
4.7
|
22.2
|
1.0
|
|
N
|
B:ILE289
|
4.7
|
19.3
|
1.0
|
|
CA
|
B:ARG290
|
4.8
|
19.4
|
1.0
|
|
OD1
|
B:ASP292
|
4.8
|
16.2
|
1.0
|
|
N
|
B:ARG290
|
4.8
|
19.1
|
1.0
|
|
CA
|
B:ILE289
|
4.9
|
19.9
|
1.0
|
|
C
|
B:VAL287
|
4.9
|
18.6
|
1.0
|
|
N
|
B:VAL251
|
4.9
|
19.6
|
1.0
|
|
O
|
B:VAL251
|
5.0
|
21.8
|
1.0
|
|
Potassium binding site 3 out
of 12 in 2dcn
Go back to
Potassium Binding Sites List in 2dcn
Potassium binding site 3 out
of 12 in the Crystal Structure of 2-Keto-3-Deoxygluconate Kinase From Sulfolobus Tokodaii Complexed with 2-Keto-6-Phosphogluconate (Alpha-Furanose Form)
 Mono view
 Stereo pair view
|
|
A full contact list of Potassium with other atoms in the K binding
site number 3 of Crystal Structure of 2-Keto-3-Deoxygluconate Kinase From Sulfolobus Tokodaii Complexed with 2-Keto-6-Phosphogluconate (Alpha-Furanose Form) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:K5003
b:22.2
occ:1.00
|
O
|
C:ASN286
|
2.8
|
17.6
|
1.0
|
|
O
|
C:ILE289
|
2.8
|
17.7
|
1.0
|
|
O
|
C:THR252
|
2.8
|
19.0
|
1.0
|
|
O
|
C:ASP250
|
2.9
|
19.7
|
1.0
|
|
O
|
C:HOH5015
|
2.9
|
16.6
|
1.0
|
|
ND2
|
C:ASN286
|
3.1
|
17.3
|
1.0
|
|
O
|
C:GLY291
|
3.1
|
18.6
|
1.0
|
|
C
|
C:ASN286
|
3.7
|
17.2
|
1.0
|
|
C
|
C:GLY291
|
3.8
|
18.6
|
1.0
|
|
C
|
C:ASP250
|
3.9
|
19.9
|
1.0
|
|
C
|
C:ILE289
|
4.0
|
17.7
|
1.0
|
|
CG
|
C:ASN286
|
4.0
|
18.9
|
1.0
|
|
C
|
C:THR252
|
4.0
|
19.2
|
1.0
|
|
N
|
C:GLY291
|
4.1
|
17.6
|
1.0
|
|
CB
|
C:ASP250
|
4.3
|
20.2
|
1.0
|
|
OD2
|
C:ASP250
|
4.3
|
19.9
|
1.0
|
|
N
|
C:ASP292
|
4.3
|
19.3
|
1.0
|
|
CA
|
C:ASP292
|
4.4
|
19.5
|
1.0
|
|
CG
|
C:ASP250
|
4.4
|
20.5
|
1.0
|
|
N
|
C:THR252
|
4.5
|
19.5
|
1.0
|
|
N
|
C:VAL287
|
4.5
|
17.0
|
1.0
|
|
CA
|
C:VAL287
|
4.5
|
17.1
|
1.0
|
|
CA
|
C:ASN286
|
4.6
|
17.4
|
1.0
|
|
CA
|
C:GLY291
|
4.6
|
17.6
|
1.0
|
|
OD1
|
C:ASN286
|
4.6
|
21.4
|
1.0
|
|
CG1
|
C:ILE289
|
4.6
|
18.7
|
1.0
|
|
C
|
C:ARG290
|
4.6
|
17.1
|
1.0
|
|
C
|
C:VAL251
|
4.7
|
19.8
|
1.0
|
|
CA
|
C:ASP250
|
4.7
|
20.3
|
1.0
|
|
O
|
C:HOH5033
|
4.7
|
19.2
|
1.0
|
|
CB
|
C:ASN286
|
4.7
|
17.1
|
1.0
|
|
OD1
|
C:ASP292
|
4.7
|
18.8
|
1.0
|
|
N
|
C:ILE289
|
4.7
|
18.9
|
1.0
|
|
CA
|
C:ARG290
|
4.7
|
16.6
|
1.0
|
|
CA
|
C:THR252
|
4.8
|
19.4
|
1.0
|
|
N
|
C:ARG290
|
4.8
|
17.0
|
1.0
|
|
CA
|
C:ILE289
|
4.9
|
18.6
|
1.0
|
|
N
|
C:VAL251
|
4.9
|
19.7
|
1.0
|
|
C
|
C:VAL287
|
4.9
|
17.7
|
1.0
|
|
Potassium binding site 4 out
of 12 in 2dcn
Go back to
Potassium Binding Sites List in 2dcn
Potassium binding site 4 out
of 12 in the Crystal Structure of 2-Keto-3-Deoxygluconate Kinase From Sulfolobus Tokodaii Complexed with 2-Keto-6-Phosphogluconate (Alpha-Furanose Form)
 Mono view
 Stereo pair view
|
|
A full contact list of Potassium with other atoms in the K binding
site number 4 of Crystal Structure of 2-Keto-3-Deoxygluconate Kinase From Sulfolobus Tokodaii Complexed with 2-Keto-6-Phosphogluconate (Alpha-Furanose Form) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:K5004
b:20.7
occ:1.00
|
O
|
D:ASP250
|
2.7
|
19.7
|
1.0
|
|
O
|
D:ASN286
|
2.8
|
18.4
|
1.0
|
|
O
|
D:THR252
|
2.8
|
19.4
|
1.0
|
|
O
|
D:ILE289
|
2.8
|
16.4
|
1.0
|
|
O
|
D:HOH5065
|
3.1
|
18.4
|
1.0
|
|
O
|
D:GLY291
|
3.1
|
20.2
|
1.0
|
|
ND2
|
D:ASN286
|
3.3
|
18.1
|
1.0
|
|
C
|
D:ASN286
|
3.8
|
18.2
|
1.0
|
|
C
|
D:ASP250
|
3.8
|
19.6
|
1.0
|
|
C
|
D:GLY291
|
3.9
|
18.9
|
1.0
|
|
C
|
D:ILE289
|
4.0
|
17.3
|
1.0
|
|
C
|
D:THR252
|
4.0
|
19.4
|
1.0
|
|
N
|
D:GLY291
|
4.1
|
18.2
|
1.0
|
|
CG
|
D:ASN286
|
4.1
|
19.3
|
1.0
|
|
CB
|
D:ASP250
|
4.2
|
18.7
|
1.0
|
|
OD2
|
D:ASP250
|
4.3
|
17.0
|
1.0
|
|
CG
|
D:ASP250
|
4.4
|
17.6
|
1.0
|
|
N
|
D:THR252
|
4.4
|
19.2
|
1.0
|
|
CA
|
D:ASP292
|
4.4
|
18.4
|
1.0
|
|
N
|
D:ASP292
|
4.5
|
18.6
|
1.0
|
|
CA
|
D:ASP250
|
4.5
|
19.1
|
1.0
|
|
CA
|
D:VAL287
|
4.5
|
17.0
|
1.0
|
|
N
|
D:VAL287
|
4.6
|
17.7
|
1.0
|
|
CA
|
D:ASN286
|
4.6
|
18.4
|
1.0
|
|
C
|
D:VAL251
|
4.6
|
19.5
|
1.0
|
|
CA
|
D:GLY291
|
4.7
|
18.8
|
1.0
|
|
CG1
|
D:ILE289
|
4.7
|
16.8
|
1.0
|
|
CB
|
D:ASN286
|
4.7
|
18.3
|
1.0
|
|
O
|
D:HOH5063
|
4.7
|
15.5
|
1.0
|
|
C
|
D:ARG290
|
4.7
|
18.1
|
1.0
|
|
OD1
|
D:ASP292
|
4.7
|
14.9
|
1.0
|
|
N
|
D:ILE289
|
4.8
|
18.4
|
1.0
|
|
N
|
D:VAL251
|
4.8
|
19.5
|
1.0
|
|
CA
|
D:THR252
|
4.8
|
19.3
|
1.0
|
|
CA
|
D:ARG290
|
4.8
|
17.3
|
1.0
|
|
N
|
D:ARG290
|
4.8
|
17.5
|
1.0
|
|
C
|
D:VAL287
|
4.9
|
17.5
|
1.0
|
|
OD1
|
D:ASN286
|
4.9
|
20.9
|
1.0
|
|
CA
|
D:ILE289
|
4.9
|
17.8
|
1.0
|
|
CA
|
D:VAL251
|
4.9
|
19.4
|
1.0
|
|
N
|
D:GLY253
|
5.0
|
19.1
|
1.0
|
|
Potassium binding site 5 out
of 12 in 2dcn
Go back to
Potassium Binding Sites List in 2dcn
Potassium binding site 5 out
of 12 in the Crystal Structure of 2-Keto-3-Deoxygluconate Kinase From Sulfolobus Tokodaii Complexed with 2-Keto-6-Phosphogluconate (Alpha-Furanose Form)
 Mono view
 Stereo pair view
|
|
A full contact list of Potassium with other atoms in the K binding
site number 5 of Crystal Structure of 2-Keto-3-Deoxygluconate Kinase From Sulfolobus Tokodaii Complexed with 2-Keto-6-Phosphogluconate (Alpha-Furanose Form) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:K5005
b:23.4
occ:1.00
|
O
|
E:ASP250
|
2.7
|
21.2
|
1.0
|
|
O
|
E:ASN286
|
2.8
|
19.8
|
1.0
|
|
O
|
E:THR252
|
2.8
|
20.6
|
1.0
|
|
O
|
E:ILE289
|
2.8
|
20.4
|
1.0
|
|
O
|
E:HOH5029
|
3.0
|
25.1
|
1.0
|
|
O
|
E:GLY291
|
3.0
|
19.5
|
1.0
|
|
ND2
|
E:ASN286
|
3.3
|
16.8
|
1.0
|
|
C
|
E:ASN286
|
3.7
|
19.8
|
1.0
|
|
C
|
E:GLY291
|
3.8
|
19.8
|
1.0
|
|
C
|
E:ASP250
|
3.8
|
21.1
|
1.0
|
|
C
|
E:ILE289
|
4.0
|
20.6
|
1.0
|
|
C
|
E:THR252
|
4.0
|
20.4
|
1.0
|
|
N
|
E:GLY291
|
4.2
|
18.9
|
1.0
|
|
CB
|
E:ASP250
|
4.2
|
20.8
|
1.0
|
|
CG
|
E:ASN286
|
4.2
|
20.7
|
1.0
|
|
CA
|
E:ASP292
|
4.3
|
19.4
|
1.0
|
|
CG
|
E:ASP250
|
4.3
|
20.7
|
1.0
|
|
N
|
E:ASP292
|
4.4
|
20.0
|
1.0
|
|
N
|
E:THR252
|
4.4
|
20.4
|
1.0
|
|
OD2
|
E:ASP250
|
4.4
|
19.1
|
1.0
|
|
C
|
E:VAL251
|
4.5
|
21.1
|
1.0
|
|
N
|
E:VAL287
|
4.5
|
19.6
|
1.0
|
|
CG2
|
E:ILE289
|
4.5
|
21.2
|
1.0
|
|
CA
|
E:ASN286
|
4.6
|
19.6
|
1.0
|
|
CA
|
E:ASP250
|
4.6
|
21.2
|
1.0
|
|
CA
|
E:VAL287
|
4.6
|
20.0
|
1.0
|
|
O
|
E:HOH5021
|
4.6
|
23.4
|
1.0
|
|
C
|
E:ARG290
|
4.6
|
18.9
|
1.0
|
|
CA
|
E:GLY291
|
4.6
|
18.7
|
1.0
|
|
CA
|
E:THR252
|
4.7
|
20.3
|
1.0
|
|
CB
|
E:ASN286
|
4.7
|
19.2
|
1.0
|
|
CA
|
E:ARG290
|
4.7
|
19.5
|
1.0
|
|
N
|
E:ILE289
|
4.7
|
20.8
|
1.0
|
|
OD1
|
E:ASP292
|
4.7
|
15.0
|
1.0
|
|
N
|
E:VAL251
|
4.8
|
21.3
|
1.0
|
|
N
|
E:ARG290
|
4.8
|
20.4
|
1.0
|
|
O
|
E:VAL251
|
4.8
|
21.2
|
1.0
|
|
CA
|
E:ILE289
|
4.8
|
21.4
|
1.0
|
|
CA
|
E:VAL251
|
4.9
|
21.0
|
1.0
|
|
OD1
|
E:ASP250
|
4.9
|
21.2
|
1.0
|
|
C
|
E:VAL287
|
4.9
|
20.5
|
1.0
|
|
N
|
E:GLY253
|
5.0
|
20.1
|
1.0
|
|
Potassium binding site 6 out
of 12 in 2dcn
Go back to
Potassium Binding Sites List in 2dcn
Potassium binding site 6 out
of 12 in the Crystal Structure of 2-Keto-3-Deoxygluconate Kinase From Sulfolobus Tokodaii Complexed with 2-Keto-6-Phosphogluconate (Alpha-Furanose Form)
 Mono view
 Stereo pair view
|
|
A full contact list of Potassium with other atoms in the K binding
site number 6 of Crystal Structure of 2-Keto-3-Deoxygluconate Kinase From Sulfolobus Tokodaii Complexed with 2-Keto-6-Phosphogluconate (Alpha-Furanose Form) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:K5006
b:24.3
occ:1.00
|
O
|
F:ASN286
|
2.7
|
19.1
|
1.0
|
|
O
|
F:THR252
|
2.8
|
19.2
|
1.0
|
|
O
|
F:ASP250
|
2.8
|
18.4
|
1.0
|
|
O
|
F:HOH5015
|
2.8
|
17.3
|
1.0
|
|
O
|
F:ILE289
|
2.8
|
18.9
|
1.0
|
|
O
|
F:GLY291
|
3.1
|
19.8
|
1.0
|
|
ND2
|
F:ASN286
|
3.2
|
17.2
|
1.0
|
|
C
|
F:ASN286
|
3.7
|
18.6
|
1.0
|
|
C
|
F:GLY291
|
3.9
|
19.3
|
1.0
|
|
C
|
F:ASP250
|
3.9
|
18.5
|
1.0
|
|
C
|
F:THR252
|
3.9
|
19.4
|
1.0
|
|
C
|
F:ILE289
|
4.0
|
19.6
|
1.0
|
|
CG
|
F:ASN286
|
4.0
|
19.2
|
1.0
|
|
CB
|
F:ASP250
|
4.2
|
18.1
|
1.0
|
|
N
|
F:GLY291
|
4.3
|
18.8
|
1.0
|
|
CA
|
F:ASP292
|
4.3
|
18.4
|
1.0
|
|
N
|
F:THR252
|
4.4
|
19.0
|
1.0
|
|
OD2
|
F:ASP250
|
4.4
|
18.0
|
1.0
|
|
CG
|
F:ASP250
|
4.4
|
17.7
|
1.0
|
|
N
|
F:ASP292
|
4.4
|
19.0
|
1.0
|
|
CA
|
F:ASN286
|
4.5
|
17.9
|
1.0
|
|
C
|
F:VAL251
|
4.5
|
18.8
|
1.0
|
|
N
|
F:VAL287
|
4.5
|
18.7
|
1.0
|
|
CA
|
F:VAL287
|
4.6
|
19.4
|
1.0
|
|
CA
|
F:ASP250
|
4.6
|
18.3
|
1.0
|
|
CB
|
F:ASN286
|
4.6
|
17.5
|
1.0
|
|
OD1
|
F:ASP292
|
4.7
|
18.7
|
1.0
|
|
CA
|
F:THR252
|
4.7
|
19.3
|
1.0
|
|
O
|
F:HOH5012
|
4.7
|
15.1
|
1.0
|
|
CG1
|
F:ILE289
|
4.7
|
20.8
|
1.0
|
|
CA
|
F:GLY291
|
4.7
|
18.7
|
1.0
|
|
C
|
F:ARG290
|
4.8
|
19.1
|
1.0
|
|
OD1
|
F:ASN286
|
4.8
|
21.8
|
1.0
|
|
CA
|
F:ARG290
|
4.8
|
19.0
|
1.0
|
|
N
|
F:ILE289
|
4.8
|
20.2
|
1.0
|
|
N
|
F:VAL251
|
4.9
|
18.6
|
1.0
|
|
N
|
F:ARG290
|
4.9
|
19.2
|
1.0
|
|
O
|
F:VAL251
|
4.9
|
18.0
|
1.0
|
|
N
|
F:GLY253
|
4.9
|
19.1
|
1.0
|
|
CA
|
F:ILE289
|
4.9
|
20.3
|
1.0
|
|
C
|
F:VAL287
|
5.0
|
19.9
|
1.0
|
|
CA
|
F:VAL251
|
5.0
|
18.4
|
1.0
|
|
Potassium binding site 7 out
of 12 in 2dcn
Go back to
Potassium Binding Sites List in 2dcn
Potassium binding site 7 out
of 12 in the Crystal Structure of 2-Keto-3-Deoxygluconate Kinase From Sulfolobus Tokodaii Complexed with 2-Keto-6-Phosphogluconate (Alpha-Furanose Form)
 Mono view
 Stereo pair view
|
|
A full contact list of Potassium with other atoms in the K binding
site number 7 of Crystal Structure of 2-Keto-3-Deoxygluconate Kinase From Sulfolobus Tokodaii Complexed with 2-Keto-6-Phosphogluconate (Alpha-Furanose Form) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:K5007
b:26.1
occ:1.00
|
O
|
G:ASN286
|
2.8
|
21.8
|
1.0
|
|
O
|
G:THR252
|
2.8
|
20.0
|
1.0
|
|
O
|
G:HOH5016
|
2.8
|
17.3
|
1.0
|
|
O
|
G:ASP250
|
2.9
|
19.8
|
1.0
|
|
O
|
G:ILE289
|
2.9
|
20.4
|
1.0
|
|
ND2
|
G:ASN286
|
3.1
|
18.5
|
1.0
|
|
O
|
G:GLY291
|
3.1
|
22.6
|
1.0
|
|
C
|
G:ASN286
|
3.8
|
21.4
|
1.0
|
|
C
|
G:GLY291
|
3.8
|
22.4
|
1.0
|
|
C
|
G:THR252
|
4.0
|
20.4
|
1.0
|
|
C
|
G:ASP250
|
4.0
|
20.9
|
1.0
|
|
C
|
G:ILE289
|
4.1
|
20.7
|
1.0
|
|
CG
|
G:ASN286
|
4.1
|
21.3
|
1.0
|
|
N
|
G:GLY291
|
4.2
|
21.4
|
1.0
|
|
CB
|
G:ASP250
|
4.3
|
20.9
|
1.0
|
|
CA
|
G:ASP292
|
4.3
|
22.1
|
1.0
|
|
N
|
G:ASP292
|
4.4
|
22.5
|
1.0
|
|
N
|
G:THR252
|
4.4
|
20.9
|
1.0
|
|
CA
|
G:VAL287
|
4.5
|
20.7
|
1.0
|
|
OD2
|
G:ASP250
|
4.5
|
20.4
|
1.0
|
|
N
|
G:VAL287
|
4.6
|
21.0
|
1.0
|
|
CG
|
G:ASP250
|
4.6
|
20.7
|
1.0
|
|
O
|
G:HOH5011
|
4.6
|
14.2
|
1.0
|
|
C
|
G:VAL251
|
4.6
|
21.0
|
1.0
|
|
CA
|
G:ASN286
|
4.6
|
21.1
|
1.0
|
|
CA
|
G:GLY291
|
4.7
|
21.9
|
1.0
|
|
CA
|
G:THR252
|
4.7
|
20.2
|
1.0
|
|
CA
|
G:ASP250
|
4.7
|
21.1
|
1.0
|
|
C
|
G:ARG290
|
4.7
|
21.5
|
1.0
|
|
CB
|
G:ASN286
|
4.8
|
21.0
|
1.0
|
|
OD1
|
G:ASP292
|
4.8
|
22.7
|
1.0
|
|
OD1
|
G:ASN286
|
4.8
|
22.7
|
1.0
|
|
CG1
|
G:ILE289
|
4.8
|
22.2
|
1.0
|
|
CA
|
G:ARG290
|
4.8
|
20.9
|
1.0
|
|
O
|
G:VAL251
|
4.8
|
21.6
|
1.0
|
|
N
|
G:ILE289
|
4.9
|
20.8
|
1.0
|
|
N
|
G:ARG290
|
4.9
|
21.0
|
1.0
|
|
C
|
G:VAL287
|
4.9
|
20.6
|
1.0
|
|
N
|
G:GLY253
|
5.0
|
20.2
|
1.0
|
|
N
|
G:VAL251
|
5.0
|
20.8
|
1.0
|
|
CA
|
G:ILE289
|
5.0
|
21.1
|
1.0
|
|
Potassium binding site 8 out
of 12 in 2dcn
Go back to
Potassium Binding Sites List in 2dcn
Potassium binding site 8 out
of 12 in the Crystal Structure of 2-Keto-3-Deoxygluconate Kinase From Sulfolobus Tokodaii Complexed with 2-Keto-6-Phosphogluconate (Alpha-Furanose Form)
 Mono view
 Stereo pair view
|
|
A full contact list of Potassium with other atoms in the K binding
site number 8 of Crystal Structure of 2-Keto-3-Deoxygluconate Kinase From Sulfolobus Tokodaii Complexed with 2-Keto-6-Phosphogluconate (Alpha-Furanose Form) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:K5008
b:23.1
occ:1.00
|
O
|
H:ASN286
|
2.6
|
18.5
|
1.0
|
|
O
|
H:ASP250
|
2.7
|
18.1
|
1.0
|
|
O
|
H:ILE289
|
2.8
|
20.4
|
1.0
|
|
O
|
H:THR252
|
2.9
|
19.6
|
1.0
|
|
O
|
H:HOH5044
|
3.1
|
13.1
|
1.0
|
|
O
|
H:GLY291
|
3.2
|
21.0
|
1.0
|
|
ND2
|
H:ASN286
|
3.2
|
17.4
|
1.0
|
|
C
|
H:ASN286
|
3.6
|
18.6
|
1.0
|
|
C
|
H:ASP250
|
3.8
|
18.2
|
1.0
|
|
C
|
H:GLY291
|
3.9
|
20.6
|
1.0
|
|
C
|
H:ILE289
|
4.0
|
20.4
|
1.0
|
|
CG
|
H:ASN286
|
4.1
|
19.2
|
1.0
|
|
C
|
H:THR252
|
4.1
|
19.1
|
1.0
|
|
CB
|
H:ASP250
|
4.2
|
17.6
|
1.0
|
|
N
|
H:GLY291
|
4.3
|
20.5
|
1.0
|
|
OD2
|
H:ASP250
|
4.4
|
17.5
|
1.0
|
|
CA
|
H:ASP292
|
4.4
|
19.2
|
1.0
|
|
N
|
H:THR252
|
4.4
|
18.9
|
1.0
|
|
CG
|
H:ASP250
|
4.4
|
17.7
|
1.0
|
|
CA
|
H:VAL287
|
4.4
|
18.7
|
1.0
|
|
N
|
H:VAL287
|
4.5
|
18.7
|
1.0
|
|
N
|
H:ASP292
|
4.5
|
20.2
|
1.0
|
|
CA
|
H:ASN286
|
4.5
|
18.3
|
1.0
|
|
CA
|
H:ASP250
|
4.6
|
17.9
|
1.0
|
|
C
|
H:VAL251
|
4.6
|
19.4
|
1.0
|
|
CB
|
H:ASN286
|
4.6
|
17.8
|
1.0
|
|
O
|
H:HOH5025
|
4.6
|
23.0
|
1.0
|
|
CG1
|
H:ILE289
|
4.7
|
21.3
|
1.0
|
|
C
|
H:ARG290
|
4.8
|
20.6
|
1.0
|
|
CA
|
H:GLY291
|
4.8
|
20.6
|
1.0
|
|
C
|
H:VAL287
|
4.8
|
18.9
|
1.0
|
|
N
|
H:ILE289
|
4.8
|
20.1
|
1.0
|
|
CA
|
H:THR252
|
4.8
|
19.1
|
1.0
|
|
OD1
|
H:ASN286
|
4.8
|
21.4
|
1.0
|
|
N
|
H:ARG290
|
4.8
|
20.1
|
1.0
|
|
CA
|
H:ARG290
|
4.8
|
20.2
|
1.0
|
|
N
|
H:VAL251
|
4.8
|
18.6
|
1.0
|
|
OD1
|
H:ASP292
|
4.9
|
18.3
|
1.0
|
|
CA
|
H:ILE289
|
4.9
|
20.5
|
1.0
|
|
CA
|
H:VAL251
|
5.0
|
19.0
|
1.0
|
|
O
|
H:VAL251
|
5.0
|
20.2
|
1.0
|
|
Potassium binding site 9 out
of 12 in 2dcn
Go back to
Potassium Binding Sites List in 2dcn
Potassium binding site 9 out
of 12 in the Crystal Structure of 2-Keto-3-Deoxygluconate Kinase From Sulfolobus Tokodaii Complexed with 2-Keto-6-Phosphogluconate (Alpha-Furanose Form)
 Mono view
 Stereo pair view
|
|
A full contact list of Potassium with other atoms in the K binding
site number 9 of Crystal Structure of 2-Keto-3-Deoxygluconate Kinase From Sulfolobus Tokodaii Complexed with 2-Keto-6-Phosphogluconate (Alpha-Furanose Form) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:K5009
b:21.6
occ:1.00
|
O
|
I:THR252
|
2.8
|
18.0
|
1.0
|
|
O
|
I:ASP250
|
2.8
|
18.4
|
1.0
|
|
O
|
I:ASN286
|
2.8
|
18.5
|
1.0
|
|
O
|
I:ILE289
|
3.0
|
18.8
|
1.0
|
|
O
|
I:HOH5047
|
3.0
|
20.0
|
1.0
|
|
O
|
I:GLY291
|
3.2
|
17.2
|
1.0
|
|
ND2
|
I:ASN286
|
3.2
|
16.2
|
1.0
|
|
C
|
I:ASN286
|
3.8
|
18.2
|
1.0
|
|
C
|
I:GLY291
|
3.8
|
17.3
|
1.0
|
|
C
|
I:ASP250
|
3.9
|
18.2
|
1.0
|
|
C
|
I:THR252
|
3.9
|
18.2
|
1.0
|
|
CG
|
I:ASN286
|
4.0
|
19.2
|
1.0
|
|
C
|
I:ILE289
|
4.1
|
18.7
|
1.0
|
|
N
|
I:GLY291
|
4.2
|
17.1
|
1.0
|
|
CB
|
I:ASP250
|
4.3
|
18.8
|
1.0
|
|
CA
|
I:ASP292
|
4.3
|
18.2
|
1.0
|
|
N
|
I:THR252
|
4.4
|
18.3
|
1.0
|
|
OD2
|
I:ASP250
|
4.4
|
20.0
|
1.0
|
|
N
|
I:ASP292
|
4.4
|
17.6
|
1.0
|
|
CG
|
I:ASP250
|
4.4
|
20.2
|
1.0
|
|
CA
|
I:VAL287
|
4.5
|
18.9
|
1.0
|
|
N
|
I:VAL287
|
4.5
|
18.4
|
1.0
|
|
C
|
I:VAL251
|
4.6
|
18.4
|
1.0
|
|
CA
|
I:ASP250
|
4.6
|
18.7
|
1.0
|
|
CA
|
I:ASN286
|
4.6
|
18.2
|
1.0
|
|
CA
|
I:THR252
|
4.6
|
18.2
|
1.0
|
|
O
|
I:HOH5037
|
4.7
|
18.3
|
1.0
|
|
CA
|
I:GLY291
|
4.7
|
16.6
|
1.0
|
|
CB
|
I:ASN286
|
4.7
|
18.0
|
1.0
|
|
OD1
|
I:ASN286
|
4.7
|
21.4
|
1.0
|
|
OD1
|
I:ASP292
|
4.7
|
19.4
|
1.0
|
|
C
|
I:ARG290
|
4.7
|
17.1
|
1.0
|
|
N
|
I:VAL251
|
4.8
|
18.2
|
1.0
|
|
CA
|
I:ARG290
|
4.8
|
17.2
|
1.0
|
|
CG1
|
I:ILE289
|
4.9
|
19.5
|
1.0
|
|
N
|
I:ILE289
|
4.9
|
19.4
|
1.0
|
|
C
|
I:VAL287
|
4.9
|
19.4
|
1.0
|
|
N
|
I:ARG290
|
4.9
|
18.1
|
1.0
|
|
CA
|
I:VAL251
|
4.9
|
17.9
|
1.0
|
|
N
|
I:GLY253
|
5.0
|
18.4
|
1.0
|
|
O
|
I:VAL251
|
5.0
|
19.6
|
1.0
|
|
CB
|
I:THR252
|
5.0
|
18.8
|
1.0
|
|
Potassium binding site 10 out
of 12 in 2dcn
Go back to
Potassium Binding Sites List in 2dcn
Potassium binding site 10 out
of 12 in the Crystal Structure of 2-Keto-3-Deoxygluconate Kinase From Sulfolobus Tokodaii Complexed with 2-Keto-6-Phosphogluconate (Alpha-Furanose Form)
 Mono view
 Stereo pair view
|
|
A full contact list of Potassium with other atoms in the K binding
site number 10 of Crystal Structure of 2-Keto-3-Deoxygluconate Kinase From Sulfolobus Tokodaii Complexed with 2-Keto-6-Phosphogluconate (Alpha-Furanose Form) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
J:K5010
b:20.2
occ:1.00
|
O
|
J:ASP250
|
2.8
|
18.6
|
1.0
|
|
O
|
J:ASN286
|
2.8
|
21.8
|
1.0
|
|
O
|
J:ILE289
|
2.8
|
20.2
|
1.0
|
|
O
|
J:THR252
|
2.9
|
19.9
|
1.0
|
|
O
|
J:HOH5021
|
3.0
|
16.3
|
1.0
|
|
O
|
J:GLY291
|
3.1
|
20.9
|
1.0
|
|
ND2
|
J:ASN286
|
3.2
|
20.0
|
1.0
|
|
C
|
J:ASN286
|
3.8
|
21.5
|
1.0
|
|
C
|
J:GLY291
|
3.8
|
20.4
|
1.0
|
|
C
|
J:ASP250
|
3.8
|
19.3
|
1.0
|
|
C
|
J:ILE289
|
3.9
|
20.3
|
1.0
|
|
C
|
J:THR252
|
4.1
|
19.6
|
1.0
|
|
CG
|
J:ASN286
|
4.1
|
22.9
|
1.0
|
|
CB
|
J:ASP250
|
4.2
|
19.3
|
1.0
|
|
N
|
J:GLY291
|
4.2
|
20.1
|
1.0
|
|
CA
|
J:ASP292
|
4.4
|
20.2
|
1.0
|
|
OD2
|
J:ASP250
|
4.4
|
18.2
|
1.0
|
|
CG
|
J:ASP250
|
4.4
|
19.7
|
1.0
|
|
N
|
J:ASP292
|
4.4
|
20.1
|
1.0
|
|
N
|
J:THR252
|
4.5
|
19.5
|
1.0
|
|
CA
|
J:ASP250
|
4.6
|
19.6
|
1.0
|
|
CA
|
J:VAL287
|
4.6
|
19.6
|
1.0
|
|
C
|
J:VAL251
|
4.6
|
19.2
|
1.0
|
|
CA
|
J:ASN286
|
4.6
|
22.2
|
1.0
|
|
OD1
|
J:ASP292
|
4.6
|
19.6
|
1.0
|
|
N
|
J:VAL287
|
4.6
|
20.6
|
1.0
|
|
CA
|
J:GLY291
|
4.7
|
20.2
|
1.0
|
|
CG2
|
J:ILE289
|
4.7
|
21.0
|
1.0
|
|
O
|
J:HOH5112
|
4.7
|
20.8
|
1.0
|
|
C
|
J:ARG290
|
4.7
|
19.9
|
1.0
|
|
CB
|
J:ASN286
|
4.7
|
21.4
|
1.0
|
|
CA
|
J:ARG290
|
4.7
|
19.4
|
1.0
|
|
OD1
|
J:ASN286
|
4.8
|
25.3
|
1.0
|
|
N
|
J:ARG290
|
4.8
|
19.9
|
1.0
|
|
N
|
J:ILE289
|
4.8
|
20.6
|
1.0
|
|
N
|
J:VAL251
|
4.8
|
19.3
|
1.0
|
|
CA
|
J:ILE289
|
4.8
|
20.6
|
1.0
|
|
CA
|
J:THR252
|
4.8
|
19.4
|
1.0
|
|
C
|
J:VAL287
|
4.9
|
19.8
|
1.0
|
|
CA
|
J:VAL251
|
5.0
|
18.9
|
1.0
|
|
O
|
J:VAL287
|
5.0
|
19.4
|
1.0
|
|
Reference:
S.Okazaki,
H.Onda,
A.Suzuki,
S.Kuramitsu,
R.Masui,
T.Yamane.
Crystal Structure of 2-Keto-3-Deoxygluconate Kinase From Sulfolobus Tokodaii Complexed with 2-Keto-6-Phosphogluconate To Be Published.
Page generated: Sat Aug 9 03:19:20 2025
|
