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Zinc in PDB 2v0a: Atomic Resolution Crystal Structure of Human Superoxide Dismutase

Enzymatic activity of Atomic Resolution Crystal Structure of Human Superoxide Dismutase

All present enzymatic activity of Atomic Resolution Crystal Structure of Human Superoxide Dismutase:
1.15.1.1;

Protein crystallography data

The structure of Atomic Resolution Crystal Structure of Human Superoxide Dismutase, PDB code: 2v0a was solved by R.W.Strange, S.Antonyuk, C.W.Yong, W.Smith, S.S.Hasnain, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 21.50 / 1.15
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 38.545, 68.220, 50.306, 90.00, 105.14, 90.00
R / Rfree (%) 15.5 / 20.6

Other elements in 2v0a:

The structure of Atomic Resolution Crystal Structure of Human Superoxide Dismutase also contains other interesting chemical elements:

Copper (Cu) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Atomic Resolution Crystal Structure of Human Superoxide Dismutase (pdb code 2v0a). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Atomic Resolution Crystal Structure of Human Superoxide Dismutase, PDB code: 2v0a:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 2v0a

Go back to Zinc Binding Sites List in 2v0a
Zinc binding site 1 out of 2 in the Atomic Resolution Crystal Structure of Human Superoxide Dismutase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Atomic Resolution Crystal Structure of Human Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1155

b:11.0
occ:1.00
OD1 A:ASP83 1.9 9.7 1.0
ND1 A:HIS63 2.0 10.8 1.0
ND1 A:HIS80 2.0 12.6 1.0
ND1 A:HIS71 2.1 11.0 1.0
CG A:ASP83 2.8 11.1 1.0
OD2 A:ASP83 2.9 11.2 1.0
CE1 A:HIS80 2.9 11.6 1.0
CE1 A:HIS63 3.0 11.9 1.0
CE1 A:HIS71 3.0 11.2 1.0
CG A:HIS63 3.0 10.9 1.0
CG A:HIS80 3.1 11.6 1.0
CG A:HIS71 3.2 11.4 1.0
CB A:HIS63 3.4 10.9 1.0
CB A:HIS80 3.5 10.4 1.0
CB A:HIS71 3.7 12.1 1.0
O A:LYS136 4.0 14.7 1.0
CA A:HIS71 4.0 11.9 1.0
NE2 A:HIS80 4.0 14.4 1.0
NE2 A:HIS63 4.1 13.1 1.0
NE2 A:HIS71 4.1 10.9 1.0
CD2 A:HIS63 4.1 13.3 1.0
CB A:ASP83 4.1 10.5 1.0
CD2 A:HIS80 4.2 13.3 1.0
CD2 A:HIS71 4.3 11.1 1.0
CA A:ASP83 4.7 9.6 1.0
N A:HIS80 4.7 11.3 1.0
CA A:HIS80 4.8 10.8 1.0
N A:GLY72 4.8 11.4 1.0
O A:HOH2230 4.8 16.0 1.0
CA A:HIS63 4.9 9.5 1.0
N A:ASP83 4.9 9.0 1.0
CD2 A:HIS46 4.9 13.7 1.0
C A:HIS71 4.9 12.3 1.0
C A:LYS136 5.0 14.3 1.0
N A:HIS71 5.0 13.2 1.0

Zinc binding site 2 out of 2 in 2v0a

Go back to Zinc Binding Sites List in 2v0a
Zinc binding site 2 out of 2 in the Atomic Resolution Crystal Structure of Human Superoxide Dismutase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Atomic Resolution Crystal Structure of Human Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn1157

b:10.5
occ:1.00
OD1 F:ASP83 2.0 9.1 1.0
ND1 F:HIS80 2.0 10.7 1.0
ND1 F:HIS63 2.0 10.7 1.0
ND1 F:HIS71 2.1 10.4 1.0
CG F:ASP83 2.8 10.2 1.0
CE1 F:HIS80 2.8 10.7 1.0
OD2 F:ASP83 2.8 11.1 1.0
CE1 F:HIS71 3.0 11.9 1.0
CE1 F:HIS63 3.0 12.6 1.0
CG F:HIS80 3.1 11.1 1.0
CG F:HIS63 3.1 9.6 1.0
CG F:HIS71 3.2 12.1 1.0
CB F:HIS63 3.5 9.6 1.0
CB F:HIS80 3.5 11.0 1.0
CB F:HIS71 3.6 11.7 1.0
CA F:HIS71 3.9 12.4 1.0
O F:LYS136 3.9 14.0 1.0
NE2 F:HIS80 4.0 12.2 1.0
NE2 F:HIS71 4.1 12.1 1.0
NE2 F:HIS63 4.1 12.2 1.0
CD2 F:HIS80 4.1 11.4 1.0
CB F:ASP83 4.2 11.1 1.0
CD2 F:HIS63 4.2 12.2 1.0
CD2 F:HIS71 4.2 12.2 1.0
N F:HIS80 4.7 11.7 1.0
N F:GLY72 4.7 11.8 1.0
CA F:ASP83 4.7 10.5 1.0
CA F:HIS80 4.8 10.5 1.0
N F:HIS71 4.8 13.3 1.0
C F:HIS71 4.8 12.0 1.0
C F:LYS136 4.9 13.8 1.0
O F:HOH2275 4.9 16.4 1.0
CD2 F:HIS46 5.0 12.1 1.0
CA F:HIS63 5.0 9.2 1.0
N F:ASP83 5.0 10.2 1.0

Reference:

R.W.Strange, C.W.Yong, W.Smith, S.S.Hasnain. Molecular Dynamics Using Atomic-Resolution Structure Reveal Structural Fluctuations That May Lead to Polymerization of Human Cu-Zn Superoxide Dismutase. Proc.Natl.Acad.Sci.Usa V. 104 10040 2007.
ISSN: ISSN 0027-8424
PubMed: 17548825
DOI: 10.1073/PNAS.0703857104
Page generated: Wed Dec 16 03:54:12 2020

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