Magnesium 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:
Magnesium Binding Sites:
The binding sites of Magnesium 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 Magnesium atom.
In total 7 binding sites of Magnesium where determined in the
Crystal Structure of E. Coli Guanosine Kinase in Complex with Ppgpp, PDB code: 6vwp:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
Magnesium binding site 1 out
of 7 in 6vwp
Go back to
Magnesium Binding Sites List in 6vwp
Magnesium binding site 1 out
of 7 in the Crystal Structure of E. Coli Guanosine Kinase in Complex with Ppgpp
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg 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:Mg505
b:0.4
occ:1.00
|
OE2
|
A:GLU257
|
2.8
|
0.4
|
1.0
|
O
|
A:LEU227
|
2.8
|
0.6
|
1.0
|
CD
|
A:GLU257
|
3.7
|
0.1
|
1.0
|
OD1
|
A:ASP358
|
3.8
|
0.1
|
1.0
|
OE1
|
A:GLU257
|
3.9
|
0.4
|
1.0
|
HA2
|
A:GLY228
|
3.9
|
0.6
|
1.0
|
C
|
A:LEU227
|
4.0
|
0.1
|
1.0
|
HD22
|
A:ASN254
|
4.1
|
0.1
|
1.0
|
HD21
|
A:ASN254
|
4.3
|
0.1
|
1.0
|
H
|
A:THR229
|
4.4
|
0.9
|
1.0
|
ND2
|
A:ASN254
|
4.4
|
0.1
|
1.0
|
O
|
A:ASN354
|
4.4
|
0.0
|
1.0
|
OG1
|
A:THR226
|
4.6
|
0.8
|
1.0
|
HG1
|
A:THR226
|
4.6
|
0.7
|
1.0
|
H
|
A:LEU227
|
4.6
|
0.8
|
1.0
|
HG21
|
A:THR94
|
4.6
|
0.1
|
1.0
|
CA
|
A:GLY228
|
4.7
|
0.8
|
1.0
|
CG
|
A:ASP358
|
4.8
|
0.4
|
1.0
|
HO5'
|
A:GMP502
|
4.8
|
0.7
|
1.0
|
N
|
A:GLY228
|
4.8
|
0.3
|
1.0
|
N
|
A:THR229
|
4.9
|
0.5
|
1.0
|
|
Magnesium binding site 2 out
of 7 in 6vwp
Go back to
Magnesium Binding Sites List in 6vwp
Magnesium binding site 2 out
of 7 in the Crystal Structure of E. Coli Guanosine Kinase in Complex with Ppgpp
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg 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
|
C:Mg506
b:0.7
occ:1.00
|
HG1
|
C:THR226
|
2.6
|
0.0
|
1.0
|
OG1
|
C:THR226
|
2.8
|
0.2
|
1.0
|
O
|
C:LEU227
|
3.0
|
0.4
|
1.0
|
H
|
C:LEU227
|
3.3
|
0.8
|
1.0
|
OE2
|
C:GLU257
|
3.6
|
0.4
|
1.0
|
OE1
|
C:GLU257
|
3.6
|
0.3
|
1.0
|
OD1
|
C:ASP358
|
3.7
|
0.7
|
1.0
|
N
|
C:LEU227
|
3.9
|
0.0
|
1.0
|
CD
|
C:GLU257
|
4.1
|
0.1
|
1.0
|
C
|
C:LEU227
|
4.1
|
0.5
|
1.0
|
CB
|
C:THR226
|
4.2
|
0.4
|
1.0
|
HA3
|
C:GLY357
|
4.4
|
0.9
|
1.0
|
CA
|
C:LEU227
|
4.6
|
98.6
|
1.0
|
HA
|
C:MET253
|
4.6
|
0.3
|
1.0
|
HB2
|
C:LEU227
|
4.6
|
0.6
|
1.0
|
HA
|
C:THR226
|
4.7
|
0.6
|
1.0
|
C
|
C:THR226
|
4.7
|
0.9
|
1.0
|
HB
|
C:THR226
|
4.7
|
0.9
|
1.0
|
HG21
|
C:THR94
|
4.7
|
0.6
|
1.0
|
CA
|
C:THR226
|
4.8
|
94.6
|
1.0
|
HB1
|
C:ALA252
|
4.8
|
0.3
|
1.0
|
H
|
C:ASP358
|
4.9
|
0.7
|
1.0
|
HD22
|
C:ASN254
|
4.9
|
0.9
|
1.0
|
CG
|
C:ASP358
|
4.9
|
0.7
|
1.0
|
O
|
C:ALA252
|
4.9
|
1.0
|
1.0
|
HG21
|
C:THR226
|
5.0
|
0.5
|
1.0
|
HG23
|
C:THR226
|
5.0
|
0.5
|
1.0
|
N
|
C:ASP358
|
5.0
|
0.6
|
1.0
|
|
Magnesium binding site 3 out
of 7 in 6vwp
Go back to
Magnesium Binding Sites List in 6vwp
Magnesium binding site 3 out
of 7 in the Crystal Structure of E. Coli Guanosine Kinase in Complex with Ppgpp
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg 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
|
D:Mg505
b:0.9
occ:1.00
|
O
|
D:LEU227
|
2.8
|
0.8
|
1.0
|
OD1
|
D:ASP358
|
2.8
|
0.8
|
1.0
|
OG1
|
D:THR226
|
2.9
|
0.4
|
1.0
|
HG1
|
D:THR226
|
3.0
|
0.1
|
1.0
|
OE2
|
D:GLU257
|
3.5
|
0.7
|
1.0
|
H
|
D:LEU227
|
3.6
|
0.8
|
1.0
|
OE1
|
D:GLU257
|
3.8
|
0.8
|
1.0
|
CG
|
D:ASP358
|
3.9
|
0.7
|
1.0
|
HG21
|
D:THR94
|
3.9
|
0.3
|
1.0
|
C
|
D:LEU227
|
4.0
|
0.6
|
1.0
|
N
|
D:LEU227
|
4.1
|
0.3
|
1.0
|
CD
|
D:GLU257
|
4.1
|
0.1
|
1.0
|
OD2
|
D:ASP358
|
4.3
|
0.8
|
1.0
|
HG23
|
D:THR226
|
4.3
|
0.9
|
1.0
|
CB
|
D:THR226
|
4.3
|
0.2
|
1.0
|
HG23
|
D:THR94
|
4.4
|
0.3
|
1.0
|
CA
|
D:LEU227
|
4.6
|
0.8
|
1.0
|
CG2
|
D:THR94
|
4.6
|
0.8
|
1.0
|
HA2
|
D:GLY228
|
4.7
|
0.5
|
1.0
|
H
|
D:ASP358
|
4.7
|
0.9
|
1.0
|
CG2
|
D:THR226
|
4.7
|
0.1
|
1.0
|
HB2
|
D:LEU227
|
4.8
|
0.9
|
1.0
|
C
|
D:THR226
|
4.8
|
0.1
|
1.0
|
HB
|
D:THR226
|
4.9
|
0.1
|
1.0
|
HD22
|
D:ASN254
|
4.9
|
0.3
|
1.0
|
HG21
|
D:THR226
|
4.9
|
0.9
|
1.0
|
|
Magnesium binding site 4 out
of 7 in 6vwp
Go back to
Magnesium Binding Sites List in 6vwp
Magnesium binding site 4 out
of 7 in the Crystal Structure of E. Coli Guanosine Kinase in Complex with Ppgpp
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg 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
|
E:Mg506
b:0.5
occ:1.00
|
HA2
|
E:GLY228
|
3.0
|
0.9
|
1.0
|
O
|
E:LEU227
|
3.1
|
0.5
|
1.0
|
OD1
|
E:ASP358
|
3.6
|
0.9
|
1.0
|
OE2
|
E:GLU257
|
3.7
|
0.3
|
1.0
|
HH
|
E:TYR195
|
4.0
|
0.6
|
1.0
|
O5'
|
E:GMP502
|
4.0
|
0.9
|
1.0
|
CA
|
E:GLY228
|
4.0
|
0.9
|
1.0
|
HO5'
|
E:GMP502
|
4.1
|
0.4
|
1.0
|
C
|
E:LEU227
|
4.1
|
0.6
|
1.0
|
OD2
|
E:ASP358
|
4.2
|
0.8
|
1.0
|
O
|
E:ASN354
|
4.2
|
0.9
|
1.0
|
HG1
|
E:THR94
|
4.2
|
0.2
|
1.0
|
H
|
E:THR229
|
4.3
|
0.6
|
1.0
|
CG
|
E:ASP358
|
4.3
|
0.1
|
1.0
|
N
|
E:GLY228
|
4.5
|
0.5
|
1.0
|
HA3
|
E:GLY228
|
4.6
|
0.9
|
1.0
|
HG21
|
E:THR94
|
4.6
|
1.0
|
1.0
|
HE2
|
E:TYR195
|
4.6
|
0.7
|
1.0
|
N
|
E:THR229
|
4.6
|
0.9
|
1.0
|
C
|
E:GLY228
|
4.6
|
0.4
|
1.0
|
OG1
|
E:THR94
|
4.7
|
0.8
|
1.0
|
OH
|
E:TYR195
|
4.7
|
0.8
|
1.0
|
CD
|
E:GLU257
|
4.8
|
0.2
|
1.0
|
HG23
|
E:THR229
|
4.9
|
0.7
|
1.0
|
|
Magnesium binding site 5 out
of 7 in 6vwp
Go back to
Magnesium Binding Sites List in 6vwp
Magnesium binding site 5 out
of 7 in the Crystal Structure of E. Coli Guanosine Kinase in Complex with Ppgpp
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg 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
|
F:Mg505
b:0.3
occ:1.00
|
HG1
|
F:THR226
|
2.9
|
0.1
|
1.0
|
OG1
|
F:THR226
|
3.0
|
0.1
|
1.0
|
O
|
F:LEU227
|
3.1
|
0.7
|
1.0
|
OE2
|
F:GLU257
|
3.4
|
0.7
|
1.0
|
OE1
|
F:GLU257
|
3.5
|
0.0
|
1.0
|
OD1
|
F:ASP358
|
3.6
|
0.4
|
1.0
|
H
|
F:LEU227
|
3.8
|
0.4
|
1.0
|
CD
|
F:GLU257
|
3.9
|
0.7
|
1.0
|
HA3
|
F:GLY357
|
4.2
|
0.1
|
1.0
|
C
|
F:LEU227
|
4.3
|
0.5
|
1.0
|
N
|
F:LEU227
|
4.3
|
0.3
|
1.0
|
HA
|
F:MET253
|
4.4
|
0.5
|
1.0
|
CB
|
F:THR226
|
4.4
|
0.1
|
1.0
|
HD22
|
F:ASN254
|
4.5
|
0.4
|
1.0
|
HG21
|
F:THR94
|
4.6
|
0.2
|
1.0
|
HG23
|
F:THR226
|
4.6
|
0.9
|
1.0
|
H
|
F:ASP358
|
4.6
|
0.8
|
1.0
|
HB3
|
F:ASN254
|
4.8
|
0.2
|
1.0
|
N
|
F:ASP358
|
4.8
|
0.3
|
1.0
|
CG
|
F:ASP358
|
4.8
|
0.8
|
1.0
|
ND2
|
F:ASN254
|
4.8
|
1.0
|
1.0
|
H
|
F:ASN254
|
4.8
|
0.5
|
1.0
|
HB1
|
F:ALA252
|
4.8
|
0.8
|
1.0
|
HB
|
F:THR226
|
4.8
|
0.3
|
1.0
|
HA2
|
F:GLY228
|
4.9
|
0.5
|
1.0
|
CA
|
F:LEU227
|
4.9
|
0.6
|
1.0
|
HB2
|
F:LEU227
|
4.9
|
0.2
|
1.0
|
N
|
F:MET253
|
4.9
|
0.5
|
1.0
|
C
|
F:MET253
|
4.9
|
0.5
|
1.0
|
CA
|
F:MET253
|
4.9
|
0.1
|
1.0
|
C
|
F:GLY357
|
4.9
|
0.4
|
1.0
|
CA
|
F:GLY357
|
5.0
|
0.9
|
1.0
|
|
Magnesium binding site 6 out
of 7 in 6vwp
Go back to
Magnesium Binding Sites List in 6vwp
Magnesium binding site 6 out
of 7 in the Crystal Structure of E. Coli Guanosine Kinase in Complex with Ppgpp
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg 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
|
G:Mg505
b:0.6
occ:1.00
|
O
|
G:LEU227
|
2.1
|
0.5
|
1.0
|
OD1
|
G:ASP358
|
3.3
|
0.6
|
1.0
|
C
|
G:LEU227
|
3.3
|
0.6
|
1.0
|
OE2
|
G:GLU257
|
3.5
|
0.6
|
1.0
|
HA2
|
G:GLY228
|
3.5
|
0.8
|
1.0
|
OG1
|
G:THR226
|
3.5
|
0.7
|
1.0
|
HG1
|
G:THR226
|
3.6
|
0.2
|
1.0
|
HG21
|
G:THR94
|
3.7
|
0.7
|
1.0
|
H
|
G:LEU227
|
3.8
|
0.0
|
1.0
|
O
|
G:GLY228
|
3.9
|
0.2
|
1.0
|
HG23
|
G:THR94
|
4.1
|
0.7
|
1.0
|
CA
|
G:GLY228
|
4.1
|
0.7
|
1.0
|
N
|
G:GLY228
|
4.2
|
0.1
|
1.0
|
N
|
G:LEU227
|
4.2
|
0.8
|
1.0
|
OE1
|
G:GLU257
|
4.2
|
0.3
|
1.0
|
CD
|
G:GLU257
|
4.2
|
0.4
|
1.0
|
CG
|
G:ASP358
|
4.3
|
0.9
|
1.0
|
CA
|
G:LEU227
|
4.3
|
0.1
|
1.0
|
HG1
|
G:THR94
|
4.4
|
0.5
|
1.0
|
CG2
|
G:THR94
|
4.4
|
0.4
|
1.0
|
C
|
G:GLY228
|
4.4
|
0.8
|
1.0
|
HD22
|
G:ASN254
|
4.6
|
0.7
|
1.0
|
HB2
|
G:LEU227
|
4.6
|
0.9
|
1.0
|
OD2
|
G:ASP358
|
4.6
|
0.2
|
1.0
|
HO5'
|
G:GMP502
|
4.7
|
0.8
|
1.0
|
HG23
|
G:THR226
|
4.8
|
0.2
|
1.0
|
HD21
|
G:ASN254
|
4.8
|
0.7
|
1.0
|
CB
|
G:THR226
|
4.8
|
0.6
|
1.0
|
OG1
|
G:THR94
|
4.8
|
0.9
|
1.0
|
ND2
|
G:ASN254
|
4.9
|
0.6
|
1.0
|
O
|
G:ASN354
|
5.0
|
0.2
|
1.0
|
HA3
|
G:GLY228
|
5.0
|
0.8
|
1.0
|
|
Magnesium binding site 7 out
of 7 in 6vwp
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Magnesium Binding Sites List in 6vwp
Magnesium binding site 7 out
of 7 in the Crystal Structure of E. Coli Guanosine Kinase in Complex with Ppgpp
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg 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
|
H:Mg506
b:0.2
occ:1.00
|
HG1
|
H:THR226
|
2.9
|
0.3
|
1.0
|
OG1
|
H:THR226
|
3.1
|
0.8
|
1.0
|
O
|
H:LEU227
|
3.3
|
0.7
|
1.0
|
OE1
|
H:GLU257
|
3.5
|
0.4
|
1.0
|
H
|
H:LEU227
|
3.6
|
0.6
|
1.0
|
OE2
|
H:GLU257
|
3.7
|
0.0
|
1.0
|
OD1
|
H:ASP358
|
3.7
|
0.0
|
1.0
|
HD22
|
H:ASN254
|
3.8
|
0.2
|
1.0
|
CD
|
H:GLU257
|
4.0
|
0.5
|
1.0
|
N
|
H:LEU227
|
4.2
|
0.3
|
1.0
|
HA3
|
H:GLY357
|
4.2
|
0.9
|
1.0
|
HB3
|
H:ASN254
|
4.3
|
1.0
|
1.0
|
ND2
|
H:ASN254
|
4.4
|
0.2
|
1.0
|
C
|
H:LEU227
|
4.4
|
0.3
|
1.0
|
CB
|
H:THR226
|
4.5
|
0.2
|
1.0
|
HD21
|
H:ASN254
|
4.7
|
0.2
|
1.0
|
HA
|
H:MET253
|
4.7
|
0.0
|
1.0
|
H
|
H:ASP358
|
4.8
|
0.5
|
1.0
|
HB2
|
H:LEU227
|
4.8
|
0.4
|
1.0
|
CA
|
H:LEU227
|
4.9
|
0.4
|
1.0
|
H
|
H:ASN254
|
4.9
|
0.9
|
1.0
|
HG21
|
H:THR94
|
4.9
|
0.3
|
1.0
|
HG23
|
H:THR226
|
4.9
|
0.7
|
1.0
|
CG
|
H:ASP358
|
4.9
|
0.8
|
1.0
|
N
|
H:ASN254
|
5.0
|
0.8
|
1.0
|
C
|
H:MET253
|
5.0
|
0.2
|
1.0
|
HB
|
H:THR226
|
5.0
|
0.2
|
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: Tue Oct 1 22:16:38 2024
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