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Zinc in PDB 2sod: Determination and Analysis of the 2 Angstrom Structure of Copper, Zinc Superoxide Dismutase

Enzymatic activity of Determination and Analysis of the 2 Angstrom Structure of Copper, Zinc Superoxide Dismutase

All present enzymatic activity of Determination and Analysis of the 2 Angstrom Structure of Copper, Zinc Superoxide Dismutase:
1.15.1.1;

Protein crystallography data

The structure of Determination and Analysis of the 2 Angstrom Structure of Copper, Zinc Superoxide Dismutase, PDB code: 2sod was solved by J.A.Tainer, E.D.Getzoff, J.S.Richardson, D.C.Richardson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) N/A / 2.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 93.650, 90.330, 71.650, 90.00, 95.10, 90.00
R / Rfree (%) n/a / n/a

Other elements in 2sod:

The structure of Determination and Analysis of the 2 Angstrom Structure of Copper, Zinc Superoxide Dismutase also contains other interesting chemical elements:

Copper (Cu) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Determination and Analysis of the 2 Angstrom Structure of Copper, Zinc Superoxide Dismutase (pdb code 2sod). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Determination and Analysis of the 2 Angstrom Structure of Copper, Zinc Superoxide Dismutase, PDB code: 2sod:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 2sod

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Zinc binding site 1 out of 4 in the Determination and Analysis of the 2 Angstrom Structure of Copper, Zinc Superoxide Dismutase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Determination and Analysis of the 2 Angstrom Structure of Copper, Zinc Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Zn153

b:10.7
occ:1.00
 OD1 O:ASP81 1.9 10.9 1.0
ND1 O:HIS78 2.0 9.6 1.0
ND1 O:HIS61 2.1 10.4 1.0
ND1 O:HIS69 2.1 10.1 1.0
CE1 O:HIS78 3.0 9.9 1.0
CE1 O:HIS61 3.0 9.3 1.0
CG O:HIS78 3.0 10.9 1.0
CG O:ASP81 3.0 11.2 1.0
CG O:HIS69 3.1 11.2 1.0
CG O:HIS61 3.1 10.6 1.0
CE1 O:HIS69 3.1 11.0 1.0
CB O:HIS78 3.3 11.7 1.0
CB O:HIS69 3.4 10.6 1.0
CB O:HIS61 3.5 10.8 1.0
OD2 O:ASP81 3.8 10.9 1.0
CB O:ASP81 3.9 11.8 1.0
NE2 O:HIS78 4.0 9.9 1.0
CA O:HIS69 4.1 11.9 1.0
CD2 O:HIS78 4.1 9.1 1.0
NE2 O:HIS61 4.1 9.5 1.0
O O:THR135 4.2 13.1 1.0
CD2 O:HIS61 4.2 10.0 1.0
CD2 O:HIS69 4.3 10.2 1.0
NE2 O:HIS69 4.3 11.1 1.0
NZ O:LYS134 4.6 14.2 1.0
CA O:HIS78 4.8 11.9 1.0
N O:GLY70 4.9 12.0 1.0
C O:THR135 4.9 13.1 1.0
N O:HIS69 5.0 11.9 1.0
C O:HIS69 5.0 12.0 1.0

Zinc binding site 2 out of 4 in 2sod

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Zinc binding site 2 out of 4 in the Determination and Analysis of the 2 Angstrom Structure of Copper, Zinc Superoxide Dismutase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Determination and Analysis of the 2 Angstrom Structure of Copper, Zinc Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Zn153

b:10.8
occ:1.00
 ND1 Y:HIS61 2.1 10.6 1.0
OD1 Y:ASP81 2.1 7.2 1.0
ND1 Y:HIS69 2.1 9.3 1.0
ND1 Y:HIS78 2.2 7.8 1.0
CE1 Y:HIS69 2.9 9.3 1.0
CE1 Y:HIS78 3.0 9.6 1.0
CE1 Y:HIS61 3.0 9.5 1.0
CG Y:ASP81 3.0 8.9 1.0
CG Y:HIS61 3.1 10.6 1.0
CG Y:HIS69 3.1 10.1 1.0
CG Y:HIS78 3.2 8.1 1.0
OD2 Y:ASP81 3.5 8.4 1.0
CB Y:HIS61 3.6 10.2 1.0
CB Y:HIS69 3.7 9.7 1.0
CB Y:HIS78 3.8 9.7 1.0
O Y:LYS134 3.9 13.0 1.0
NE2 Y:HIS69 4.0 9.4 1.0
NE2 Y:HIS61 4.1 9.2 1.0
CD2 Y:HIS61 4.2 8.8 1.0
NE2 Y:HIS78 4.2 9.6 1.0
CD2 Y:HIS69 4.2 10.8 1.0
CA Y:HIS69 4.2 11.9 1.0
CD2 Y:HIS78 4.3 8.0 1.0
CB Y:ASP81 4.3 10.5 1.0
C Y:LYS134 4.5 13.3 1.0
N Y:ASP81 4.6 11.9 1.0
CA Y:ASP81 4.7 11.9 1.0
O Y:THR135 4.7 13.6 1.0
N Y:GLY70 4.8 12.3 1.0
C Y:THR135 4.9 12.4 1.0
N Y:THR135 4.9 13.7 1.0
N Y:HIS78 5.0 11.9 1.0
CA Y:HIS78 5.0 11.8 1.0
NE2 Y:HIS44 5.0 7.4 1.0

Zinc binding site 3 out of 4 in 2sod

Go back to Zinc Binding Sites List in 2sod
Zinc binding site 3 out of 4 in the Determination and Analysis of the 2 Angstrom Structure of Copper, Zinc Superoxide Dismutase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Determination and Analysis of the 2 Angstrom Structure of Copper, Zinc Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn153

b:10.5
occ:1.00
 OD1 B:ASP81 2.0 8.5 1.0
ND1 B:HIS78 2.0 8.4 1.0
ND1 B:HIS61 2.1 9.1 1.0
ND1 B:HIS69 2.1 8.1 1.0
CG B:ASP81 2.8 8.0 1.0
CE1 B:HIS78 3.0 9.3 1.0
OD2 B:ASP81 3.0 10.8 1.0
CE1 B:HIS61 3.0 7.2 1.0
CE1 B:HIS69 3.0 7.0 1.0
CG B:HIS61 3.1 9.3 1.0
CG B:HIS78 3.1 9.6 1.0
CG B:HIS69 3.1 8.2 1.0
CB B:HIS61 3.5 9.9 1.0
CB B:HIS78 3.5 10.4 1.0
CB B:HIS69 3.6 9.8 1.0
O B:LYS134 3.8 12.0 1.0
NE2 B:HIS78 4.1 10.8 1.0
CA B:HIS69 4.1 11.9 1.0
NE2 B:HIS61 4.1 8.3 1.0
CD2 B:HIS61 4.2 7.4 1.0
NE2 B:HIS69 4.2 7.4 1.0
CD2 B:HIS78 4.2 9.4 1.0
CB B:ASP81 4.2 9.3 1.0
CD2 B:HIS69 4.2 8.1 1.0
N B:HIS78 4.5 11.9 1.0
CA B:HIS78 4.5 11.8 1.0
O B:THR135 4.6 12.1 1.0
N B:ASP81 4.6 11.8 1.0
CA B:ASP81 4.7 11.9 1.0
C B:LYS134 4.8 10.2 1.0
N B:HIS69 4.9 11.9 1.0
CA B:HIS61 5.0 12.0 1.0

Zinc binding site 4 out of 4 in 2sod

Go back to Zinc Binding Sites List in 2sod
Zinc binding site 4 out of 4 in the Determination and Analysis of the 2 Angstrom Structure of Copper, Zinc Superoxide Dismutase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Determination and Analysis of the 2 Angstrom Structure of Copper, Zinc Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn153

b:10.7
occ:1.00
 OD1 G:ASP81 2.0 9.0 1.0
ND1 G:HIS61 2.1 9.0 1.0
ND1 G:HIS78 2.1 8.7 1.0
ND1 G:HIS69 2.1 10.3 1.0
CG G:ASP81 2.9 8.2 1.0
CE1 G:HIS61 3.0 9.1 1.0
OD2 G:ASP81 3.0 7.2 1.0
CE1 G:HIS78 3.0 9.0 1.0
CG G:HIS61 3.0 10.1 1.0
CE1 G:HIS69 3.0 9.7 1.0
CG G:HIS78 3.1 8.4 1.0
CG G:HIS69 3.2 10.2 1.0
CB G:HIS61 3.5 10.3 1.0
CB G:HIS78 3.6 8.7 1.0
CB G:HIS69 3.6 11.4 1.0
O G:LYS134 3.8 12.6 1.0
NE2 G:HIS61 4.1 9.6 1.0
NE2 G:HIS69 4.2 10.0 1.0
CA G:HIS69 4.2 12.0 1.0
CD2 G:HIS61 4.2 10.0 1.0
NE2 G:HIS78 4.2 7.1 1.0
CD2 G:HIS78 4.2 7.6 1.0
CB G:ASP81 4.2 10.2 1.0
CD2 G:HIS69 4.3 10.3 1.0
N G:ASP81 4.6 11.9 1.0
C G:LYS134 4.6 12.2 1.0
CA G:HIS78 4.7 11.8 1.0
CA G:ASP81 4.7 11.9 1.0
N G:HIS78 4.7 11.9 1.0
O G:LYS68 4.8 16.2 1.0
CD2 G:HIS44 5.0 8.5 1.0

Reference:

J.A.Tainer, E.D.Getzoff, K.M.Beem, J.S.Richardson, D.C.Richardson. Determination and Analysis of the 2 A-Structure of Copper, Zinc Superoxide Dismutase. J.Mol.Biol. V. 160 181 1982.
ISSN: ISSN 0022-2836
PubMed: 7175933
DOI: 10.1016/0022-2836(82)90174-7
Page generated: Wed Dec 16 03:53:16 2020

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