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Vanadium in PDB 3gw8: Crystal Structure of Phosphoglyceromutase From Burkholderia Pseudomallei with Vanadate and Glycerol

Enzymatic activity of Crystal Structure of Phosphoglyceromutase From Burkholderia Pseudomallei with Vanadate and Glycerol

All present enzymatic activity of Crystal Structure of Phosphoglyceromutase From Burkholderia Pseudomallei with Vanadate and Glycerol:
5.4.2.1;

Protein crystallography data

The structure of Crystal Structure of Phosphoglyceromutase From Burkholderia Pseudomallei with Vanadate and Glycerol, PDB code: 3gw8 was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.93
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 45.175, 49.112, 62.590, 106.42, 91.18, 107.61
R / Rfree (%) 18.7 / 22.7

Vanadium Binding Sites:

The binding sites of Vanadium atom in the Crystal Structure of Phosphoglyceromutase From Burkholderia Pseudomallei with Vanadate and Glycerol (pdb code 3gw8). This binding sites where shown within 5.0 Angstroms radius around Vanadium atom.
In total 4 binding sites of Vanadium where determined in the Crystal Structure of Phosphoglyceromutase From Burkholderia Pseudomallei with Vanadate and Glycerol, PDB code: 3gw8:
Jump to Vanadium binding site number: 1; 2; 3; 4;

Vanadium binding site 1 out of 4 in 3gw8

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Vanadium binding site 1 out of 4 in the Crystal Structure of Phosphoglyceromutase From Burkholderia Pseudomallei with Vanadate and Glycerol


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 1 of Crystal Structure of Phosphoglyceromutase From Burkholderia Pseudomallei with Vanadate and Glycerol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:V401

b:24.2
occ:1.00
 V A:VO4401 0.0 24.2 1.0
O3 A:VO4401 1.9 26.0 1.0
O2 A:VO4401 1.9 21.7 1.0
O1 A:VO4401 1.9 20.2 1.0
O2 A:GOL402 1.9 34.5 0.5
O2 A:GOL402 2.0 40.8 0.5
NE2 A:HIS9 2.3 16.6 1.0
C2 A:GOL402 3.2 34.6 0.5
CE1 A:HIS9 3.2 17.0 1.0
C2 A:GOL402 3.3 41.4 0.5
CD2 A:HIS9 3.3 16.1 1.0
OE1 A:GLU87 3.4 26.9 1.0
C1 A:GOL402 3.6 33.6 0.5
O1 A:GOL402 3.6 41.6 0.5
C1 A:GOL402 3.7 40.8 0.5
NE A:ARG60 3.9 13.2 1.0
C3 A:GOL402 3.9 34.2 0.5
NH2 A:ARG8 3.9 20.1 1.0
O A:HOH255 4.0 35.5 1.0
CD A:GLU87 4.0 21.8 1.0
NE A:ARG8 4.1 19.8 1.0
O A:HOH313 4.1 22.0 1.0
C3 A:GOL402 4.1 40.8 0.5
NH2 A:ARG60 4.2 13.4 1.0
ND1 A:HIS182 4.2 14.8 1.0
N A:GLY183 4.3 15.4 1.0
CG A:GLU87 4.3 17.7 1.0
CB A:HIS182 4.3 14.3 1.0
ND1 A:HIS9 4.4 14.7 1.0
CG A:HIS9 4.4 16.1 1.0
CZ A:ARG8 4.5 20.6 1.0
CZ A:ARG60 4.5 14.7 1.0
CA A:HIS182 4.7 14.4 1.0
CG A:HIS182 4.8 14.8 1.0
ND2 A:ASN15 4.8 22.8 1.0
CB A:GLU87 4.8 16.0 1.0
OE2 A:GLU87 4.9 23.2 1.0
CD A:ARG60 4.9 13.0 1.0
O1 A:GOL402 5.0 34.2 0.5

Vanadium binding site 2 out of 4 in 3gw8

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Vanadium binding site 2 out of 4 in the Crystal Structure of Phosphoglyceromutase From Burkholderia Pseudomallei with Vanadate and Glycerol


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 2 of Crystal Structure of Phosphoglyceromutase From Burkholderia Pseudomallei with Vanadate and Glycerol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:V403

b:47.3
occ:0.50
 V A:VO4403 0.0 47.3 0.5
O4 A:VO4403 1.9 47.5 0.5
O3 A:VO4403 1.9 46.9 0.5
O2 A:VO4403 1.9 46.7 0.5
O1 A:VO4403 1.9 46.9 0.5
NZ A:LYS98 3.1 36.7 1.0
C2 A:GOL402 3.7 41.4 0.5
C2 A:GOL402 3.7 34.6 0.5
O1 A:GOL402 4.0 34.2 0.5
OH A:TYR90 4.0 37.0 1.0
O3 A:GOL402 4.0 41.8 0.5
O3 A:GOL402 4.0 35.2 0.5
O A:HOH255 4.0 35.5 1.0
C1 A:GOL402 4.1 40.8 0.5
CE A:LYS98 4.1 35.8 1.0
C3 A:GOL402 4.2 34.2 0.5
O1 A:GOL402 4.2 41.6 0.5
CE2 A:TYR90 4.2 30.8 1.0
C3 A:GOL402 4.3 40.8 0.5
C1 A:GOL402 4.3 33.6 0.5
CZ A:TYR90 4.4 31.7 1.0
CD1 A:PHE20 4.6 23.6 1.0
O2 A:GOL402 4.7 34.5 0.5
O2 A:GOL402 4.7 40.8 0.5
CD A:LYS98 4.9 34.5 1.0
CE1 A:PHE20 5.0 24.5 1.0

Vanadium binding site 3 out of 4 in 3gw8

Go back to Vanadium Binding Sites List in 3gw8
Vanadium binding site 3 out of 4 in the Crystal Structure of Phosphoglyceromutase From Burkholderia Pseudomallei with Vanadate and Glycerol


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 3 of Crystal Structure of Phosphoglyceromutase From Burkholderia Pseudomallei with Vanadate and Glycerol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:V401

b:23.6
occ:1.00
 V B:VO4401 0.0 23.6 1.0
O1 B:VO4401 1.9 23.7 1.0
O3 B:VO4401 1.9 24.9 1.0
O2 B:VO4401 1.9 22.9 1.0
O2 B:GOL402 1.9 21.6 0.5
O2 B:GOL402 2.0 28.6 0.5
NE2 B:HIS9 2.2 12.4 1.0
C2 B:GOL402 3.1 21.6 0.5
C2 B:GOL402 3.1 27.1 0.5
CE1 B:HIS9 3.2 12.7 1.0
CD2 B:HIS9 3.2 13.7 1.0
O1 B:GOL402 3.4 20.7 0.5
C1 B:GOL402 3.5 20.8 0.5
OE1 B:GLU87 3.5 27.2 1.0
C1 B:GOL402 3.8 27.1 0.5
NH2 B:ARG8 3.8 17.0 1.0
NE B:ARG60 3.9 13.3 1.0
NE B:ARG8 4.0 17.4 1.0
O B:HOH277 4.0 20.9 1.0
CD B:GLU87 4.1 20.3 1.0
NH2 B:ARG60 4.2 13.0 1.0
C3 B:GOL402 4.3 20.4 0.5
ND1 B:HIS182 4.3 12.2 1.0
N B:GLY183 4.3 15.3 1.0
ND1 B:HIS9 4.3 13.9 1.0
C3 B:GOL402 4.3 26.5 0.5
CG B:GLU87 4.3 17.6 1.0
CG B:HIS9 4.4 14.4 1.0
O3 B:GOL402 4.4 19.2 0.5
CZ B:ARG8 4.4 19.4 1.0
CB B:HIS182 4.4 14.3 1.0
CZ B:ARG60 4.6 13.8 1.0
O3 B:GOL402 4.7 25.5 0.5
ND2 B:ASN15 4.7 17.1 1.0
CA B:HIS182 4.8 14.5 1.0
CG B:HIS182 4.9 14.1 1.0
CB B:GLU87 4.9 15.2 1.0
CD B:ARG60 4.9 12.5 1.0
O2 B:VO4403 5.0 37.6 0.5

Vanadium binding site 4 out of 4 in 3gw8

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Vanadium binding site 4 out of 4 in the Crystal Structure of Phosphoglyceromutase From Burkholderia Pseudomallei with Vanadate and Glycerol


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 4 of Crystal Structure of Phosphoglyceromutase From Burkholderia Pseudomallei with Vanadate and Glycerol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:V403

b:38.3
occ:0.50
 V B:VO4403 0.0 38.3 0.5
O3 B:VO4403 1.9 36.7 0.5
O2 B:VO4403 1.9 37.6 0.5
O1 B:VO4403 1.9 38.6 0.5
O4 B:VO4403 1.9 38.3 0.5
C3 B:GOL402 3.4 26.5 0.5
C3 B:GOL402 3.4 20.4 0.5
C2 B:GOL402 3.6 21.6 0.5
OH B:TYR90 3.6 28.2 1.0
C2 B:GOL402 3.7 27.1 0.5
NZ B:LYS98 3.8 27.1 1.0
C1 B:GOL402 4.0 20.8 0.5
O1 B:GOL402 4.0 27.9 0.5
CE2 B:TYR90 4.1 25.9 1.0
NH1 B:ARG114 4.2 42.1 1.0
ND2 B:ASN184 4.2 26.0 1.0
O1 B:GOL402 4.3 20.7 0.5
CZ B:TYR90 4.3 26.0 1.0
C1 B:GOL402 4.4 27.1 0.5
NE B:ARG114 4.4 38.8 1.0
O3 B:GOL402 4.6 25.5 0.5
O3 B:GOL402 4.7 19.2 0.5
NH2 B:ARG115 4.7 47.3 1.0
CZ B:ARG114 4.7 41.1 1.0
O2 B:GOL402 4.8 21.6 0.5
O2 B:GOL402 4.9 28.6 0.5
CE B:LYS98 5.0 26.5 1.0

Reference:

D.R.Davies, B.L.Staker, J.A.Abendroth, T.E.Edwards, R.Hartley, J.Leonard, H.Kim, A.L.Rychel, S.N.Hewitt, P.J.Myler, L.J.Stewart. An Ensemble of Structures of Burkholderia Pseudomallei 2,3-Bisphosphoglycerate-Dependent Phosphoglycerate Mutase. Acta Crystallogr.,Sect.F V. 67 1044 2011.
ISSN: ESSN 1744-3091
PubMed: 21904048
DOI: 10.1107/S1744309111030405
Page generated: Fri Oct 11 19:19:28 2024

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