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Zinc in PDB 2c9v: Atomic Resolution Structure of Cu-Zn Human Superoxide Dismutase

Enzymatic activity of Atomic Resolution Structure of Cu-Zn Human Superoxide Dismutase

All present enzymatic activity of Atomic Resolution Structure of Cu-Zn Human Superoxide Dismutase:
1.15.1.1;

Protein crystallography data

The structure of Atomic Resolution Structure of Cu-Zn Human Superoxide Dismutase, PDB code: 2c9v was solved by R.W.Strange, S.V.Antonyuk, M.A.Hough, P.A.Doucette, J.S.Valentine, S.S.Hasnain, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.00 / 1.07
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 38.605, 67.368, 52.532, 90.00, 106.54, 90.00
R / Rfree (%) 13.1 / 15.8

Other elements in 2c9v:

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

Copper (Cu) 4 atoms
Sodium (Na) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Atomic Resolution Structure of Cu-Zn Human Superoxide Dismutase (pdb code 2c9v). 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 Structure of Cu-Zn Human Superoxide Dismutase, PDB code: 2c9v:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 2c9v

Go back to Zinc Binding Sites List in 2c9v
Zinc binding site 1 out of 2 in the Atomic Resolution Structure of Cu-Zn 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 Structure of Cu-Zn Human Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn155

b:7.8
occ:1.00
OD1 A:ASP83 1.9 7.4 1.0
ND1 A:HIS71 2.0 8.0 1.0
ND1 A:HIS63 2.0 7.8 1.0
ND1 A:HIS80 2.0 7.6 1.0
CG A:ASP83 2.7 8.0 1.0
OD2 A:ASP83 2.9 8.0 1.0
CE1 A:HIS71 2.9 7.9 1.0
CE1 A:HIS80 2.9 8.3 1.0
CE1 A:HIS63 3.0 9.1 1.0
CG A:HIS63 3.1 8.2 1.0
CG A:HIS80 3.1 7.5 1.0
CG A:HIS71 3.1 8.1 1.0
CB A:HIS63 3.5 8.7 1.0
CB A:HIS80 3.6 7.2 1.0
CB A:HIS71 3.7 8.5 1.0
O A:LYS136 3.9 10.8 1.0
CA A:HIS71 4.0 8.6 1.0
NE2 A:HIS80 4.0 8.8 1.0
NE2 A:HIS71 4.1 7.6 1.0
NE2 A:HIS63 4.1 10.2 1.0
CD2 A:HIS80 4.1 8.4 1.0
CD2 A:HIS63 4.2 9.9 1.0
CB A:ASP83 4.2 8.1 1.0
CD2 A:HIS71 4.2 8.9 1.0
CA A:ASP83 4.7 8.1 1.0
N A:HIS80 4.7 7.8 1.0
N A:GLY72 4.8 8.7 1.0
CA A:HIS80 4.8 7.4 1.0
CD2 A:HIS46 4.9 8.8 1.0
C A:HIS71 4.9 8.8 1.0
O A:HOH2128 4.9 14.4 1.0
C A:LYS136 4.9 10.4 1.0
N A:HIS71 5.0 9.4 1.0
N A:ASP83 5.0 7.5 1.0
CA A:HIS63 5.0 7.6 1.0

Zinc binding site 2 out of 2 in 2c9v

Go back to Zinc Binding Sites List in 2c9v
Zinc binding site 2 out of 2 in the Atomic Resolution Structure of Cu-Zn 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 Structure of Cu-Zn Human Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn155

b:8.1
occ:1.00
OD1 F:ASP83 1.9 7.7 1.0
ND1 F:HIS63 2.0 7.8 1.0
ND1 F:HIS80 2.0 7.8 1.0
ND1 F:HIS71 2.0 8.3 1.0
CG F:ASP83 2.7 8.7 1.0
OD2 F:ASP83 2.8 8.5 1.0
CE1 F:HIS71 2.9 8.1 1.0
CE1 F:HIS80 2.9 8.6 1.0
CE1 F:HIS63 3.0 9.0 1.0
CG F:HIS63 3.0 8.3 1.0
CG F:HIS80 3.1 7.7 1.0
CG F:HIS71 3.2 8.6 1.0
CB F:HIS63 3.4 8.9 1.0
CB F:HIS80 3.5 8.8 1.0
CB F:HIS71 3.7 9.1 1.0
O F:LYS136 3.9 11.9 1.0
CA F:HIS71 4.0 9.7 1.0
NE2 F:HIS80 4.0 8.9 1.0
NE2 F:HIS63 4.1 10.1 1.0
NE2 F:HIS71 4.1 8.1 1.0
CD2 F:HIS80 4.1 8.7 1.0
CD2 F:HIS63 4.1 9.9 1.0
CB F:ASP83 4.2 7.9 1.0
CD2 F:HIS71 4.2 9.3 1.0
CA F:ASP83 4.7 8.3 1.0
N F:HIS80 4.7 8.2 1.0
CA F:HIS80 4.8 8.0 1.0
N F:GLY72 4.8 9.0 1.0
O F:HOH2271 4.9 15.3 1.0
CD2 F:HIS46 4.9 8.7 1.0
N F:ASP83 4.9 7.3 1.0
C F:LYS136 4.9 11.5 1.0
C F:HIS71 5.0 8.8 1.0
CA F:HIS63 5.0 8.1 1.0

Reference:

R.W.Strange, S.V.Antonyuk, M.A.Hough, P.A.Doucette, J.S.Valentine, S.S.Hasnain. Variable Metallation of Human Superoxide Dismutase: Atomic Resolution Crystal Structures of Cu-Zn, Zn-Zn and As-Isolated Wild-Type Enzymes. J.Mol.Biol. V. 356 1152 2006.
ISSN: ISSN 0022-2836
PubMed: 16406071
DOI: 10.1016/J.JMB.2005.11.081
Page generated: Wed Dec 16 03:19:06 2020

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