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Zinc in PDB 2wwn: Yersinia Pseudotuberculosis Superoxide Dismutase C with Bound Azide

Enzymatic activity of Yersinia Pseudotuberculosis Superoxide Dismutase C with Bound Azide

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

Protein crystallography data

The structure of Yersinia Pseudotuberculosis Superoxide Dismutase C with Bound Azide, PDB code: 2wwn 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) 41.812 / 2.60
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 96.561, 96.561, 81.716, 90.00, 90.00, 120.00
R / Rfree (%) 18.59 / 23.2

Zinc Binding Sites:

The binding sites of Zinc atom in the Yersinia Pseudotuberculosis Superoxide Dismutase C with Bound Azide (pdb code 2wwn). 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 with Bound Azide, PDB code: 2wwn:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 2wwn

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


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 with Bound Azide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1162

b:41.9
occ:1.00
 NE2 A:HIS79 2.2 50.1 1.0
NE2 A:HIS135 2.2 39.3 1.0
NE2 A:HIS56 2.3 42.2 1.0
ND1 A:HIS54 2.4 43.0 1.0
CD2 A:HIS79 2.9 48.1 1.0
CE1 A:HIS56 3.0 44.6 1.0
CE1 A:HIS135 3.1 41.0 1.0
CD2 A:HIS135 3.2 40.2 1.0
CE1 A:HIS54 3.3 41.8 1.0
CG A:HIS54 3.3 41.2 1.0
CE1 A:HIS79 3.4 51.5 1.0
CD2 A:HIS56 3.5 45.2 1.0
CB A:HIS54 3.6 42.2 1.0
O A:HOH2056 3.8 33.4 1.0
O A:HOH2021 4.1 60.4 1.0
CG A:HIS79 4.1 46.8 1.0
ND1 A:HIS56 4.2 48.5 1.0
ND1 A:HIS135 4.2 44.0 1.0
CG A:HIS135 4.3 43.8 1.0
ND1 A:HIS79 4.3 51.2 1.0
NE2 A:HIS54 4.4 41.3 1.0
CD2 A:HIS54 4.4 42.2 1.0
CG A:HIS56 4.5 47.8 1.0
CG A:MET133 4.5 45.9 1.0
CB A:MET133 4.6 42.6 1.0
CA A:HIS54 4.7 42.7 1.0
N A:HIS54 4.8 44.3 1.0

Zinc binding site 2 out of 7 in 2wwn

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


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 with Bound Azide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1163

b:41.1
occ:1.00
 OD1 A:ASP100 2.1 45.1 1.0
ND1 A:HIS88 2.3 35.8 1.0
ND1 A:HIS79 2.3 51.2 1.0
ND1 A:HIS97 2.4 37.5 1.0
CG A:ASP100 2.9 45.3 1.0
OD2 A:ASP100 3.1 47.2 1.0
CE1 A:HIS88 3.1 38.6 1.0
CE1 A:HIS79 3.1 51.5 1.0
CG A:HIS79 3.2 46.8 1.0
CG A:HIS97 3.2 43.2 1.0
CG A:HIS88 3.3 42.7 1.0
CB A:HIS97 3.3 36.3 1.0
CE1 A:HIS97 3.4 38.8 1.0
CB A:HIS79 3.5 44.4 1.0
CB A:HIS88 3.7 37.5 1.0
CA A:HIS88 3.9 44.2 1.0
NE2 A:HIS79 4.1 50.1 1.0
CD2 A:HIS79 4.2 48.1 1.0
NE2 A:HIS88 4.2 35.1 1.0
CD2 A:HIS88 4.3 41.7 1.0
CB A:ASP100 4.4 43.4 1.0
CD2 A:LEU148 4.4 42.4 1.0
CD2 A:HIS97 4.4 45.9 1.0
NE2 A:HIS97 4.5 49.8 1.0
CA A:HIS97 4.6 39.1 1.0
O A:VAL87 4.7 45.1 1.0
CA A:ASP100 4.8 40.6 1.0
N A:HIS88 4.9 43.8 1.0
N A:HIS97 4.9 38.0 1.0
N A:ASP100 4.9 39.9 1.0
C A:HIS88 5.0 44.2 1.0
CD2 A:HIS54 5.0 42.2 1.0

Zinc binding site 3 out of 7 in 2wwn

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


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 with Bound Azide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1164

b:52.9
occ:1.00
 NE2 A:HIS130 2.2 43.4 1.0
O A:HOH2064 2.4 39.0 1.0
O A:HOH2066 2.5 41.7 1.0
O A:HOH2065 2.5 40.2 1.0
CE1 A:HIS130 3.1 43.0 1.0
CD2 A:HIS130 3.2 43.1 1.0
O A:GLU126 3.9 41.7 1.0
O A:LYS128 4.0 46.7 1.0
O A:HOH2047 4.2 57.6 1.0
O A:SER125 4.2 47.9 1.0
ND1 A:HIS130 4.3 43.0 1.0
O A:HOH2017 4.3 39.0 1.0
CG A:HIS130 4.3 42.4 1.0
C A:GLU126 4.3 43.6 1.0
CA A:GLU126 4.7 44.5 1.0
CD1 A:LEU80 4.8 41.3 1.0

Zinc binding site 4 out of 7 in 2wwn

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


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 with Bound Azide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1165

b:75.1
occ:1.00
 NE2 A:HIS144 2.2 55.3 1.0
CE1 A:HIS144 3.0 57.7 1.0
CD2 A:HIS144 3.1 54.8 1.0
ND1 A:HIS144 4.1 59.2 1.0
CG A:HIS144 4.1 56.8 1.0

Zinc binding site 5 out of 7 in 2wwn

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


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 with Bound Azide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1166

b:47.5
occ:1.00
 OD2 A:ASP5 2.0 58.4 1.0
O A:HOH2067 2.4 34.0 1.0
ND2 A:ASN4 2.9 66.8 1.0
CG A:ASP5 3.0 62.8 1.0
OD1 A:ASN4 3.2 72.6 1.0
CG A:ASN4 3.3 73.6 1.0
OD1 A:ASP5 3.4 64.3 1.0
N A:ASP5 4.2 78.6 1.0
CB A:ASP5 4.3 64.7 1.0
CA A:ASP5 4.5 72.1 1.0
CB A:ASN4 4.6 76.6 1.0
C A:ASN4 5.0 80.1 1.0

Zinc binding site 6 out of 7 in 2wwn

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


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 with Bound Azide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1162

b:42.0
occ:1.00
 NE2 B:HIS79 2.2 49.6 1.0
NE2 B:HIS135 2.3 39.8 1.0
ND1 B:HIS54 2.3 42.8 1.0
NE2 B:HIS56 2.3 42.9 1.0
CD2 B:HIS79 3.0 49.0 1.0
CD2 B:HIS135 3.0 38.9 1.0
CE1 B:HIS56 3.1 45.8 1.0
CG B:HIS54 3.2 41.6 1.0
CE1 B:HIS54 3.3 45.4 1.0
CE1 B:HIS135 3.3 43.5 1.0
CE1 B:HIS79 3.3 45.8 1.0
CB B:HIS54 3.4 38.7 1.0
CD2 B:HIS56 3.4 42.9 1.0
O B:HOH2057 4.0 44.0 1.0
CG B:HIS135 4.2 44.3 1.0
CG B:HIS79 4.2 48.0 1.0
CD2 B:HIS54 4.3 42.7 1.0
NE2 B:HIS54 4.3 45.8 1.0
ND1 B:HIS56 4.3 47.8 1.0
ND1 B:HIS135 4.3 44.2 1.0
ND1 B:HIS79 4.4 43.8 1.0
CG B:MET133 4.4 39.0 1.0
CB B:MET133 4.5 37.5 1.0
CG B:HIS56 4.5 48.4 1.0
CA B:HIS54 4.7 39.8 1.0
N B:HIS54 4.9 36.0 1.0

Zinc binding site 7 out of 7 in 2wwn

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


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 with Bound Azide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1163

b:39.9
occ:1.00
 OD1 B:ASP100 2.1 49.3 1.0
ND1 B:HIS79 2.2 43.8 1.0
ND1 B:HIS88 2.2 38.0 1.0
ND1 B:HIS97 2.4 39.3 1.0
CG B:ASP100 2.9 43.3 1.0
CE1 B:HIS79 3.0 45.8 1.0
OD2 B:ASP100 3.1 42.9 1.0
CE1 B:HIS88 3.1 37.2 1.0
CG B:HIS97 3.2 46.5 1.0
CG B:HIS79 3.2 48.0 1.0
CG B:HIS88 3.2 39.1 1.0
CB B:HIS97 3.3 43.9 1.0
CE1 B:HIS97 3.4 44.8 1.0
CB B:HIS88 3.5 40.4 1.0
CB B:HIS79 3.6 38.1 1.0
CA B:HIS88 3.8 43.9 1.0
NE2 B:HIS79 4.1 49.6 1.0
CD2 B:HIS79 4.2 49.0 1.0
CD2 B:LEU148 4.2 44.3 1.0
NE2 B:HIS88 4.3 37.7 1.0
CD2 B:HIS88 4.3 50.4 1.0
CD2 B:HIS97 4.3 47.8 1.0
CB B:ASP100 4.4 40.5 1.0
NE2 B:HIS97 4.4 50.9 1.0
CA B:HIS97 4.6 41.8 1.0
N B:HIS88 4.7 41.4 1.0
CA B:ASP100 4.8 38.5 1.0
N B:HIS97 4.9 39.3 1.0
C B:HIS88 4.9 39.7 1.0
CD2 B:HIS54 4.9 42.7 1.0
O B:HIS97 4.9 39.4 1.0
O B:VAL87 4.9 40.1 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.
Page generated: Thu Oct 17 05:02:58 2024

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