Potassium in PDB 6vwp: Crystal Structure of E. Coli Guanosine Kinase in Complex with Ppgpp
Enzymatic activity of Crystal Structure of E. Coli Guanosine Kinase in Complex with Ppgpp
All present enzymatic activity of Crystal Structure of E. Coli Guanosine Kinase in Complex with Ppgpp:
2.7.1.73;
Protein crystallography data
The structure of Crystal Structure of E. Coli Guanosine Kinase in Complex with Ppgpp, PDB code: 6vwp
was solved by
B.Wang,
R.A.Grant,
M.T.Laub,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
49.16 /
3.45
|
|
Space group
|
P 31 2 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
245.949,
245.949,
221.680,
90.00,
90.00,
120.00
|
|
R / Rfree (%)
|
20 /
24.2
|
Other elements in 6vwp:
The structure of Crystal Structure of E. Coli Guanosine Kinase in Complex with Ppgpp 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 E. Coli Guanosine Kinase in Complex with Ppgpp
(pdb code 6vwp). 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 E. Coli Guanosine Kinase in Complex with Ppgpp, PDB code: 6vwp:
Jump to Potassium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Potassium binding site 1 out
of 12 in 6vwp
Go back to
Potassium Binding Sites List in 6vwp
Potassium binding site 1 out
of 12 in the Crystal Structure of E. Coli Guanosine Kinase in Complex with Ppgpp
 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 E. Coli Guanosine Kinase in Complex with Ppgpp within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K504
b:0.6
occ:1.00
|
O
|
A:VAL248
|
2.6
|
0.6
|
1.0
|
|
O
|
A:LYS245
|
2.7
|
0.7
|
1.0
|
|
O
|
A:TRP277
|
2.7
|
0.8
|
1.0
|
|
O
|
A:LEU244
|
3.0
|
0.9
|
1.0
|
|
HA
|
A:VAL278
|
3.3
|
0.2
|
1.0
|
|
HA
|
A:LYS245
|
3.4
|
0.4
|
1.0
|
|
C
|
A:LYS245
|
3.5
|
1.0
|
1.0
|
|
C
|
A:VAL248
|
3.8
|
0.4
|
1.0
|
|
CA
|
A:LYS245
|
3.9
|
0.2
|
1.0
|
|
HG12
|
A:VAL278
|
3.9
|
0.9
|
1.0
|
|
C
|
A:TRP277
|
3.9
|
0.2
|
1.0
|
|
HA
|
A:SER249
|
4.1
|
0.1
|
1.0
|
|
C
|
A:LEU244
|
4.1
|
0.6
|
1.0
|
|
CA
|
A:VAL278
|
4.2
|
0.2
|
1.0
|
|
N
|
A:VAL248
|
4.3
|
0.6
|
1.0
|
|
H
|
A:VAL248
|
4.4
|
0.9
|
1.0
|
|
C
|
A:HIS247
|
4.5
|
0.1
|
1.0
|
|
N
|
A:LYS245
|
4.5
|
0.1
|
1.0
|
|
N
|
A:VAL278
|
4.5
|
0.8
|
1.0
|
|
N
|
A:ASP246
|
4.6
|
0.2
|
1.0
|
|
O
|
A:HIS247
|
4.6
|
0.4
|
1.0
|
|
C
|
A:ASP246
|
4.6
|
0.0
|
1.0
|
|
CA
|
A:VAL248
|
4.7
|
0.3
|
1.0
|
|
N
|
A:HIS247
|
4.7
|
0.4
|
1.0
|
|
OD1
|
A:ASP279
|
4.7
|
0.5
|
1.0
|
|
N
|
A:SER249
|
4.7
|
0.1
|
1.0
|
|
O
|
A:ASP246
|
4.7
|
0.7
|
1.0
|
|
CG1
|
A:VAL278
|
4.7
|
0.8
|
1.0
|
|
H
|
A:HIS247
|
4.8
|
0.1
|
1.0
|
|
CA
|
A:SER249
|
4.8
|
0.4
|
1.0
|
|
HA
|
A:TRP277
|
4.9
|
1.0
|
1.0
|
|
HB
|
A:VAL248
|
4.9
|
0.5
|
1.0
|
|
HG13
|
A:VAL278
|
5.0
|
0.9
|
1.0
|
|
CB
|
A:VAL278
|
5.0
|
0.8
|
1.0
|
|
Potassium binding site 2 out
of 12 in 6vwp
Go back to
Potassium Binding Sites List in 6vwp
Potassium binding site 2 out
of 12 in the Crystal Structure of E. Coli Guanosine Kinase in Complex with Ppgpp
 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 E. Coli Guanosine Kinase in Complex with Ppgpp within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:K504
b:0.6
occ:1.00
|
O
|
B:LEU130
|
2.4
|
94.6
|
1.0
|
|
O
|
A:THR133
|
2.6
|
0.4
|
1.0
|
|
O
|
A:LEU130
|
2.7
|
0.3
|
1.0
|
|
O
|
B:THR133
|
2.7
|
0.5
|
1.0
|
|
O
|
B:CYS131
|
3.2
|
94.6
|
1.0
|
|
HA
|
B:CYS131
|
3.3
|
1.0
|
1.0
|
|
C
|
B:CYS131
|
3.4
|
0.5
|
1.0
|
|
C
|
B:LEU130
|
3.6
|
0.4
|
1.0
|
|
C
|
A:THR133
|
3.7
|
94.6
|
1.0
|
|
HA
|
A:CYS131
|
3.7
|
0.7
|
1.0
|
|
CA
|
B:CYS131
|
3.7
|
0.7
|
1.0
|
|
HB
|
A:THR133
|
3.8
|
0.7
|
1.0
|
|
C
|
A:LEU130
|
3.8
|
0.7
|
1.0
|
|
HA
|
A:SER135
|
3.8
|
0.3
|
1.0
|
|
O
|
A:CYS131
|
3.9
|
0.1
|
1.0
|
|
C
|
B:THR133
|
3.9
|
94.6
|
1.0
|
|
C
|
A:CYS131
|
4.0
|
0.2
|
1.0
|
|
N
|
B:ASN132
|
4.0
|
0.2
|
1.0
|
|
H
|
B:THR133
|
4.1
|
0.6
|
1.0
|
|
N
|
B:THR133
|
4.1
|
94.6
|
1.0
|
|
HB
|
B:THR133
|
4.1
|
0.8
|
1.0
|
|
O
|
A:SER134
|
4.1
|
94.6
|
1.0
|
|
N
|
B:CYS131
|
4.1
|
0.5
|
1.0
|
|
H
|
A:THR133
|
4.1
|
0.4
|
1.0
|
|
N
|
A:THR133
|
4.2
|
0.0
|
1.0
|
|
CA
|
A:CYS131
|
4.2
|
99.8
|
1.0
|
|
C
|
A:SER134
|
4.3
|
0.4
|
1.0
|
|
C
|
B:ASN132
|
4.3
|
95.8
|
1.0
|
|
CA
|
A:THR133
|
4.3
|
94.6
|
1.0
|
|
H
|
B:ASN132
|
4.4
|
0.0
|
1.0
|
|
CA
|
B:THR133
|
4.4
|
94.6
|
1.0
|
|
HA
|
B:SER135
|
4.4
|
0.1
|
1.0
|
|
CB
|
A:THR133
|
4.5
|
0.7
|
1.0
|
|
HG22
|
A:THR133
|
4.5
|
0.0
|
1.0
|
|
N
|
A:CYS131
|
4.5
|
0.6
|
1.0
|
|
N
|
A:ASN132
|
4.5
|
94.6
|
1.0
|
|
N
|
A:SER135
|
4.5
|
0.7
|
1.0
|
|
C
|
A:ASN132
|
4.6
|
94.6
|
1.0
|
|
O
|
B:SER134
|
4.6
|
0.5
|
1.0
|
|
CA
|
A:SER135
|
4.6
|
0.5
|
1.0
|
|
CA
|
B:ASN132
|
4.6
|
0.8
|
1.0
|
|
HA
|
A:LEU130
|
4.7
|
0.1
|
1.0
|
|
N
|
A:SER134
|
4.7
|
94.6
|
1.0
|
|
HA
|
B:LEU130
|
4.7
|
0.1
|
1.0
|
|
C
|
B:SER134
|
4.7
|
0.8
|
1.0
|
|
CB
|
B:THR133
|
4.7
|
99.9
|
1.0
|
|
HA
|
B:ASN132
|
4.8
|
0.7
|
1.0
|
|
CA
|
B:LEU130
|
4.8
|
0.6
|
1.0
|
|
O
|
B:ASN132
|
4.9
|
94.6
|
1.0
|
|
H
|
A:ASN132
|
4.9
|
0.6
|
1.0
|
|
HA
|
A:SER134
|
4.9
|
0.2
|
1.0
|
|
CA
|
A:LEU130
|
4.9
|
0.4
|
1.0
|
|
CA
|
A:SER134
|
4.9
|
1.0
|
1.0
|
|
H
|
A:SER135
|
4.9
|
0.9
|
1.0
|
|
N
|
B:SER134
|
4.9
|
94.6
|
1.0
|
|
HB3
|
A:SER135
|
5.0
|
0.7
|
1.0
|
|
N
|
B:SER135
|
5.0
|
0.8
|
1.0
|
|
H
|
B:CYS131
|
5.0
|
0.8
|
1.0
|
|
HG22
|
B:THR133
|
5.0
|
0.8
|
1.0
|
|
Potassium binding site 3 out
of 12 in 6vwp
Go back to
Potassium Binding Sites List in 6vwp
Potassium binding site 3 out
of 12 in the Crystal Structure of E. Coli Guanosine Kinase in Complex with Ppgpp
 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 E. Coli Guanosine Kinase in Complex with Ppgpp within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:K505
b:0.8
occ:1.00
|
O
|
B:LYS245
|
2.8
|
0.3
|
1.0
|
|
O
|
B:VAL248
|
3.3
|
0.6
|
1.0
|
|
O
|
B:TRP277
|
3.7
|
0.8
|
1.0
|
|
C
|
B:LYS245
|
3.9
|
0.8
|
1.0
|
|
O
|
B:LEU244
|
4.0
|
0.8
|
1.0
|
|
HA
|
B:VAL278
|
4.0
|
0.9
|
1.0
|
|
O
|
B:ASP246
|
4.2
|
0.6
|
1.0
|
|
HA
|
B:LYS245
|
4.2
|
0.6
|
1.0
|
|
HN22
|
B:GMP503
|
4.2
|
0.7
|
1.0
|
|
HA
|
B:SER249
|
4.3
|
0.1
|
1.0
|
|
C
|
B:VAL248
|
4.4
|
0.8
|
1.0
|
|
C
|
B:ASP246
|
4.4
|
0.5
|
1.0
|
|
O2'
|
B:GMP503
|
4.6
|
0.1
|
1.0
|
|
CA
|
B:LYS245
|
4.7
|
0.0
|
1.0
|
|
C
|
B:HIS247
|
4.7
|
0.7
|
1.0
|
|
OD2
|
B:ASP279
|
4.7
|
0.2
|
1.0
|
|
O
|
B:HIS247
|
4.7
|
0.1
|
1.0
|
|
HO2'
|
B:GMP503
|
4.7
|
0.7
|
1.0
|
|
N
|
B:HIS247
|
4.8
|
0.8
|
1.0
|
|
C
|
B:TRP277
|
4.8
|
0.3
|
1.0
|
|
N
|
B:ASP246
|
4.8
|
0.6
|
1.0
|
|
HG12
|
B:VAL278
|
4.8
|
0.2
|
1.0
|
|
HA
|
B:ASP246
|
4.9
|
0.8
|
1.0
|
|
N
|
B:VAL248
|
4.9
|
0.8
|
1.0
|
|
HB2
|
B:SER249
|
4.9
|
0.4
|
1.0
|
|
CA
|
B:ASP246
|
5.0
|
0.5
|
1.0
|
|
CA
|
B:VAL278
|
5.0
|
0.9
|
1.0
|
|
Potassium binding site 4 out
of 12 in 6vwp
Go back to
Potassium Binding Sites List in 6vwp
Potassium binding site 4 out
of 12 in the Crystal Structure of E. Coli Guanosine Kinase in Complex with Ppgpp
 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 E. Coli Guanosine Kinase in Complex with Ppgpp within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:K504
b:94.6
occ:1.00
|
O
|
C:LEU130
|
2.5
|
0.9
|
1.0
|
|
O
|
D:LEU130
|
2.6
|
0.3
|
1.0
|
|
O
|
C:THR133
|
2.6
|
94.6
|
1.0
|
|
O
|
D:THR133
|
2.7
|
0.6
|
1.0
|
|
O
|
C:CYS131
|
3.1
|
0.3
|
1.0
|
|
HA
|
C:CYS131
|
3.3
|
0.5
|
1.0
|
|
C
|
C:CYS131
|
3.3
|
0.1
|
1.0
|
|
HA
|
D:CYS131
|
3.6
|
0.6
|
1.0
|
|
O
|
D:CYS131
|
3.6
|
0.1
|
1.0
|
|
C
|
C:LEU130
|
3.6
|
1.0
|
1.0
|
|
C
|
D:LEU130
|
3.7
|
0.7
|
1.0
|
|
C
|
C:THR133
|
3.7
|
94.6
|
1.0
|
|
C
|
D:THR133
|
3.7
|
0.0
|
1.0
|
|
CA
|
C:CYS131
|
3.8
|
0.4
|
1.0
|
|
C
|
D:CYS131
|
3.8
|
0.1
|
1.0
|
|
H
|
C:THR133
|
3.9
|
0.1
|
1.0
|
|
N
|
C:THR133
|
3.9
|
98.4
|
1.0
|
|
N
|
C:ASN132
|
3.9
|
99.1
|
1.0
|
|
HB
|
D:THR133
|
4.0
|
0.3
|
1.0
|
|
HB
|
C:THR133
|
4.0
|
0.3
|
1.0
|
|
CA
|
D:CYS131
|
4.0
|
0.2
|
1.0
|
|
HA
|
D:SER135
|
4.1
|
0.1
|
1.0
|
|
H
|
D:THR133
|
4.2
|
1.0
|
1.0
|
|
N
|
D:THR133
|
4.2
|
0.3
|
1.0
|
|
N
|
C:CYS131
|
4.2
|
0.1
|
1.0
|
|
C
|
C:ASN132
|
4.2
|
94.8
|
1.0
|
|
O
|
D:SER134
|
4.2
|
96.8
|
1.0
|
|
CA
|
C:THR133
|
4.3
|
0.1
|
1.0
|
|
N
|
D:CYS131
|
4.3
|
0.2
|
1.0
|
|
N
|
D:ASN132
|
4.3
|
0.1
|
1.0
|
|
H
|
C:ASN132
|
4.4
|
0.9
|
1.0
|
|
C
|
D:SER134
|
4.4
|
1.0
|
1.0
|
|
CA
|
D:THR133
|
4.4
|
0.8
|
1.0
|
|
HA
|
C:SER135
|
4.4
|
0.7
|
1.0
|
|
C
|
D:ASN132
|
4.5
|
0.1
|
1.0
|
|
CA
|
C:ASN132
|
4.5
|
0.0
|
1.0
|
|
O
|
C:SER134
|
4.6
|
0.2
|
1.0
|
|
N
|
D:SER135
|
4.6
|
0.7
|
1.0
|
|
CB
|
D:THR133
|
4.6
|
0.6
|
1.0
|
|
C
|
C:SER134
|
4.6
|
0.0
|
1.0
|
|
CB
|
C:THR133
|
4.7
|
0.1
|
1.0
|
|
HA
|
C:ASN132
|
4.7
|
0.1
|
1.0
|
|
HG22
|
D:THR133
|
4.7
|
0.6
|
1.0
|
|
HA
|
D:LEU130
|
4.7
|
0.1
|
1.0
|
|
H
|
D:ASN132
|
4.7
|
0.3
|
1.0
|
|
O
|
C:ASN132
|
4.8
|
94.6
|
1.0
|
|
N
|
D:SER134
|
4.8
|
0.3
|
1.0
|
|
HA
|
C:LEU130
|
4.8
|
0.7
|
1.0
|
|
CA
|
D:SER135
|
4.8
|
0.1
|
1.0
|
|
N
|
C:SER134
|
4.8
|
0.3
|
1.0
|
|
CA
|
D:LEU130
|
4.8
|
0.8
|
1.0
|
|
HG22
|
C:THR133
|
4.8
|
0.6
|
1.0
|
|
CA
|
C:LEU130
|
4.9
|
0.1
|
1.0
|
|
N
|
C:SER135
|
4.9
|
94.6
|
1.0
|
|
HA
|
D:SER134
|
4.9
|
0.5
|
1.0
|
|
CA
|
D:ASN132
|
4.9
|
0.1
|
1.0
|
|
CA
|
D:SER134
|
5.0
|
0.1
|
1.0
|
|
Potassium binding site 5 out
of 12 in 6vwp
Go back to
Potassium Binding Sites List in 6vwp
Potassium binding site 5 out
of 12 in the Crystal Structure of E. Coli Guanosine Kinase in Complex with Ppgpp
 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 E. Coli Guanosine Kinase in Complex with Ppgpp within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:K505
b:0.4
occ:1.00
|
O
|
C:VAL248
|
2.6
|
0.2
|
1.0
|
|
O
|
C:LYS245
|
2.7
|
0.4
|
1.0
|
|
O
|
C:TRP277
|
2.8
|
94.6
|
1.0
|
|
O
|
C:LEU244
|
3.2
|
99.6
|
1.0
|
|
HA
|
C:VAL278
|
3.3
|
0.2
|
1.0
|
|
HA
|
C:LYS245
|
3.5
|
0.8
|
1.0
|
|
C
|
C:LYS245
|
3.6
|
0.1
|
1.0
|
|
C
|
C:VAL248
|
3.8
|
0.7
|
1.0
|
|
HA
|
C:SER249
|
3.9
|
0.8
|
1.0
|
|
C
|
C:TRP277
|
3.9
|
0.4
|
1.0
|
|
HG12
|
C:VAL278
|
4.1
|
0.3
|
1.0
|
|
CA
|
C:LYS245
|
4.1
|
0.6
|
1.0
|
|
CA
|
C:VAL278
|
4.2
|
95.2
|
1.0
|
|
C
|
C:LEU244
|
4.3
|
1.0
|
1.0
|
|
HN22
|
C:GMP503
|
4.4
|
0.9
|
1.0
|
|
N
|
C:VAL248
|
4.5
|
0.3
|
1.0
|
|
N
|
C:VAL278
|
4.5
|
99.7
|
1.0
|
|
H
|
C:VAL248
|
4.6
|
0.4
|
1.0
|
|
C
|
C:HIS247
|
4.6
|
0.6
|
1.0
|
|
N
|
C:ASP246
|
4.6
|
0.8
|
1.0
|
|
C
|
C:ASP246
|
4.7
|
0.4
|
1.0
|
|
OD1
|
C:ASP279
|
4.7
|
0.0
|
1.0
|
|
N
|
C:SER249
|
4.7
|
0.6
|
1.0
|
|
O
|
C:HIS247
|
4.7
|
0.5
|
1.0
|
|
CA
|
C:SER249
|
4.7
|
0.0
|
1.0
|
|
N
|
C:LYS245
|
4.7
|
0.5
|
1.0
|
|
O
|
C:ASP246
|
4.7
|
0.2
|
1.0
|
|
CA
|
C:VAL248
|
4.8
|
0.8
|
1.0
|
|
N
|
C:HIS247
|
4.8
|
0.1
|
1.0
|
|
CG1
|
C:VAL278
|
4.9
|
0.2
|
1.0
|
|
H
|
C:HIS247
|
4.9
|
0.7
|
1.0
|
|
HA
|
C:TRP277
|
5.0
|
0.6
|
1.0
|
|
HB
|
C:VAL248
|
5.0
|
0.9
|
1.0
|
|
Potassium binding site 6 out
of 12 in 6vwp
Go back to
Potassium Binding Sites List in 6vwp
Potassium binding site 6 out
of 12 in the Crystal Structure of E. Coli Guanosine Kinase in Complex with Ppgpp
 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 E. Coli Guanosine Kinase in Complex with Ppgpp within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:K504
b:0.6
occ:1.00
|
O
|
D:LYS245
|
2.9
|
0.4
|
1.0
|
|
O
|
D:VAL248
|
3.1
|
0.6
|
1.0
|
|
O
|
D:TRP277
|
3.2
|
0.6
|
1.0
|
|
O
|
D:LEU244
|
3.7
|
0.5
|
1.0
|
|
C
|
D:LYS245
|
3.8
|
0.3
|
1.0
|
|
HA
|
D:VAL278
|
3.9
|
0.5
|
1.0
|
|
HN22
|
D:GMP503
|
3.9
|
0.5
|
1.0
|
|
HA
|
D:LYS245
|
4.0
|
0.7
|
1.0
|
|
C
|
D:VAL248
|
4.2
|
0.0
|
1.0
|
|
C
|
D:TRP277
|
4.4
|
0.7
|
1.0
|
|
O
|
D:ASP246
|
4.4
|
0.2
|
1.0
|
|
CA
|
D:LYS245
|
4.5
|
0.6
|
1.0
|
|
HA
|
D:SER249
|
4.5
|
0.3
|
1.0
|
|
O
|
D:HIS247
|
4.5
|
0.6
|
1.0
|
|
C
|
D:ASP246
|
4.5
|
0.1
|
1.0
|
|
C
|
D:HIS247
|
4.6
|
0.9
|
1.0
|
|
HO2'
|
D:GMP503
|
4.6
|
0.2
|
1.0
|
|
N
|
D:VAL248
|
4.7
|
0.6
|
1.0
|
|
N2
|
D:GMP503
|
4.7
|
0.9
|
1.0
|
|
O2'
|
D:GMP503
|
4.7
|
0.3
|
1.0
|
|
N
|
D:HIS247
|
4.8
|
0.5
|
1.0
|
|
CA
|
D:VAL278
|
4.8
|
0.3
|
1.0
|
|
H
|
D:VAL248
|
4.8
|
0.6
|
1.0
|
|
OD1
|
D:ASP279
|
4.8
|
0.7
|
1.0
|
|
N
|
D:ASP246
|
4.8
|
1.0
|
1.0
|
|
C
|
D:LEU244
|
4.8
|
0.7
|
1.0
|
|
HG12
|
D:VAL278
|
4.9
|
0.4
|
1.0
|
|
Potassium binding site 7 out
of 12 in 6vwp
Go back to
Potassium Binding Sites List in 6vwp
Potassium binding site 7 out
of 12 in the Crystal Structure of E. Coli Guanosine Kinase in Complex with Ppgpp
 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 E. Coli Guanosine Kinase in Complex with Ppgpp within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:K504
b:0.7
occ:1.00
|
O
|
E:LEU130
|
2.6
|
0.7
|
1.0
|
|
O
|
E:THR133
|
2.6
|
1.0
|
1.0
|
|
O
|
F:LEU130
|
2.6
|
0.3
|
1.0
|
|
O
|
F:THR133
|
2.6
|
0.1
|
1.0
|
|
O
|
E:CYS131
|
3.3
|
0.9
|
1.0
|
|
O
|
F:CYS131
|
3.5
|
0.2
|
1.0
|
|
HA
|
E:CYS131
|
3.5
|
0.0
|
1.0
|
|
C
|
E:CYS131
|
3.6
|
0.6
|
1.0
|
|
HA
|
F:CYS131
|
3.6
|
0.1
|
1.0
|
|
C
|
F:CYS131
|
3.7
|
0.5
|
1.0
|
|
C
|
E:THR133
|
3.7
|
0.7
|
1.0
|
|
C
|
F:THR133
|
3.7
|
0.1
|
1.0
|
|
C
|
E:LEU130
|
3.7
|
0.5
|
1.0
|
|
C
|
F:LEU130
|
3.8
|
0.2
|
1.0
|
|
HB
|
F:THR133
|
3.8
|
0.9
|
1.0
|
|
H
|
F:THR133
|
3.9
|
1.0
|
1.0
|
|
N
|
F:THR133
|
4.0
|
0.5
|
1.0
|
|
CA
|
E:CYS131
|
4.0
|
0.5
|
1.0
|
|
HB
|
E:THR133
|
4.0
|
0.4
|
1.0
|
|
N
|
E:THR133
|
4.0
|
0.1
|
1.0
|
|
H
|
E:THR133
|
4.0
|
0.6
|
1.0
|
|
CA
|
F:CYS131
|
4.1
|
0.9
|
1.0
|
|
HA
|
F:SER135
|
4.1
|
0.0
|
1.0
|
|
N
|
E:ASN132
|
4.1
|
0.1
|
1.0
|
|
N
|
F:ASN132
|
4.2
|
0.5
|
1.0
|
|
HA
|
E:SER135
|
4.2
|
0.7
|
1.0
|
|
CA
|
F:THR133
|
4.2
|
0.9
|
1.0
|
|
C
|
E:ASN132
|
4.3
|
0.3
|
1.0
|
|
CA
|
E:THR133
|
4.3
|
1.0
|
1.0
|
|
C
|
F:ASN132
|
4.3
|
0.4
|
1.0
|
|
N
|
E:CYS131
|
4.3
|
0.3
|
1.0
|
|
N
|
F:CYS131
|
4.4
|
0.7
|
1.0
|
|
O
|
F:SER134
|
4.4
|
0.3
|
1.0
|
|
O
|
E:SER134
|
4.4
|
0.6
|
1.0
|
|
CB
|
F:THR133
|
4.5
|
0.9
|
1.0
|
|
C
|
F:SER134
|
4.5
|
0.9
|
1.0
|
|
C
|
E:SER134
|
4.5
|
0.8
|
1.0
|
|
H
|
E:ASN132
|
4.5
|
0.7
|
1.0
|
|
H
|
F:ASN132
|
4.6
|
0.2
|
1.0
|
|
CB
|
E:THR133
|
4.6
|
0.7
|
1.0
|
|
HG22
|
F:THR133
|
4.7
|
0.3
|
1.0
|
|
CA
|
E:ASN132
|
4.7
|
0.4
|
1.0
|
|
N
|
F:SER135
|
4.7
|
0.2
|
1.0
|
|
N
|
E:SER135
|
4.7
|
0.2
|
1.0
|
|
CA
|
F:ASN132
|
4.7
|
0.4
|
1.0
|
|
N
|
E:SER134
|
4.7
|
0.7
|
1.0
|
|
HA
|
E:LEU130
|
4.8
|
0.7
|
1.0
|
|
HA
|
F:LEU130
|
4.8
|
0.1
|
1.0
|
|
N
|
F:SER134
|
4.8
|
0.3
|
1.0
|
|
HA
|
E:ASN132
|
4.8
|
0.3
|
1.0
|
|
O
|
E:ASN132
|
4.8
|
0.4
|
1.0
|
|
O
|
F:ASN132
|
4.8
|
0.1
|
1.0
|
|
HG22
|
E:THR133
|
4.8
|
0.8
|
1.0
|
|
CA
|
F:SER135
|
4.8
|
0.4
|
1.0
|
|
HA
|
E:SER134
|
4.9
|
0.6
|
1.0
|
|
HA
|
F:ASN132
|
4.9
|
0.7
|
1.0
|
|
CA
|
F:LEU130
|
4.9
|
0.5
|
1.0
|
|
CA
|
E:LEU130
|
4.9
|
0.4
|
1.0
|
|
CA
|
E:SER135
|
5.0
|
0.9
|
1.0
|
|
HA
|
F:SER134
|
5.0
|
0.6
|
1.0
|
|
CA
|
E:SER134
|
5.0
|
0.0
|
1.0
|
|
Potassium binding site 8 out
of 12 in 6vwp
Go back to
Potassium Binding Sites List in 6vwp
Potassium binding site 8 out
of 12 in the Crystal Structure of E. Coli Guanosine Kinase in Complex with Ppgpp
 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 E. Coli Guanosine Kinase in Complex with Ppgpp within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:K505
b:0.9
occ:1.00
|
O
|
E:VAL248
|
2.6
|
0.3
|
1.0
|
|
O
|
E:LYS245
|
2.8
|
0.9
|
1.0
|
|
O
|
E:TRP277
|
2.9
|
0.7
|
1.0
|
|
HA
|
E:VAL278
|
3.2
|
0.4
|
1.0
|
|
O
|
E:LEU244
|
3.2
|
0.0
|
1.0
|
|
C
|
E:LYS245
|
3.7
|
0.0
|
1.0
|
|
HA
|
E:LYS245
|
3.7
|
0.5
|
1.0
|
|
C
|
E:VAL248
|
3.8
|
0.9
|
1.0
|
|
HG12
|
E:VAL278
|
3.9
|
0.5
|
1.0
|
|
HA
|
E:SER249
|
3.9
|
0.2
|
1.0
|
|
C
|
E:TRP277
|
4.1
|
0.7
|
1.0
|
|
CA
|
E:VAL278
|
4.2
|
0.8
|
1.0
|
|
CA
|
E:LYS245
|
4.2
|
0.9
|
1.0
|
|
C
|
E:LEU244
|
4.3
|
0.2
|
1.0
|
|
HN22
|
E:GMP503
|
4.4
|
0.1
|
1.0
|
|
N
|
E:VAL248
|
4.4
|
0.8
|
1.0
|
|
C
|
E:HIS247
|
4.5
|
0.8
|
1.0
|
|
O
|
E:HIS247
|
4.5
|
0.3
|
1.0
|
|
O
|
E:ASP246
|
4.5
|
0.1
|
1.0
|
|
C
|
E:ASP246
|
4.6
|
0.7
|
1.0
|
|
H
|
E:VAL248
|
4.6
|
0.4
|
1.0
|
|
N
|
E:VAL278
|
4.6
|
0.5
|
1.0
|
|
N
|
E:SER249
|
4.6
|
0.1
|
1.0
|
|
N
|
E:ASP246
|
4.7
|
0.9
|
1.0
|
|
CA
|
E:SER249
|
4.7
|
0.5
|
1.0
|
|
CG1
|
E:VAL278
|
4.7
|
0.7
|
1.0
|
|
OD1
|
E:ASP279
|
4.7
|
0.7
|
1.0
|
|
CA
|
E:VAL248
|
4.7
|
0.9
|
1.0
|
|
N
|
E:HIS247
|
4.7
|
0.5
|
1.0
|
|
N
|
E:LYS245
|
4.8
|
1.0
|
1.0
|
|
CB
|
E:VAL278
|
4.9
|
0.7
|
1.0
|
|
HB2
|
E:SER249
|
4.9
|
0.6
|
1.0
|
|
HB
|
E:VAL278
|
4.9
|
0.9
|
1.0
|
|
H
|
E:HIS247
|
5.0
|
0.5
|
1.0
|
|
Potassium binding site 9 out
of 12 in 6vwp
Go back to
Potassium Binding Sites List in 6vwp
Potassium binding site 9 out
of 12 in the Crystal Structure of E. Coli Guanosine Kinase in Complex with Ppgpp
 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 E. Coli Guanosine Kinase in Complex with Ppgpp within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:K504
b:0.6
occ:1.00
|
HN22
|
F:GMP503
|
3.6
|
0.8
|
1.0
|
|
HE2
|
F:LYS328
|
3.8
|
0.3
|
1.0
|
|
HH21
|
F:ARG326
|
3.8
|
0.3
|
1.0
|
|
OD1
|
F:ASP279
|
4.1
|
0.2
|
1.0
|
|
O
|
F:LYS245
|
4.1
|
0.8
|
1.0
|
|
HZ2
|
F:LYS328
|
4.4
|
0.9
|
1.0
|
|
OD2
|
F:ASP279
|
4.5
|
0.3
|
1.0
|
|
N2
|
F:GMP503
|
4.5
|
0.9
|
1.0
|
|
HZ1
|
F:LYS328
|
4.5
|
0.9
|
1.0
|
|
NH2
|
F:ARG326
|
4.5
|
0.9
|
1.0
|
|
HB3
|
F:LYS328
|
4.6
|
0.7
|
1.0
|
|
CE
|
F:LYS328
|
4.7
|
0.2
|
1.0
|
|
CG
|
F:ASP279
|
4.7
|
0.6
|
1.0
|
|
NZ
|
F:LYS328
|
4.7
|
0.6
|
1.0
|
|
HH22
|
F:ARG326
|
4.8
|
0.3
|
1.0
|
|
O
|
F:VAL248
|
4.8
|
0.3
|
1.0
|
|
HN21
|
F:GMP503
|
5.0
|
0.8
|
1.0
|
|
HA
|
F:SER249
|
5.0
|
0.3
|
1.0
|
|
Potassium binding site 10 out
of 12 in 6vwp
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Potassium Binding Sites List in 6vwp
Potassium binding site 10 out
of 12 in the Crystal Structure of E. Coli Guanosine Kinase in Complex with Ppgpp
 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 E. Coli Guanosine Kinase in Complex with Ppgpp within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:K504
b:0.1
occ:1.00
|
O
|
G:LYS245
|
3.3
|
0.9
|
1.0
|
|
O
|
G:VAL248
|
3.5
|
0.6
|
1.0
|
|
OD1
|
G:ASP279
|
3.8
|
0.3
|
1.0
|
|
O2'
|
G:GMP503
|
4.0
|
0.5
|
1.0
|
|
HO2'
|
G:GMP503
|
4.0
|
1.0
|
1.0
|
|
O
|
G:TRP277
|
4.0
|
0.2
|
1.0
|
|
HH21
|
G:ARG326
|
4.0
|
0.6
|
1.0
|
|
O
|
G:ASP246
|
4.1
|
0.8
|
1.0
|
|
HA
|
G:VAL278
|
4.2
|
0.1
|
1.0
|
|
HA
|
G:SER249
|
4.3
|
0.1
|
1.0
|
|
HN22
|
G:GMP503
|
4.3
|
0.6
|
1.0
|
|
C
|
G:LYS245
|
4.5
|
0.6
|
1.0
|
|
C
|
G:VAL248
|
4.5
|
0.6
|
1.0
|
|
HZ2
|
G:LYS328
|
4.5
|
0.7
|
1.0
|
|
C
|
G:ASP246
|
4.6
|
0.5
|
1.0
|
|
HB2
|
G:SER249
|
4.6
|
0.6
|
1.0
|
|
O
|
G:HIS247
|
4.7
|
0.8
|
1.0
|
|
O
|
G:LEU244
|
4.7
|
0.4
|
1.0
|
|
HZ1
|
G:LYS328
|
4.7
|
0.7
|
1.0
|
|
NH2
|
G:ARG326
|
4.8
|
0.7
|
1.0
|
|
HE2
|
G:LYS328
|
4.8
|
0.7
|
1.0
|
|
C
|
G:HIS247
|
4.9
|
0.6
|
1.0
|
|
HE3
|
G:LYS328
|
4.9
|
0.7
|
1.0
|
|
HH22
|
G:ARG326
|
4.9
|
0.6
|
1.0
|
|
HA
|
G:LYS245
|
4.9
|
0.8
|
1.0
|
|
CG
|
G:ASP279
|
5.0
|
0.1
|
1.0
|
|
NZ
|
G:LYS328
|
5.0
|
0.7
|
1.0
|
|
Reference:
B.Wang,
R.A.Grant,
M.T.Laub.
Ppgpp Coordinates Nucleotide and Amino-Acid Synthesis in E. Coli During Starvation. Mol.Cell V. 80 29 2020.
ISSN: ISSN 1097-2765
PubMed: 32857952
DOI: 10.1016/J.MOLCEL.2020.08.005
Page generated: Mon Aug 12 18:02:28 2024
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