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Zinc in PDB 3mnd: Crystallographic Analysis of the Cystosolic Cu/Zn Superoxide Dismutase From Taenia Solium

Enzymatic activity of Crystallographic Analysis of the Cystosolic Cu/Zn Superoxide Dismutase From Taenia Solium

All present enzymatic activity of Crystallographic Analysis of the Cystosolic Cu/Zn Superoxide Dismutase From Taenia Solium:
1.15.1.1;

Protein crystallography data

The structure of Crystallographic Analysis of the Cystosolic Cu/Zn Superoxide Dismutase From Taenia Solium, PDB code: 3mnd was solved by A.Hernandez-Santoyo, A.Rodriguez-Romero, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.64 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 42.171, 53.798, 117.264, 90.00, 90.00, 90.00
R / Rfree (%) 19.2 / 24.9

Other elements in 3mnd:

The structure of Crystallographic Analysis of the Cystosolic Cu/Zn Superoxide Dismutase From Taenia Solium also contains other interesting chemical elements:

Copper (Cu) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystallographic Analysis of the Cystosolic Cu/Zn Superoxide Dismutase From Taenia Solium (pdb code 3mnd). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Crystallographic Analysis of the Cystosolic Cu/Zn Superoxide Dismutase From Taenia Solium, PDB code: 3mnd:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in 3mnd

Go back to Zinc Binding Sites List in 3mnd
Zinc binding site 1 out of 5 in the Crystallographic Analysis of the Cystosolic Cu/Zn Superoxide Dismutase From Taenia Solium


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystallographic Analysis of the Cystosolic Cu/Zn Superoxide Dismutase From Taenia Solium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn153

b:15.0
occ:1.00
 ND1 A:HIS60 2.1 14.8 1.0
ND1 A:HIS77 2.1 14.0 1.0
OD1 A:ASP80 2.1 11.6 1.0
ND1 A:HIS68 2.3 15.6 1.0
CG A:ASP80 2.8 15.6 1.0
OD2 A:ASP80 3.0 17.2 1.0
CE1 A:HIS77 3.0 13.5 1.0
CE1 A:HIS60 3.0 14.7 1.0
CG A:HIS60 3.1 18.4 1.0
CG A:HIS77 3.1 16.9 1.0
CE1 A:HIS68 3.3 13.8 1.0
CG A:HIS68 3.3 17.5 1.0
CB A:HIS60 3.5 12.9 1.0
CB A:HIS77 3.5 12.3 1.0
CB A:HIS68 3.6 13.0 1.0
O A:ILE133 3.8 16.3 1.0
CA A:HIS68 4.0 15.1 1.0
NE2 A:HIS77 4.1 14.2 1.0
NE2 A:HIS60 4.1 17.2 1.0
CD2 A:HIS77 4.2 14.3 1.0
CB A:ASP80 4.2 13.1 1.0
CD2 A:HIS60 4.2 18.4 1.0
NE2 A:HIS68 4.4 15.6 1.0
CD2 A:HIS68 4.5 13.9 1.0
CA A:ASP80 4.7 13.1 1.0
O A:HOH182 4.7 16.1 1.0
CA A:HIS77 4.7 12.4 1.0
N A:HIS77 4.8 12.9 1.0
C A:ILE133 4.8 19.8 1.0
CD2 A:HIS43 4.8 15.1 1.0
CA A:THR134 4.9 16.0 1.0
N A:GLY69 4.9 16.0 1.0
N A:HIS68 4.9 11.3 1.0
N A:ASP80 5.0 10.3 1.0
C A:HIS68 5.0 19.9 1.0
CA A:HIS60 5.0 15.3 1.0

Zinc binding site 2 out of 5 in 3mnd

Go back to Zinc Binding Sites List in 3mnd
Zinc binding site 2 out of 5 in the Crystallographic Analysis of the Cystosolic Cu/Zn Superoxide Dismutase From Taenia Solium


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystallographic Analysis of the Cystosolic Cu/Zn Superoxide Dismutase From Taenia Solium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn154

b:34.4
occ:1.00
 NE2 A:HIS107 2.1 24.8 1.0
NE2 A:HIS64 2.1 23.9 1.0
O A:HOH165 2.3 16.9 1.0
CE1 A:HIS107 2.9 24.7 1.0
CE1 A:HIS64 3.0 30.0 1.0
CD2 A:HIS64 3.1 26.1 1.0
CD2 A:HIS107 3.3 18.6 1.0
OE2 A:GLU106 4.1 24.5 1.0
ND1 A:HIS107 4.1 25.7 1.0
ND1 A:HIS64 4.1 23.7 1.0
CG A:HIS64 4.2 20.8 1.0
CG A:HIS107 4.3 22.2 1.0
CD A:GLU106 4.8 22.4 1.0

Zinc binding site 3 out of 5 in 3mnd

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Zinc binding site 3 out of 5 in the Crystallographic Analysis of the Cystosolic Cu/Zn Superoxide Dismutase From Taenia Solium


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystallographic Analysis of the Cystosolic Cu/Zn Superoxide Dismutase From Taenia Solium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn153

b:19.6
occ:1.00
 OD1 B:ASP80 2.0 15.2 1.0
ND1 B:HIS77 2.1 15.1 1.0
ND1 B:HIS60 2.1 13.6 1.0
ND1 B:HIS68 2.2 19.4 1.0
CE1 B:HIS77 2.8 18.5 1.0
CG B:ASP80 2.9 18.4 1.0
CE1 B:HIS60 3.1 17.5 1.0
CG B:HIS60 3.1 15.8 1.0
OD2 B:ASP80 3.1 17.9 1.0
CE1 B:HIS68 3.1 19.1 1.0
CG B:HIS77 3.2 19.0 1.0
CG B:HIS68 3.2 22.8 1.0
CB B:HIS60 3.4 18.9 1.0
CB B:HIS68 3.6 19.2 1.0
CB B:HIS77 3.7 15.7 1.0
CA B:HIS68 3.9 22.0 1.0
O B:ILE133 4.0 23.4 1.0
NE2 B:HIS77 4.0 19.9 1.0
NE2 B:HIS60 4.2 17.1 1.0
CD2 B:HIS77 4.2 17.7 1.0
CD2 B:HIS60 4.2 16.7 1.0
NE2 B:HIS68 4.2 24.0 1.0
CB B:ASP80 4.3 17.5 1.0
CD2 B:HIS68 4.3 25.6 1.0
CD2 B:HIS43 4.7 18.4 1.0
CA B:ASP80 4.7 14.3 1.0
N B:GLY69 4.8 22.1 1.0
N B:HIS77 4.8 22.2 1.0
N B:HIS68 4.9 21.7 1.0
CA B:HIS77 4.9 19.0 1.0
C B:HIS68 4.9 26.1 1.0
C B:ILE133 4.9 19.4 1.0
CA B:HIS60 4.9 15.4 1.0
N B:ASP80 5.0 18.0 1.0

Zinc binding site 4 out of 5 in 3mnd

Go back to Zinc Binding Sites List in 3mnd
Zinc binding site 4 out of 5 in the Crystallographic Analysis of the Cystosolic Cu/Zn Superoxide Dismutase From Taenia Solium


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystallographic Analysis of the Cystosolic Cu/Zn Superoxide Dismutase From Taenia Solium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn154

b:25.1
occ:1.00
 O3 B:GOL157 2.0 19.0 1.0
OE2 B:GLU31 2.2 25.2 1.0
NE2 B:HIS29 2.2 20.1 1.0
O1 B:GOL157 2.5 23.0 1.0
C1 B:GOL157 2.6 31.2 1.0
CD B:GLU31 2.8 29.4 1.0
C3 B:GOL157 3.0 22.7 1.0
CD2 B:HIS29 3.1 17.2 1.0
C2 B:GOL157 3.2 28.5 1.0
OE1 B:GLU31 3.2 29.6 1.0
CE1 B:HIS29 3.3 20.1 1.0
CG B:GLU31 3.7 20.6 1.0
O B:HOH192 3.9 21.7 1.0
CG B:HIS29 4.3 19.4 1.0
ND1 B:HIS29 4.4 18.8 1.0
O2 B:GOL157 4.5 34.6 1.0
O B:HOH166 4.8 32.9 1.0
CB B:GLU31 4.9 15.0 1.0

Zinc binding site 5 out of 5 in 3mnd

Go back to Zinc Binding Sites List in 3mnd
Zinc binding site 5 out of 5 in the Crystallographic Analysis of the Cystosolic Cu/Zn Superoxide Dismutase From Taenia Solium


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystallographic Analysis of the Cystosolic Cu/Zn Superoxide Dismutase From Taenia Solium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn155

b:51.0
occ:1.00
 O B:HOH205 1.9 31.0 1.0
NE2 B:HIS64 2.2 39.2 1.0
CE1 B:HIS64 2.2 38.3 1.0
NE2 B:HIS107 2.3 45.7 1.0
CD2 B:HIS107 3.2 35.5 1.0
CE1 B:HIS107 3.4 42.0 1.0
CD2 B:HIS64 3.5 40.8 1.0
ND1 B:HIS64 3.6 34.9 1.0
CG B:HIS64 4.2 36.9 1.0
CG B:HIS107 4.4 37.6 1.0
ND1 B:HIS107 4.5 36.9 1.0

Reference:

A.Hernandez-Santoyo, A.Landa, E.Gonzalez-Mondragon, M.Pedraza-Escalona, R.Parra-Unda, A.Rodriguez-Romero. Crystal Structure of Cu / Zn Superoxide Dismutase From Taenia Solium Reveals Metal-Mediated Self-Assembly Febs J. V. 278 3308 2011.
ISSN: ISSN 1742-464X
PubMed: 21767346
DOI: 10.1111/J.1742-4658.2011.08247.X
Page generated: Sat Oct 26 09:37:56 2024

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