Atomistry » Zinc » PDB 2gd8-2gze » 2gso
Atomistry »
  Zinc »
    PDB 2gd8-2gze »
      2gso »

Zinc in PDB 2gso: Structure of Xac Nucleotide Pyrophosphatase/Phosphodiesterase in Complex with Vanadate

Enzymatic activity of Structure of Xac Nucleotide Pyrophosphatase/Phosphodiesterase in Complex with Vanadate

All present enzymatic activity of Structure of Xac Nucleotide Pyrophosphatase/Phosphodiesterase in Complex with Vanadate:
3.6.1.9;

Protein crystallography data

The structure of Structure of Xac Nucleotide Pyrophosphatase/Phosphodiesterase in Complex with Vanadate, PDB code: 2gso was solved by J.G.Zalatan, T.D.Fenn, A.T.Brunger, D.Herschlag, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 66.040, 78.776, 129.686, 90.00, 90.00, 90.00
R / Rfree (%) 17.2 / 19.3

Other elements in 2gso:

The structure of Structure of Xac Nucleotide Pyrophosphatase/Phosphodiesterase in Complex with Vanadate also contains other interesting chemical elements:

Vanadium (V) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of Xac Nucleotide Pyrophosphatase/Phosphodiesterase in Complex with Vanadate (pdb code 2gso). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Structure of Xac Nucleotide Pyrophosphatase/Phosphodiesterase in Complex with Vanadate, PDB code: 2gso:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 2gso

Go back to Zinc Binding Sites List in 2gso
Zinc binding site 1 out of 4 in the Structure of Xac Nucleotide Pyrophosphatase/Phosphodiesterase in Complex with Vanadate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Xac Nucleotide Pyrophosphatase/Phosphodiesterase in Complex with Vanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1000

b:12.0
occ:1.00
NE2 A:HIS258 2.0 10.7 1.0
OD1 A:ASP54 2.0 12.2 1.0
OG1 A:THR90 2.1 11.2 1.0
OD2 A:ASP257 2.1 11.7 1.0
O3 A:VO41004 2.3 16.0 1.0
CG A:ASP54 2.8 12.2 1.0
OD2 A:ASP54 2.9 15.3 1.0
CE1 A:HIS258 2.9 9.8 1.0
CG A:ASP257 3.0 11.1 1.0
CD2 A:HIS258 3.0 11.6 1.0
CB A:THR90 3.1 11.8 1.0
OD1 A:ASP257 3.2 11.3 1.0
V A:VO41004 3.3 17.7 1.0
CA A:THR90 3.5 11.1 1.0
CG2 A:THR90 3.5 11.9 1.0
O A:HOH1431 4.0 40.3 1.0
N A:THR90 4.0 11.0 1.0
ND1 A:HIS258 4.1 10.0 1.0
OD1 A:ASP210 4.1 14.9 1.0
CE1 A:HIS363 4.1 10.9 1.0
CG A:HIS258 4.1 10.4 1.0
ZN A:ZN1001 4.1 12.2 1.0
CB A:ASP54 4.2 11.6 1.0
NE2 A:HIS363 4.3 11.3 1.0
CB A:ASP257 4.3 11.2 1.0
CG A:ASP210 4.3 13.2 1.0
N A:GLY55 4.3 11.3 1.0
O1 A:VO41004 4.3 16.0 1.0
CE1 A:HIS94 4.5 12.5 1.0
O2 A:VO41004 4.6 18.9 1.0
CA A:ASP54 4.6 11.4 1.0
OD2 A:ASP210 4.6 13.6 1.0
O4 A:VO41004 4.7 17.1 1.0
C A:ASP54 4.8 11.4 1.0
C A:LEU89 4.8 11.4 1.0
C A:THR90 4.8 11.7 1.0
CB A:ASP210 4.9 12.1 1.0
ND1 A:HIS363 4.9 10.8 1.0
ND1 A:HIS94 4.9 11.6 1.0

Zinc binding site 2 out of 4 in 2gso

Go back to Zinc Binding Sites List in 2gso
Zinc binding site 2 out of 4 in the Structure of Xac Nucleotide Pyrophosphatase/Phosphodiesterase in Complex with Vanadate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Xac Nucleotide Pyrophosphatase/Phosphodiesterase in Complex with Vanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1001

b:12.2
occ:1.00
NE2 A:HIS214 2.0 12.7 1.0
NE2 A:HIS363 2.1 11.3 1.0
O3 A:VO41004 2.1 16.0 1.0
OD1 A:ASP210 2.2 14.9 1.0
O4 A:VO41004 2.2 17.1 1.0
OD2 A:ASP210 2.5 13.6 1.0
CG A:ASP210 2.6 13.2 1.0
CE1 A:HIS214 3.0 12.6 1.0
CD2 A:HIS363 3.1 11.7 1.0
CD2 A:HIS214 3.1 13.8 1.0
CE1 A:HIS363 3.1 10.9 1.0
V A:VO41004 3.1 17.7 1.0
O A:HOH1033 4.0 21.4 1.0
CE1 A:HIS258 4.0 9.8 1.0
O1 A:VO41004 4.1 16.0 1.0
ND1 A:HIS214 4.1 14.1 1.0
CB A:ASP210 4.1 12.1 1.0
ZN A:ZN1000 4.1 12.0 1.0
CG A:HIS214 4.2 13.1 1.0
ND1 A:HIS363 4.2 10.8 1.0
CG A:HIS363 4.2 10.0 1.0
NE2 A:HIS258 4.2 10.7 1.0
O A:HOH1431 4.2 40.3 1.0
OG1 A:THR90 4.3 11.2 1.0
O A:HOH1283 4.4 37.6 1.0
O2 A:VO41004 4.4 18.9 1.0
OD1 A:ASP54 4.5 12.2 1.0
CE A:MET260 4.7 13.0 1.0
O A:HOH1022 4.8 14.2 1.0
O A:ASP210 4.9 12.4 1.0
CA A:ASP210 5.0 12.4 1.0

Zinc binding site 3 out of 4 in 2gso

Go back to Zinc Binding Sites List in 2gso
Zinc binding site 3 out of 4 in the Structure of Xac Nucleotide Pyrophosphatase/Phosphodiesterase in Complex with Vanadate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Xac Nucleotide Pyrophosphatase/Phosphodiesterase in Complex with Vanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1002

b:13.1
occ:1.00
NE2 B:HIS258 2.0 12.6 1.0
OD1 B:ASP54 2.0 11.5 1.0
OG1 B:THR90 2.1 12.0 1.0
OD2 B:ASP257 2.1 12.0 1.0
O3 B:VO41005 2.3 16.8 1.0
CG B:ASP54 2.8 12.3 1.0
CE1 B:HIS258 3.0 11.4 1.0
OD2 B:ASP54 3.0 15.5 1.0
CG B:ASP257 3.0 12.3 1.0
CD2 B:HIS258 3.0 11.5 1.0
CB B:THR90 3.1 12.7 1.0
OD1 B:ASP257 3.2 11.8 1.0
V B:VO41005 3.3 17.4 1.0
CA B:THR90 3.5 11.9 1.0
CG2 B:THR90 3.5 12.6 1.0
O B:HOH1234 3.8 32.4 1.0
N B:THR90 3.9 12.0 1.0
ND1 B:HIS258 4.1 11.4 1.0
OD1 B:ASP210 4.1 14.6 1.0
CE1 B:HIS363 4.1 11.6 1.0
CG B:HIS258 4.1 12.1 1.0
O1 B:VO41005 4.1 16.1 1.0
ZN B:ZN1003 4.2 12.8 1.0
CB B:ASP54 4.2 11.4 1.0
N B:GLY55 4.3 11.6 1.0
CB B:ASP257 4.3 11.7 1.0
CG B:ASP210 4.3 13.0 1.0
NE2 B:HIS363 4.3 12.3 1.0
O2 B:VO41005 4.6 19.1 1.0
CA B:ASP54 4.6 11.2 1.0
O4 B:VO41005 4.6 16.5 1.0
OD2 B:ASP210 4.6 14.5 1.0
CE1 B:HIS94 4.6 11.6 1.0
C B:LEU89 4.7 11.9 1.0
C B:ASP54 4.7 11.4 1.0
C B:THR90 4.8 12.0 1.0
CB B:ASP210 4.9 12.1 1.0
ND1 B:HIS363 4.9 11.3 1.0
CA B:GLY55 4.9 11.7 1.0

Zinc binding site 4 out of 4 in 2gso

Go back to Zinc Binding Sites List in 2gso
Zinc binding site 4 out of 4 in the Structure of Xac Nucleotide Pyrophosphatase/Phosphodiesterase in Complex with Vanadate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Xac Nucleotide Pyrophosphatase/Phosphodiesterase in Complex with Vanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1003

b:12.8
occ:1.00
NE2 B:HIS214 2.0 12.8 1.0
NE2 B:HIS363 2.0 12.3 1.0
O4 B:VO41005 2.1 16.5 1.0
O3 B:VO41005 2.1 16.8 1.0
OD1 B:ASP210 2.2 14.6 1.0
OD2 B:ASP210 2.6 14.5 1.0
CG B:ASP210 2.7 13.0 1.0
CE1 B:HIS214 2.9 12.6 1.0
CE1 B:HIS363 3.0 11.6 1.0
CD2 B:HIS363 3.0 12.3 1.0
CD2 B:HIS214 3.1 13.4 1.0
V B:VO41005 3.2 17.4 1.0
O B:HOH1292 3.7 24.0 1.0
CE1 B:HIS258 4.0 11.4 1.0
O1 B:VO41005 4.0 16.1 1.0
ND1 B:HIS214 4.1 14.3 1.0
ND1 B:HIS363 4.1 11.3 1.0
CB B:ASP210 4.2 12.1 1.0
ZN B:ZN1002 4.2 13.1 1.0
CG B:HIS363 4.2 10.6 1.0
CG B:HIS214 4.2 13.8 1.0
NE2 B:HIS258 4.2 12.6 1.0
O B:HOH1234 4.2 32.4 1.0
OG1 B:THR90 4.4 12.0 1.0
O2 B:VO41005 4.4 19.1 1.0
OD1 B:ASP54 4.6 11.5 1.0
CE B:MET260 4.6 14.4 1.0
O B:HOH1329 4.8 46.5 1.0
O B:HOH1025 4.8 16.0 1.0
O B:ASP210 4.9 12.1 1.0

Reference:

J.G.Zalatan, T.D.Fenn, A.T.Brunger, D.Herschlag. Structural and Functional Comparisons of Nucleotide Pyrophosphatase/Phosphodiesterase and Alkaline Phosphatase: Implications For Mechanism and Evolution Biochemistry V. 45 9788 2006.
ISSN: ISSN 0006-2960
PubMed: 16893180
DOI: 10.1021/BI060847T
Page generated: Wed Dec 16 03:29:36 2020

Last articles

Zn in 7L3L
Zn in 7KSO
Zn in 7KSR
Zn in 7KTP
Zn in 7LMM
Zn in 7LMK
Zn in 7LLZ
Zn in 7LLF
Zn in 7L0N
Zn in 7LBR
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy