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Zinc in PDB 2c9s: 1.24 Angstroms Resolution Structure of Zn-Zn Human Superoxide Dismutase

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

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

Protein crystallography data

The structure of 1.24 Angstroms Resolution Structure of Zn-Zn Human Superoxide Dismutase, PDB code: 2c9s 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) 19.90 / 1.24
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 38.243, 67.742, 51.260, 90.00, 106.44, 90.00
R / Rfree (%) 15.2 / 19.4

Zinc Binding Sites:

The binding sites of Zinc atom in the 1.24 Angstroms Resolution Structure of Zn-Zn Human Superoxide Dismutase (pdb code 2c9s). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the 1.24 Angstroms Resolution Structure of Zn-Zn Human Superoxide Dismutase, PDB code: 2c9s:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 2c9s

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Zinc binding site 1 out of 6 in the 1.24 Angstroms Resolution Structure of Zn-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 Zn-Zn Human Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1155

b:9.6
occ:1.00
 NE2 A:HIS48 2.0 7.5 1.0
NE2 A:HIS120 2.0 9.0 1.0
ND1 A:HIS46 2.1 9.1 1.0
O4 A:SO41161 2.1 10.6 1.0
CE1 A:HIS48 2.9 8.1 1.0
CE1 A:HIS120 3.0 10.6 1.0
CE1 A:HIS46 3.0 8.9 1.0
CD2 A:HIS120 3.0 7.7 1.0
CG A:HIS46 3.1 7.7 1.0
CD2 A:HIS48 3.2 8.2 1.0
S A:SO41161 3.2 10.9 1.0
O2 A:SO41161 3.3 11.4 1.0
CB A:HIS46 3.5 7.7 1.0
NE2 A:HIS63 3.6 9.2 1.0
CD2 A:HIS63 4.0 9.1 1.0
ND1 A:HIS120 4.0 9.2 1.0
ND1 A:HIS48 4.1 8.9 1.0
O1 A:SO41161 4.1 16.0 1.0
CG A:HIS120 4.1 8.6 1.0
NE2 A:HIS46 4.1 9.6 1.0
O3 A:SO41161 4.1 14.1 1.0
CD2 A:HIS46 4.2 8.5 1.0
CG A:HIS48 4.2 7.3 1.0
O A:HOH2211 4.5 13.0 1.0
CG1 A:VAL118 4.5 8.8 1.0
CB A:VAL118 4.6 7.7 1.0
CE1 A:HIS63 4.6 9.2 1.0
NE A:ARG143 4.9 9.8 1.0
CA A:HIS46 4.9 6.7 1.0

Zinc binding site 2 out of 6 in 2c9s

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Zinc binding site 2 out of 6 in the 1.24 Angstroms Resolution Structure of Zn-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 Zn-Zn Human Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1156

b:9.1
occ:1.00
 OD1 A:ASP83 2.0 8.2 1.0
ND1 A:HIS63 2.0 8.5 1.0
ND1 A:HIS80 2.0 8.1 1.0
ND1 A:HIS71 2.1 7.7 1.0
CG A:ASP83 2.7 9.6 1.0
OD2 A:ASP83 2.8 8.4 1.0
CE1 A:HIS80 2.9 10.0 1.0
CE1 A:HIS63 2.9 9.2 1.0
CE1 A:HIS71 2.9 9.2 1.0
CG A:HIS80 3.1 9.2 1.0
CG A:HIS63 3.1 8.2 1.0
CG A:HIS71 3.2 8.7 1.0
CB A:HIS63 3.5 8.7 1.0
CB A:HIS71 3.6 8.1 1.0
CB A:HIS80 3.6 7.9 1.0
CA A:HIS71 3.9 8.9 1.0
NE2 A:HIS80 4.0 9.9 1.0
O A:LYS136 4.0 12.8 1.0
NE2 A:HIS63 4.0 9.2 1.0
CD2 A:HIS80 4.1 10.5 1.0
NE2 A:HIS71 4.1 9.6 1.0
CD2 A:HIS63 4.2 9.1 1.0
CB A:ASP83 4.2 8.8 1.0
CD2 A:HIS71 4.2 10.5 1.0
N A:GLY72 4.7 8.5 1.0
CA A:ASP83 4.7 7.5 1.0
N A:HIS80 4.7 8.0 1.0
CA A:HIS80 4.8 7.9 1.0
O A:HOH2208 4.8 17.4 1.0
C A:HIS71 4.8 8.4 1.0
N A:HIS71 4.9 8.8 1.0
N A:ASP83 4.9 7.7 1.0
O A:GLY72 5.0 9.4 1.0
C A:LYS136 5.0 11.0 1.0

Zinc binding site 3 out of 6 in 2c9s

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Zinc binding site 3 out of 6 in the 1.24 Angstroms Resolution Structure of Zn-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 Zn-Zn Human Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1157

b:10.4
occ:0.15
 O4 A:SO41163 1.9 13.7 0.4
O A:HOH2229 1.9 30.6 1.0
O A:ARG143 2.4 12.2 1.0
N A:ARG143 2.4 8.9 1.0
OG A:SER142 2.4 17.6 0.5
O A:HOH2245 2.6 14.7 0.6
C A:ARG143 2.7 8.8 1.0
CB A:SER142 3.0 12.3 1.0
CA A:ARG143 3.0 8.9 1.0
C A:SER142 3.1 9.7 1.0
S A:SO41163 3.3 19.9 0.4
CA A:SER142 3.3 11.4 1.0
CB A:ARG143 3.6 8.3 1.0
O A:HOH2247 3.7 31.8 1.0
N A:LEU144 3.8 8.8 1.0
O3 A:SO41163 3.9 20.9 0.4
OG A:SER142 3.9 12.8 0.5
O2 A:SO41163 4.0 21.6 0.4
O A:SER142 4.1 10.6 1.0
O1 A:SO41163 4.1 16.5 0.4
O A:HOH2016 4.3 45.7 1.0
O A:HOH2217 4.3 17.7 0.5
CA A:LEU144 4.3 9.2 1.0
CG A:ARG143 4.5 9.4 1.0
CD2 A:LEU144 4.6 17.6 1.0
N A:SER142 4.8 10.6 1.0
O A:HOH2017 4.9 12.6 0.5

Zinc binding site 4 out of 6 in 2c9s

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Zinc binding site 4 out of 6 in the 1.24 Angstroms Resolution Structure of Zn-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 Zn-Zn Human Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn1157

b:9.7
occ:1.00
 O1 F:SO41154 2.0 9.7 1.0
NE2 F:HIS120 2.0 8.8 1.0
NE2 F:HIS48 2.0 7.9 1.0
ND1 F:HIS46 2.1 9.1 1.0
CE1 F:HIS120 2.9 9.0 1.0
CE1 F:HIS48 2.9 9.6 1.0
CE1 F:HIS46 3.0 9.2 1.0
CD2 F:HIS120 3.0 8.0 1.0
CG F:HIS46 3.1 8.6 1.0
CD2 F:HIS48 3.2 9.1 1.0
S F:SO41154 3.2 11.0 1.0
O3 F:SO41154 3.3 11.6 1.0
CB F:HIS46 3.5 7.7 1.0
NE2 F:HIS63 3.6 9.2 1.0
CD2 F:HIS63 3.9 10.3 1.0
ND1 F:HIS120 4.0 10.1 1.0
O4 F:SO41154 4.0 16.1 1.0
ND1 F:HIS48 4.1 8.6 1.0
CG F:HIS120 4.1 8.8 1.0
NE2 F:HIS46 4.1 9.7 1.0
O2 F:SO41154 4.1 15.3 1.0
CD2 F:HIS46 4.2 8.7 1.0
CG F:HIS48 4.2 7.8 1.0
CG1 F:VAL118 4.5 8.9 1.0
O F:HOH2229 4.5 13.0 1.0
CE1 F:HIS63 4.5 9.1 1.0
CB F:VAL118 4.6 7.2 1.0
NE F:ARG143 4.9 12.8 1.0
CA F:HIS46 4.9 7.0 1.0
O F:HOH2250 4.9 7.7 0.5

Zinc binding site 5 out of 6 in 2c9s

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Zinc binding site 5 out of 6 in the 1.24 Angstroms Resolution Structure of Zn-Zn Human Superoxide Dismutase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of 1.24 Angstroms Resolution Structure of Zn-Zn Human Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn1158

b:8.6
occ:1.00
 OD1 F:ASP83 2.0 8.7 1.0
ND1 F:HIS80 2.0 8.2 1.0
ND1 F:HIS71 2.0 7.5 1.0
ND1 F:HIS63 2.1 8.2 1.0
CG F:ASP83 2.7 8.6 1.0
OD2 F:ASP83 2.8 9.3 1.0
CE1 F:HIS80 2.9 9.3 1.0
CE1 F:HIS71 2.9 7.8 1.0
CE1 F:HIS63 2.9 9.1 1.0
CG F:HIS80 3.1 9.6 1.0
CG F:HIS63 3.1 7.5 1.0
CG F:HIS71 3.2 8.6 1.0
CB F:HIS63 3.5 7.8 1.0
CB F:HIS80 3.6 7.5 1.0
CB F:HIS71 3.6 8.2 1.0
CA F:HIS71 3.9 8.9 1.0
NE2 F:HIS80 4.0 9.6 1.0
O F:LYS136 4.0 12.2 1.0
NE2 F:HIS71 4.1 8.6 1.0
NE2 F:HIS63 4.1 9.2 1.0
CD2 F:HIS80 4.1 10.1 1.0
CD2 F:HIS63 4.2 10.3 1.0
CB F:ASP83 4.2 8.2 1.0
CD2 F:HIS71 4.2 8.4 1.0
N F:HIS80 4.6 8.6 1.0
N F:GLY72 4.7 8.9 1.0
CA F:HIS80 4.7 8.3 1.0
CA F:ASP83 4.7 8.6 1.0
C F:HIS71 4.8 9.0 1.0
N F:HIS71 4.9 8.5 1.0
N F:ASP83 4.9 8.1 1.0
O F:HOH2228 4.9 17.7 1.0
C F:LYS136 5.0 11.1 1.0
O F:GLY72 5.0 9.8 1.0

Zinc binding site 6 out of 6 in 2c9s

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Zinc binding site 6 out of 6 in the 1.24 Angstroms Resolution Structure of Zn-Zn Human Superoxide Dismutase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of 1.24 Angstroms Resolution Structure of Zn-Zn Human Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn1160

b:12.1
occ:0.15
 O F:HOH2260 2.1 14.0 0.3
O F:ARG143 2.2 13.4 1.0
N F:ARG143 2.2 10.3 1.0
O1 F:SO41155 2.3 18.0 0.6
C F:ARG143 2.6 10.1 1.0
CA F:ARG143 2.8 9.7 1.0
CB F:SER142 2.9 13.5 1.0
C F:SER142 2.9 9.9 1.0
CA F:SER142 3.3 12.4 1.0
OG F:SER142 3.3 19.9 1.0
CB F:ARG143 3.4 9.6 1.0
O F:HOH2252 3.4 43.6 1.0
S F:SO41155 3.6 26.1 0.6
N F:LEU144 3.6 9.8 1.0
O F:SER142 3.9 11.7 1.0
O4 F:SO41155 3.9 20.5 0.6
O F:HOH2255 4.2 33.0 1.0
O3 F:SO41155 4.3 25.9 0.6
CG F:ARG143 4.3 9.4 1.0
CA F:LEU144 4.3 10.2 1.0
O F:HOH2232 4.4 27.7 1.0
O2 F:SO41155 4.6 26.9 0.6
N F:SER142 4.7 10.9 1.0
CD2 F:LEU144 5.0 18.1 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 Oct 16 22:14:25 2024

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