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Zinc in PDB 2c9u: 1.24 Angstroms Resolution Structure of As-Isolated Cu-Zn Human Superoxide Dismutase

Enzymatic activity of 1.24 Angstroms Resolution Structure of As-Isolated Cu-Zn Human Superoxide Dismutase

All present enzymatic activity of 1.24 Angstroms Resolution Structure of As-Isolated Cu-Zn Human Superoxide Dismutase:
1.15.1.1;

Protein crystallography data

The structure of 1.24 Angstroms Resolution Structure of As-Isolated Cu-Zn Human Superoxide Dismutase, PDB code: 2c9u 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) 50.19 / 1.24
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 38.638, 67.553, 52.320, 90.00, 106.48, 90.00
R / Rfree (%) 13.9 / 17.6

Other elements in 2c9u:

The structure of 1.24 Angstroms Resolution Structure of As-Isolated Cu-Zn Human Superoxide Dismutase also contains other interesting chemical elements:

Copper (Cu) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the 1.24 Angstroms Resolution Structure of As-Isolated Cu-Zn Human Superoxide Dismutase (pdb code 2c9u). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the 1.24 Angstroms Resolution Structure of As-Isolated Cu-Zn Human Superoxide Dismutase, PDB code: 2c9u:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 2c9u

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Zinc binding site 1 out of 4 in the 1.24 Angstroms Resolution Structure of As-Isolated 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 1.24 Angstroms Resolution Structure of As-Isolated Cu-Zn Human Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1158

b:9.1
occ:1.00
OD1 A:ASP83 2.0 8.3 1.0
ND1 A:HIS80 2.0 8.0 1.0
ND1 A:HIS63 2.0 9.6 1.0
ND1 A:HIS71 2.1 8.2 1.0
CG A:ASP83 2.7 9.0 1.0
OD2 A:ASP83 2.9 8.9 1.0
CE1 A:HIS71 2.9 8.0 1.0
CE1 A:HIS80 2.9 10.8 1.0
CE1 A:HIS63 2.9 11.7 1.0
CG A:HIS80 3.1 8.3 1.0
CG A:HIS63 3.1 10.9 1.0
CG A:HIS71 3.2 9.3 1.0
CB A:HIS63 3.5 9.5 1.0
CB A:HIS80 3.5 7.6 1.0
CB A:HIS71 3.7 9.9 1.0
O A:LYS136 3.9 19.4 1.0
CA A:HIS71 4.0 10.3 1.0
NE2 A:HIS80 4.0 11.9 1.0
NE2 A:HIS71 4.1 9.8 1.0
NE2 A:HIS63 4.1 14.2 1.0
CD2 A:HIS80 4.1 10.8 1.0
CB A:ASP83 4.2 8.4 1.0
CD2 A:HIS63 4.2 13.8 1.0
CD2 A:HIS71 4.2 9.0 1.0
CA A:ASP83 4.7 8.4 1.0
N A:HIS80 4.7 7.6 1.0
N A:GLY72 4.7 8.8 1.0
CA A:HIS80 4.8 8.0 1.0
C A:HIS71 4.9 9.4 1.0
N A:ASP83 4.9 8.1 1.0
C A:LYS136 4.9 17.7 1.0
N A:HIS71 4.9 10.2 1.0
CA A:HIS63 5.0 8.7 1.0

Zinc binding site 2 out of 4 in 2c9u

Go back to Zinc Binding Sites List in 2c9u
Zinc binding site 2 out of 4 in the 1.24 Angstroms Resolution Structure of As-Isolated 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 1.24 Angstroms Resolution Structure of As-Isolated Cu-Zn Human Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1159

b:9.0
occ:0.55
CU A:CU1157 1.1 10.9 0.5
NE2 A:HIS120 2.0 10.5 1.0
O1 A:SO41154 2.0 7.2 0.5
NE2 A:HIS48 2.1 10.1 1.0
ND1 A:HIS46 2.2 11.7 1.0
O A:HOH2193 2.3 27.8 0.6
CE1 A:HIS120 2.7 11.4 1.0
CE1 A:HIS48 2.8 11.2 1.0
CE1 A:HIS46 3.0 12.9 1.0
O A:HOH2191 3.1 17.2 0.5
CD2 A:HIS120 3.1 8.9 1.0
S A:SO41154 3.2 10.1 0.5
CD2 A:HIS48 3.3 9.5 1.0
NE2 A:HIS63 3.3 14.2 1.0
CG A:HIS46 3.3 10.2 1.0
O2 A:SO41154 3.4 9.9 0.5
CB A:HIS46 3.7 11.8 1.0
CD2 A:HIS63 3.8 13.8 1.0
ND1 A:HIS120 3.9 10.3 1.0
ND1 A:HIS48 4.0 9.2 1.0
O4 A:SO41154 4.0 14.4 0.5
CG A:HIS120 4.1 9.0 1.0
O3 A:SO41154 4.2 14.8 0.5
NE2 A:HIS46 4.2 10.6 1.0
CG A:HIS48 4.3 7.9 1.0
CE1 A:HIS63 4.3 11.7 1.0
O A:HOH2192 4.4 17.4 0.6
CD2 A:HIS46 4.4 12.2 1.0
O A:HOH2177 4.5 13.0 0.5
CG1 A:VAL118 4.6 9.6 1.0
CB A:VAL118 4.6 7.8 1.0
CG A:HIS63 4.9 10.9 1.0
NE A:ARG143 4.9 10.1 1.0

Zinc binding site 3 out of 4 in 2c9u

Go back to Zinc Binding Sites List in 2c9u
Zinc binding site 3 out of 4 in the 1.24 Angstroms Resolution Structure of As-Isolated 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 3 of 1.24 Angstroms Resolution Structure of As-Isolated Cu-Zn Human Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn1155

b:11.5
occ:0.55
CU F:CU1156 0.8 9.5 0.5
NE2 F:HIS120 1.9 10.1 1.0
O1 F:SO41154 2.1 19.5 0.6
O F:HOH2190 2.1 11.6 0.5
NE2 F:HIS48 2.2 10.5 1.0
ND1 F:HIS46 2.3 12.3 1.0
CE1 F:HIS120 2.6 10.9 1.0
CE1 F:HIS48 2.8 11.2 1.0
CD2 F:HIS120 3.0 9.2 1.0
O F:HOH2189 3.0 14.6 0.5
CE1 F:HIS46 3.1 12.6 1.0
NE2 F:HIS63 3.2 13.9 1.0
S F:SO41154 3.3 14.5 0.6
CD2 F:HIS48 3.4 9.7 1.0
CG F:HIS46 3.4 11.0 1.0
O2 F:SO41154 3.5 16.5 0.6
CD2 F:HIS63 3.6 14.1 1.0
ND1 F:HIS120 3.8 11.2 1.0
CB F:HIS46 3.8 12.3 1.0
CG F:HIS120 4.0 9.4 1.0
O4 F:SO41154 4.0 19.9 0.6
ND1 F:HIS48 4.1 9.8 1.0
NE2 F:HIS46 4.3 11.5 1.0
CE1 F:HIS63 4.3 10.4 1.0
O3 F:SO41154 4.4 20.7 0.6
CG F:HIS48 4.4 8.5 1.0
CD2 F:HIS46 4.4 11.2 1.0
O F:HOH2185 4.5 13.6 0.5
CG1 F:VAL118 4.5 10.4 1.0
O F:HOH2172 4.5 15.0 0.5
CB F:VAL118 4.6 8.0 1.0
CG F:HIS63 4.8 10.7 1.0
NE F:ARG143 5.0 10.1 1.0

Zinc binding site 4 out of 4 in 2c9u

Go back to Zinc Binding Sites List in 2c9u
Zinc binding site 4 out of 4 in the 1.24 Angstroms Resolution Structure of As-Isolated 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 4 of 1.24 Angstroms Resolution Structure of As-Isolated Cu-Zn Human Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn1157

b:9.1
occ:1.00
OD1 F:ASP83 2.0 8.5 1.0
ND1 F:HIS80 2.0 7.8 1.0
ND1 F:HIS63 2.1 8.7 1.0
ND1 F:HIS71 2.1 8.3 1.0
CG F:ASP83 2.7 8.1 1.0
OD2 F:ASP83 2.8 8.9 1.0
CE1 F:HIS80 2.9 10.7 1.0
CE1 F:HIS71 2.9 8.8 1.0
CE1 F:HIS63 3.0 10.4 1.0
CG F:HIS80 3.1 9.1 1.0
CG F:HIS63 3.1 10.7 1.0
CG F:HIS71 3.2 9.6 1.0
CB F:HIS63 3.5 9.6 1.0
CB F:HIS80 3.5 7.7 1.0
CB F:HIS71 3.7 10.2 1.0
O F:LYS136 3.9 18.7 1.0
CA F:HIS71 3.9 10.0 1.0
NE2 F:HIS80 4.0 12.1 1.0
NE2 F:HIS71 4.1 10.0 1.0
NE2 F:HIS63 4.1 13.9 1.0
CD2 F:HIS80 4.1 10.4 1.0
CB F:ASP83 4.2 9.1 1.0
CD2 F:HIS63 4.2 14.1 1.0
CD2 F:HIS71 4.3 10.2 1.0
N F:HIS80 4.7 8.8 1.0
N F:GLY72 4.7 9.8 1.0
CA F:ASP83 4.7 8.6 1.0
CA F:HIS80 4.8 8.7 1.0
C F:HIS71 4.9 9.1 1.0
N F:ASP83 4.9 8.4 1.0
N F:HIS71 4.9 10.4 1.0
O F:HOH2092 4.9 23.9 1.0
C F:LYS136 4.9 17.7 1.0
CA F:HIS63 5.0 8.2 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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