Potassium in PDB 6vwo: Crystal Structure of E. Coli Guanosine Kinase
Enzymatic activity of Crystal Structure of E. Coli Guanosine Kinase
All present enzymatic activity of Crystal Structure of E. Coli Guanosine Kinase:
2.7.1.73;
Protein crystallography data
The structure of Crystal Structure of E. Coli Guanosine Kinase, PDB code: 6vwo
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)
|
46.50 /
1.78
|
Space group
|
P 32 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
118.117,
118.117,
75.447,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
18.1 /
20.5
|
Other elements in 6vwo:
The structure of Crystal Structure of E. Coli Guanosine Kinase also contains other interesting chemical elements:
Potassium Binding Sites:
The binding sites of Potassium atom in the Crystal Structure of E. Coli Guanosine Kinase
(pdb code 6vwo). This binding sites where shown within
5.0 Angstroms radius around Potassium atom.
In total 3 binding sites of Potassium where determined in the
Crystal Structure of E. Coli Guanosine Kinase, PDB code: 6vwo:
Jump to Potassium binding site number:
1;
2;
3;
Potassium binding site 1 out
of 3 in 6vwo
Go back to
Potassium Binding Sites List in 6vwo
Potassium binding site 1 out
of 3 in the Crystal Structure of E. Coli Guanosine Kinase
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 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K504
b:30.2
occ:0.50
|
O
|
A:THR133
|
2.6
|
30.2
|
1.0
|
O
|
A:CYS131
|
2.7
|
29.7
|
1.0
|
O
|
A:LEU130
|
2.8
|
30.2
|
1.0
|
HA
|
A:CYS131
|
3.1
|
36.3
|
1.0
|
C
|
A:CYS131
|
3.3
|
31.7
|
1.0
|
CA
|
A:CYS131
|
3.7
|
30.3
|
1.0
|
C
|
A:THR133
|
3.8
|
31.4
|
1.0
|
H
|
A:THR133
|
3.8
|
35.4
|
1.0
|
C
|
A:LEU130
|
3.9
|
31.2
|
1.0
|
N
|
A:THR133
|
4.0
|
29.5
|
1.0
|
HB
|
A:THR133
|
4.2
|
36.2
|
1.0
|
HA
|
A:SER135
|
4.3
|
37.1
|
1.0
|
N
|
A:CYS131
|
4.3
|
30.3
|
1.0
|
N
|
A:ASN132
|
4.4
|
29.9
|
1.0
|
CA
|
A:THR133
|
4.4
|
28.6
|
1.0
|
C
|
A:ASN132
|
4.4
|
32.2
|
1.0
|
O
|
A:HOH628
|
4.7
|
36.5
|
1.0
|
C
|
A:SER134
|
4.7
|
33.9
|
1.0
|
N
|
A:SER135
|
4.8
|
31.6
|
1.0
|
CB
|
A:THR133
|
4.8
|
30.2
|
1.0
|
N
|
A:SER134
|
4.9
|
27.9
|
1.0
|
CA
|
A:ASN132
|
4.9
|
30.0
|
1.0
|
O
|
A:SER134
|
4.9
|
31.4
|
1.0
|
H
|
A:ASN132
|
5.0
|
35.8
|
1.0
|
O
|
A:ASN132
|
5.0
|
29.4
|
1.0
|
CA
|
A:SER135
|
5.0
|
30.9
|
1.0
|
CB
|
A:CYS131
|
5.0
|
32.3
|
1.0
|
HB3
|
A:CYS131
|
5.0
|
38.7
|
1.0
|
|
Potassium binding site 2 out
of 3 in 6vwo
Go back to
Potassium Binding Sites List in 6vwo
Potassium binding site 2 out
of 3 in the Crystal Structure of E. Coli Guanosine Kinase
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 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K505
b:28.0
occ:1.00
|
O
|
A:LEU227
|
2.4
|
28.6
|
1.0
|
O
|
A:HOH772
|
2.4
|
33.8
|
1.0
|
O
|
A:HOH608
|
2.4
|
37.8
|
1.0
|
O
|
A:HOH661
|
2.5
|
27.7
|
1.0
|
OE2
|
A:GLU257
|
2.5
|
30.6
|
1.0
|
O
|
A:HOH776
|
2.6
|
37.1
|
1.0
|
OE1
|
A:GLU257
|
2.7
|
28.3
|
1.0
|
CD
|
A:GLU257
|
2.9
|
32.3
|
1.0
|
C
|
A:LEU227
|
3.6
|
27.8
|
1.0
|
HA2
|
A:GLY228
|
3.6
|
34.1
|
1.0
|
H
|
A:THR229
|
3.8
|
35.9
|
1.0
|
HA
|
A:MET253
|
4.0
|
33.9
|
1.0
|
H
|
A:ASN254
|
4.1
|
34.5
|
1.0
|
OG1
|
A:THR226
|
4.2
|
33.3
|
1.0
|
HG1
|
A:THR226
|
4.2
|
40.0
|
1.0
|
HB2
|
A:LEU227
|
4.3
|
32.5
|
1.0
|
O1B
|
A:ADP501
|
4.4
|
36.6
|
1.0
|
H
|
A:LEU227
|
4.4
|
33.5
|
1.0
|
CA
|
A:GLY228
|
4.4
|
28.4
|
1.0
|
O
|
A:HOH757
|
4.4
|
42.4
|
1.0
|
N
|
A:GLY228
|
4.4
|
30.1
|
1.0
|
CG
|
A:GLU257
|
4.4
|
29.8
|
1.0
|
OD1
|
A:ASP358
|
4.4
|
37.0
|
1.0
|
O
|
A:HOH639
|
4.5
|
31.2
|
1.0
|
N
|
A:LEU227
|
4.6
|
27.9
|
1.0
|
CA
|
A:LEU227
|
4.6
|
28.0
|
1.0
|
O
|
A:HOH624
|
4.6
|
34.5
|
1.0
|
O
|
A:HOH638
|
4.6
|
33.3
|
1.0
|
N
|
A:THR229
|
4.6
|
29.9
|
1.0
|
O
|
A:HOH742
|
4.6
|
50.7
|
1.0
|
O
|
A:HOH660
|
4.7
|
30.8
|
1.0
|
N
|
A:ASN254
|
4.7
|
28.8
|
1.0
|
HG2
|
A:GLU257
|
4.7
|
35.8
|
1.0
|
ND2
|
A:ASN254
|
4.8
|
36.6
|
1.0
|
HD22
|
A:ASN254
|
4.8
|
43.9
|
1.0
|
HD21
|
A:ASN254
|
4.8
|
43.9
|
1.0
|
HG3
|
A:GLU257
|
4.9
|
35.8
|
1.0
|
CA
|
A:MET253
|
4.9
|
28.2
|
1.0
|
HB3
|
A:ASN254
|
4.9
|
34.1
|
1.0
|
CB
|
A:LEU227
|
5.0
|
27.1
|
1.0
|
O
|
A:HOH795
|
5.0
|
43.1
|
1.0
|
|
Potassium binding site 3 out
of 3 in 6vwo
Go back to
Potassium Binding Sites List in 6vwo
Potassium binding site 3 out
of 3 in the Crystal Structure of E. Coli Guanosine Kinase
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 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K506
b:33.6
occ:1.00
|
O
|
A:VAL408
|
2.7
|
29.4
|
1.0
|
O
|
A:GLN411
|
2.7
|
33.8
|
1.0
|
O
|
A:ASN354
|
2.8
|
32.7
|
1.0
|
O
|
A:ASN352
|
2.8
|
33.8
|
1.0
|
O
|
A:SER413
|
3.0
|
28.8
|
1.0
|
HB3
|
A:ASN352
|
3.1
|
48.0
|
1.0
|
O
|
A:HIS412
|
3.3
|
36.6
|
1.0
|
HG13
|
A:VAL408
|
3.3
|
35.0
|
1.0
|
HG12
|
A:VAL408
|
3.4
|
35.0
|
1.0
|
C
|
A:SER413
|
3.6
|
28.1
|
1.0
|
C
|
A:HIS412
|
3.6
|
36.1
|
1.0
|
HB3
|
A:ASN354
|
3.7
|
45.1
|
1.0
|
OD1
|
A:ASN352
|
3.7
|
40.4
|
1.0
|
HG3
|
A:GLN411
|
3.7
|
42.6
|
1.0
|
C
|
A:ASN352
|
3.7
|
35.2
|
1.0
|
HA
|
A:PRO414
|
3.7
|
32.6
|
1.0
|
CG1
|
A:VAL408
|
3.8
|
29.2
|
1.0
|
C
|
A:GLN411
|
3.8
|
38.3
|
1.0
|
H
|
A:ASN354
|
3.8
|
38.8
|
1.0
|
C
|
A:VAL408
|
3.8
|
28.1
|
1.0
|
CB
|
A:ASN352
|
3.9
|
40.0
|
1.0
|
C
|
A:ASN354
|
3.9
|
36.5
|
1.0
|
N
|
A:ASN354
|
3.9
|
32.3
|
1.0
|
HA
|
A:HIS412
|
4.0
|
47.5
|
1.0
|
HA
|
A:LEU409
|
4.0
|
36.4
|
1.0
|
N
|
A:SER413
|
4.1
|
33.4
|
1.0
|
H
|
A:GLN411
|
4.1
|
36.1
|
1.0
|
CG
|
A:ASN352
|
4.1
|
45.8
|
1.0
|
N
|
A:PRO414
|
4.2
|
28.9
|
1.0
|
CA
|
A:HIS412
|
4.3
|
39.6
|
1.0
|
CA
|
A:ASN354
|
4.3
|
37.6
|
1.0
|
C
|
A:THR353
|
4.4
|
39.4
|
1.0
|
CA
|
A:ASN352
|
4.4
|
40.5
|
1.0
|
HG11
|
A:VAL408
|
4.4
|
35.0
|
1.0
|
CA
|
A:SER413
|
4.4
|
37.0
|
1.0
|
CA
|
A:PRO414
|
4.4
|
27.2
|
1.0
|
CB
|
A:ASN354
|
4.5
|
37.6
|
1.0
|
N
|
A:HIS412
|
4.5
|
32.5
|
1.0
|
HG2
|
A:GLN411
|
4.5
|
42.6
|
1.0
|
CG
|
A:GLN411
|
4.5
|
35.5
|
1.0
|
HA
|
A:VAL408
|
4.6
|
30.5
|
1.0
|
H
|
A:SER413
|
4.6
|
40.0
|
1.0
|
HB2
|
A:ASN352
|
4.6
|
48.0
|
1.0
|
N
|
A:THR353
|
4.6
|
37.7
|
1.0
|
H
|
A:ASN352
|
4.7
|
42.5
|
1.0
|
CA
|
A:VAL408
|
4.7
|
25.4
|
1.0
|
N
|
A:LEU409
|
4.7
|
29.6
|
1.0
|
CA
|
A:LEU409
|
4.7
|
30.4
|
1.0
|
HE21
|
A:GLN411
|
4.7
|
45.5
|
1.0
|
HA
|
A:SER413
|
4.8
|
44.4
|
1.0
|
N
|
A:GLN411
|
4.8
|
30.1
|
1.0
|
HA
|
A:THR353
|
4.8
|
48.2
|
1.0
|
O
|
A:THR353
|
4.8
|
36.4
|
1.0
|
CB
|
A:VAL408
|
4.8
|
25.7
|
1.0
|
CA
|
A:GLN411
|
4.9
|
34.9
|
1.0
|
CA
|
A:THR353
|
4.9
|
40.2
|
1.0
|
N
|
A:ASN352
|
4.9
|
35.4
|
1.0
|
O
|
A:HOH647
|
4.9
|
43.1
|
1.0
|
HB2
|
A:ASN354
|
4.9
|
45.1
|
1.0
|
C
|
A:LEU409
|
4.9
|
31.2
|
1.0
|
HB3
|
A:PRO414
|
5.0
|
34.1
|
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 18:02:21 2024
|