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Vanadium in PDB 3f9b: W354F Yersinia Enterocolitica Ptpase Complexed with Divanadate

Enzymatic activity of W354F Yersinia Enterocolitica Ptpase Complexed with Divanadate

All present enzymatic activity of W354F Yersinia Enterocolitica Ptpase Complexed with Divanadate:
3.1.3.48;

Protein crystallography data

The structure of W354F Yersinia Enterocolitica Ptpase Complexed with Divanadate, PDB code: 3f9b was solved by T.A.S.Brandao, H.Robinson, S.J.Johnson, A.C.Hengge, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.10 / 1.42
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 54.196, 58.191, 90.347, 90.00, 90.00, 90.00
R / Rfree (%) 17.3 / 19.6

Vanadium Binding Sites:

The binding sites of Vanadium atom in the W354F Yersinia Enterocolitica Ptpase Complexed with Divanadate (pdb code 3f9b). This binding sites where shown within 5.0 Angstroms radius around Vanadium atom.
In total 3 binding sites of Vanadium where determined in the W354F Yersinia Enterocolitica Ptpase Complexed with Divanadate, PDB code: 3f9b:
Jump to Vanadium binding site number: 1; 2; 3;

Vanadium binding site 1 out of 3 in 3f9b

Go back to Vanadium Binding Sites List in 3f9b
Vanadium binding site 1 out of 3 in the W354F Yersinia Enterocolitica Ptpase Complexed with Divanadate


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 1 of W354F Yersinia Enterocolitica Ptpase Complexed with Divanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:V501

b:62.1
occ:1.00
V A:VO4501 0.0 62.1 1.0
O3 A:VO4501 1.9 62.5 1.0
O4 A:VO4501 1.9 62.2 1.0
O1 A:VO4501 1.9 62.4 1.0
O2 A:VO4501 1.9 62.3 1.0
O A:HOH589 3.3 46.1 1.0
O A:HOH592 3.7 47.2 1.0
OG A:SER388 3.7 26.1 1.0
NH2 A:ARG278 3.8 19.6 1.0
NE A:ARG278 4.1 21.0 1.0
OG A:SER389 4.1 29.5 1.0
N A:SER389 4.2 27.9 1.0
CB A:SER388 4.4 26.4 1.0
CA A:SER388 4.4 26.6 1.0
O A:HOH546 4.4 54.0 1.0
CZ A:ARG278 4.5 20.1 1.0
O A:HOH609 4.5 58.5 1.0
CD A:LYS342 4.7 25.4 1.0
C A:SER388 4.8 27.1 1.0
CB A:SER389 5.0 28.6 1.0

Vanadium binding site 2 out of 3 in 3f9b

Go back to Vanadium Binding Sites List in 3f9b
Vanadium binding site 2 out of 3 in the W354F Yersinia Enterocolitica Ptpase Complexed with Divanadate


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 2 of W354F Yersinia Enterocolitica Ptpase Complexed with Divanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:V502

b:23.3
occ:1.00
V2 A:PDV502 0.0 23.3 1.0
O6 A:PDV502 1.9 22.4 1.0
O5 A:PDV502 1.9 26.7 1.0
O7 A:PDV502 1.9 25.6 1.0
O3 A:PDV502 2.1 20.7 1.0
O4 A:PDV502 2.1 21.0 1.0
V1 A:PDV502 3.1 18.5 1.0
NE2 A:GLN450 3.8 16.5 1.0
NE A:ARG409 3.9 21.8 1.0
NE2 A:GLN446 4.0 22.3 1.0
O1 A:PDV502 4.1 19.7 1.0
N A:ARG409 4.1 14.4 1.0
O2 A:PDV502 4.2 17.5 1.0
CA A:GLY408 4.2 14.4 1.0
CG A:ARG409 4.3 17.1 1.0
O A:HOH63 4.4 23.3 1.0
NH2 A:ARG409 4.5 24.4 1.0
CZ A:ARG409 4.5 22.6 1.0
CE A:LYS447 4.6 26.9 1.0
O A:HOH510 4.6 37.9 1.0
CD A:ARG409 4.6 19.1 1.0
NZ A:LYS447 4.7 29.3 1.0
C A:GLY408 4.7 14.4 1.0
N A:GLY408 4.9 14.9 1.0

Vanadium binding site 3 out of 3 in 3f9b

Go back to Vanadium Binding Sites List in 3f9b
Vanadium binding site 3 out of 3 in the W354F Yersinia Enterocolitica Ptpase Complexed with Divanadate


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 3 of W354F Yersinia Enterocolitica Ptpase Complexed with Divanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:V502

b:18.5
occ:1.00
V1 A:PDV502 0.0 18.5 1.0
O2 A:PDV502 1.9 17.5 1.0
O1 A:PDV502 1.9 19.7 1.0
O3 A:PDV502 2.0 20.7 1.0
O4 A:PDV502 2.1 21.0 1.0
SG A:CYS403 2.4 17.1 1.0
V2 A:PDV502 3.1 23.3 1.0
CB A:CYS403 3.5 15.2 1.0
N A:GLY408 3.8 14.9 1.0
NE A:ARG409 3.9 21.8 1.0
N A:ALA405 3.9 15.8 1.0
NH2 A:ARG409 4.0 24.4 1.0
N A:ARG404 4.1 15.4 1.0
O7 A:PDV502 4.1 25.6 1.0
N A:ARG409 4.1 14.4 1.0
O5 A:PDV502 4.1 26.7 1.0
O6 A:PDV502 4.1 22.4 1.0
CA A:GLY408 4.2 14.4 1.0
N A:GLY406 4.2 15.5 1.0
O A:HOH510 4.3 37.9 1.0
CZ A:ARG409 4.4 22.6 1.0
CB A:ALA405 4.4 16.2 1.0
N A:VAL407 4.4 14.7 1.0
CA A:ALA405 4.6 16.1 1.0
C A:GLY408 4.6 14.4 1.0
CA A:CYS403 4.7 14.7 1.0
NE2 A:GLN446 4.7 22.3 1.0
CB A:ARG409 4.8 15.3 1.0
CA A:ARG404 4.8 16.0 1.0
C A:CYS403 4.8 14.8 1.0
C A:ALA405 4.8 15.9 1.0
CB A:ARG404 4.9 16.8 1.0
C A:ARG404 4.9 15.5 1.0
CG A:ARG409 4.9 17.1 1.0
C A:VAL407 4.9 15.1 1.0
CD A:ARG409 5.0 19.1 1.0

Reference:

T.A.Brandao, H.Robinson, S.J.Johnson, A.C.Hengge. Impaired Acid Catalysis By Mutation of A Protein Loop Hinge Residue in A Yoph Mutant Revealed By Crystal Structures. J.Am.Chem.Soc. V. 131 778 2009.
ISSN: ISSN 0002-7863
PubMed: 19140798
DOI: 10.1021/JA807418B
Page generated: Wed Dec 16 02:30:49 2020

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