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:

Potassium (K) 12 atoms

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

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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

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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

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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

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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 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 Dec 15 01:27:07 2020

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