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Zinc in PDB 2wwo: Yersinia Pseudotuberculosis Superoxide Dismutase C

Enzymatic activity of Yersinia Pseudotuberculosis Superoxide Dismutase C

All present enzymatic activity of Yersinia Pseudotuberculosis Superoxide Dismutase C:
1.15.1.1;

Protein crystallography data

The structure of Yersinia Pseudotuberculosis Superoxide Dismutase C, PDB code: 2wwo was solved by A.K.Basak, M.L.Duffield, C.E.Naylor, J.Huyet, R.W.Titball, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.773 / 2.40
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 97.546, 97.546, 81.810, 90.00, 90.00, 120.00
R / Rfree (%) 16.65 / 20.54

Zinc Binding Sites:

The binding sites of Zinc atom in the Yersinia Pseudotuberculosis Superoxide Dismutase C (pdb code 2wwo). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Yersinia Pseudotuberculosis Superoxide Dismutase C, PDB code: 2wwo:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 2wwo

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Zinc binding site 1 out of 7 in the Yersinia Pseudotuberculosis Superoxide Dismutase C


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Yersinia Pseudotuberculosis Superoxide Dismutase C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1162

b:35.7
occ:1.00
OD1 A:ASP100 2.1 40.0 1.0
ND1 A:HIS88 2.2 34.4 1.0
ND1 A:HIS79 2.2 43.6 1.0
ND1 A:HIS97 2.2 35.8 1.0
CG A:ASP100 2.9 41.0 1.0
OD2 A:ASP100 3.0 33.1 1.0
CE1 A:HIS88 3.1 33.8 1.0
CE1 A:HIS79 3.1 46.4 1.0
CG A:HIS97 3.1 37.9 1.0
CG A:HIS79 3.2 40.3 1.0
CG A:HIS88 3.2 35.5 1.0
CE1 A:HIS97 3.3 38.7 1.0
CB A:HIS97 3.3 36.9 1.0
CB A:HIS79 3.5 37.3 1.0
CB A:HIS88 3.6 36.0 1.0
CA A:HIS88 3.9 35.8 1.0
NE2 A:HIS88 4.2 34.5 1.0
NE2 A:HIS79 4.2 46.3 1.0
CB A:ASP100 4.3 39.6 1.0
CD2 A:HIS79 4.3 45.0 1.0
CD2 A:HIS97 4.3 38.6 1.0
CD2 A:HIS88 4.3 35.0 1.0
NE2 A:HIS97 4.3 39.3 1.0
CD2 A:LEU148 4.5 38.8 1.0
CA A:HIS97 4.7 34.4 1.0
CA A:ASP100 4.7 36.7 1.0
O A:VAL87 4.7 36.4 1.0
N A:ASP100 4.8 31.5 1.0
N A:HIS88 4.8 36.9 1.0
N A:HIS97 4.9 40.3 1.0
C A:HIS88 5.0 36.4 1.0
CD2 A:HIS54 5.0 35.1 1.0

Zinc binding site 2 out of 7 in 2wwo

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Zinc binding site 2 out of 7 in the Yersinia Pseudotuberculosis Superoxide Dismutase C


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Yersinia Pseudotuberculosis Superoxide Dismutase C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1163

b:55.0
occ:1.00
NE2 A:HIS130 2.2 39.8 1.0
O A:HOH2090 2.4 51.1 1.0
O A:HOH2091 2.4 49.2 1.0
O A:HOH2092 2.6 45.7 1.0
CE1 A:HIS130 3.1 38.5 1.0
CD2 A:HIS130 3.3 38.2 1.0
O A:GLU126 3.9 32.8 1.0
O A:LYS128 4.2 35.5 1.0
ND1 A:HIS130 4.3 36.2 1.0
CG A:HIS130 4.4 37.5 1.0
O A:SER125 4.4 39.7 1.0
C A:GLU126 4.4 36.0 1.0
O A:HOH2072 4.7 61.7 1.0
CD1 A:LEU80 4.8 38.5 1.0
CA A:GLU126 4.8 36.0 1.0

Zinc binding site 3 out of 7 in 2wwo

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Zinc binding site 3 out of 7 in the Yersinia Pseudotuberculosis Superoxide Dismutase C


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Yersinia Pseudotuberculosis Superoxide Dismutase C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1164

b:44.2
occ:1.00
OD2 A:ASP5 2.0 64.0 1.0
O A:HOH2094 2.3 38.9 1.0
OD1 A:ASP5 2.3 61.1 1.0
O A:HOH2093 2.3 47.2 1.0
CG A:ASP5 2.4 63.3 1.0
OD1 A:ASN4 2.9 55.4 1.0
ND2 A:ASN4 2.9 58.7 1.0
CG A:ASN4 3.2 58.6 1.0
CB A:ASP5 3.9 65.0 1.0
O A:HOH2002 4.3 44.6 1.0
O A:HOH2001 4.4 60.2 1.0
CB A:ASN4 4.6 0.3 1.0
C A:ASN4 4.8 77.9 1.0
CA A:ASP5 4.8 67.6 1.0
N A:ASP5 4.9 73.5 1.0

Zinc binding site 4 out of 7 in 2wwo

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Zinc binding site 4 out of 7 in the Yersinia Pseudotuberculosis Superoxide Dismutase C


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Yersinia Pseudotuberculosis Superoxide Dismutase C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1165

b:37.3
occ:1.00
NE2 A:HIS79 2.1 46.3 1.0
NE2 A:HIS135 2.1 35.6 1.0
NE2 A:HIS56 2.3 42.6 1.0
ND1 A:HIS54 2.3 38.1 1.0
CD2 A:HIS79 2.9 45.0 1.0
CE1 A:HIS135 3.0 36.6 1.0
CE1 A:HIS56 3.0 36.8 1.0
CE1 A:HIS54 3.1 36.0 1.0
CD2 A:HIS135 3.2 37.0 1.0
CE1 A:HIS79 3.2 46.4 1.0
CG A:HIS54 3.3 36.4 1.0
CD2 A:HIS56 3.4 43.7 1.0
CB A:HIS54 3.6 32.7 1.0
O A:HOH2082 3.9 30.9 1.0
ND1 A:HIS135 4.1 36.8 1.0
CG A:HIS79 4.1 40.3 1.0
ND1 A:HIS56 4.2 46.6 1.0
CG A:HIS135 4.2 39.5 1.0
NE2 A:HIS54 4.2 35.8 1.0
ND1 A:HIS79 4.2 43.6 1.0
CD2 A:HIS54 4.3 35.1 1.0
CG A:HIS56 4.4 43.9 1.0
CG A:MET133 4.5 35.5 1.0
CB A:MET133 4.5 36.0 1.0
CA A:HIS54 4.8 32.2 1.0
N A:HIS54 4.9 32.0 1.0
O A:HOH2085 4.9 38.0 1.0

Zinc binding site 5 out of 7 in 2wwo

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Zinc binding site 5 out of 7 in the Yersinia Pseudotuberculosis Superoxide Dismutase C


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Yersinia Pseudotuberculosis Superoxide Dismutase C within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1162

b:33.9
occ:1.00
OD1 B:ASP100 2.0 31.2 1.0
ND1 B:HIS79 2.1 32.7 1.0
ND1 B:HIS88 2.2 33.1 1.0
ND1 B:HIS97 2.3 32.8 1.0
CG B:ASP100 2.8 32.6 1.0
CE1 B:HIS79 2.9 45.0 1.0
OD2 B:ASP100 3.0 31.1 1.0
CG B:HIS88 3.1 35.7 1.0
CG B:HIS79 3.1 36.0 1.0
CG B:HIS97 3.2 35.3 1.0
CE1 B:HIS88 3.2 32.0 1.0
CE1 B:HIS97 3.3 35.6 1.0
CB B:HIS97 3.3 33.1 1.0
CB B:HIS88 3.3 36.0 1.0
CB B:HIS79 3.6 32.8 1.0
CA B:HIS88 3.7 36.1 1.0
NE2 B:HIS79 4.1 42.5 1.0
CD2 B:HIS79 4.2 38.8 1.0
CB B:ASP100 4.2 31.9 1.0
CD2 B:HIS88 4.3 33.5 1.0
NE2 B:HIS88 4.3 32.2 1.0
CD2 B:HIS97 4.3 38.1 1.0
NE2 B:HIS97 4.4 38.9 1.0
CD2 B:LEU148 4.4 37.2 1.0
N B:HIS88 4.6 35.8 1.0
CA B:HIS97 4.6 33.8 1.0
CA B:ASP100 4.7 32.2 1.0
C B:HIS88 4.8 35.3 1.0
N B:ASP100 4.8 32.3 1.0
N B:HIS97 4.8 32.6 1.0
O B:VAL87 4.9 34.5 1.0
N B:LEU89 5.0 36.5 1.0

Zinc binding site 6 out of 7 in 2wwo

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Zinc binding site 6 out of 7 in the Yersinia Pseudotuberculosis Superoxide Dismutase C


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Yersinia Pseudotuberculosis Superoxide Dismutase C within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1163

b:59.8
occ:1.00
O B:HOH2119 2.1 49.4 1.0
NE2 B:HIS144 2.2 48.5 1.0
O B:HOH2118 2.5 48.4 1.0
CE1 B:HIS144 3.2 47.3 1.0
CD2 B:HIS144 3.2 44.3 1.0
O B:HOH2052 4.0 54.5 1.0
ND1 B:HIS144 4.3 48.8 1.0
CG B:HIS144 4.4 48.0 1.0

Zinc binding site 7 out of 7 in 2wwo

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Zinc binding site 7 out of 7 in the Yersinia Pseudotuberculosis Superoxide Dismutase C


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Yersinia Pseudotuberculosis Superoxide Dismutase C within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1164

b:36.7
occ:1.00
NE2 B:HIS56 2.1 39.4 1.0
NE2 B:HIS135 2.2 36.1 1.0
ND1 B:HIS54 2.2 37.0 1.0
NE2 B:HIS79 2.3 42.5 1.0
CE1 B:HIS56 2.8 39.1 1.0
CD2 B:HIS79 3.1 38.8 1.0
CD2 B:HIS135 3.1 33.5 1.0
CE1 B:HIS54 3.2 36.6 1.0
CE1 B:HIS135 3.2 37.2 1.0
CG B:HIS54 3.2 37.5 1.0
CD2 B:HIS56 3.3 38.1 1.0
CE1 B:HIS79 3.4 45.0 1.0
CB B:HIS54 3.5 33.0 1.0
O B:HOH2110 3.8 43.4 1.0
ND1 B:HIS56 4.0 40.5 1.0
CG B:HIS135 4.2 40.1 1.0
ND1 B:HIS135 4.2 35.0 1.0
NE2 B:HIS54 4.3 36.8 1.0
CG B:HIS56 4.3 38.0 1.0
CG B:HIS79 4.3 36.0 1.0
CD2 B:HIS54 4.3 37.1 1.0
ND1 B:HIS79 4.4 32.7 1.0
CB B:MET133 4.6 32.7 1.0
CG B:MET133 4.6 33.6 1.0
CA B:HIS54 4.7 32.6 1.0
N B:HIS54 4.9 31.3 1.0

Reference:

J.Huyet, C.E.Naylor, R.W.Titball, H.Bullifent, N.Walker, H.E.Jones, M.L.Duffied, A.K.Basak. Crystal Structure of the Yersinia Pseudotuberculosis Superoxide Dismutase (Sodc) To Be Published.
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