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Zinc in PDB 1sda: Crystal Structure of Peroxynitrite-Modified Bovine Cu,Zn Superoxide Dismutase

Enzymatic activity of Crystal Structure of Peroxynitrite-Modified Bovine Cu,Zn Superoxide Dismutase

All present enzymatic activity of Crystal Structure of Peroxynitrite-Modified Bovine Cu,Zn Superoxide Dismutase:
1.15.1.1;

Protein crystallography data

The structure of Crystal Structure of Peroxynitrite-Modified Bovine Cu,Zn Superoxide Dismutase, PDB code: 1sda was solved by C.D.Smith, M.Carson, M.Van Der Woerd, J.Chen, H.Ischiropoulos, J.S.Beckman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) N/A / 2.50
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 (%) 18.7 / n/a

Other elements in 1sda:

The structure of Crystal Structure of Peroxynitrite-Modified Bovine Cu,Zn Superoxide Dismutase also contains other interesting chemical elements:

Copper (Cu) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Peroxynitrite-Modified Bovine Cu,Zn Superoxide Dismutase (pdb code 1sda). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Peroxynitrite-Modified Bovine Cu,Zn Superoxide Dismutase, PDB code: 1sda:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 1sda

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Zinc binding site 1 out of 4 in the Crystal Structure of Peroxynitrite-Modified Bovine Cu,Zn Superoxide Dismutase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Peroxynitrite-Modified Bovine Cu,Zn Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Zn802

b:13.8
occ:1.00
ND1 O:HIS78 1.8 4.8 1.0
ND1 O:HIS61 1.8 3.1 1.0
OD1 O:ASP81 2.0 12.5 1.0
ND1 O:HIS69 2.2 13.5 1.0
CE1 O:HIS78 2.5 4.5 1.0
CE1 O:HIS61 2.7 3.8 1.0
CG O:ASP81 2.8 11.9 1.0
CG O:HIS61 2.9 2.7 1.0
OD2 O:ASP81 3.0 15.6 1.0
CE1 O:HIS69 3.0 11.2 1.0
CG O:HIS78 3.0 4.8 1.0
CG O:HIS69 3.4 10.6 1.0
CB O:HIS61 3.5 3.4 1.0
O O:LYS134 3.7 10.7 1.0
CB O:HIS78 3.7 7.0 1.0
NE2 O:HIS78 3.7 5.1 1.0
NE2 O:HIS61 3.8 2.0 1.0
CB O:HIS69 3.8 10.7 1.0
CD2 O:HIS61 4.0 2.0 1.0
CD2 O:HIS78 4.0 2.0 1.0
CA O:HIS69 4.1 11.6 1.0
NE2 O:HIS69 4.2 10.4 1.0
CB O:ASP81 4.3 11.2 1.0
CD2 O:HIS69 4.4 11.2 1.0
N O:GLY70 4.7 11.4 1.0
CA O:ASP81 4.8 9.6 1.0
N O:HIS78 4.8 10.4 1.0
C O:LYS134 4.8 9.4 1.0
CA O:HIS78 4.9 7.6 1.0
CD2 O:HIS44 5.0 5.5 1.0
CA O:HIS61 5.0 4.9 1.0
C O:HIS69 5.0 11.1 1.0

Zinc binding site 2 out of 4 in 1sda

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Zinc binding site 2 out of 4 in the Crystal Structure of Peroxynitrite-Modified Bovine Cu,Zn Superoxide Dismutase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Peroxynitrite-Modified Bovine Cu,Zn Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Zn805

b:16.6
occ:1.00
ND1 Y:HIS61 1.8 8.8 1.0
ND1 Y:HIS69 1.9 10.4 1.0
ND1 Y:HIS78 1.9 7.7 1.0
OD1 Y:ASP81 2.0 6.4 1.0
CE1 Y:HIS78 2.6 8.7 1.0
CE1 Y:HIS69 2.7 11.8 1.0
CE1 Y:HIS61 2.7 6.4 1.0
CG Y:ASP81 2.8 5.9 1.0
OD2 Y:ASP81 2.9 2.8 1.0
CG Y:HIS61 2.9 4.9 1.0
CG Y:HIS69 3.0 10.4 1.0
CG Y:HIS78 3.1 10.2 1.0
CB Y:HIS61 3.5 4.2 1.0
CB Y:HIS69 3.6 9.6 1.0
O Y:LYS134 3.6 8.4 1.0
CB Y:HIS78 3.7 9.5 1.0
NE2 Y:HIS78 3.8 7.9 1.0
NE2 Y:HIS61 3.8 6.6 1.0
NE2 Y:HIS69 3.9 12.0 1.0
CD2 Y:HIS61 4.0 4.2 1.0
CA Y:HIS69 4.0 9.4 1.0
CD2 Y:HIS78 4.1 9.4 1.0
CD2 Y:HIS69 4.1 10.3 1.0
CB Y:ASP81 4.2 5.8 1.0
C Y:LYS134 4.6 11.2 1.0
N Y:HIS78 4.8 10.9 1.0
CA Y:ASP81 4.8 8.8 1.0
N Y:GLY70 4.8 8.4 1.0
CA Y:HIS78 4.9 11.1 1.0
N Y:ASP81 4.9 9.3 1.0
C Y:HIS69 5.0 9.4 1.0
CA Y:HIS61 5.0 5.1 1.0

Zinc binding site 3 out of 4 in 1sda

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Zinc binding site 3 out of 4 in the Crystal Structure of Peroxynitrite-Modified Bovine Cu,Zn Superoxide Dismutase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Peroxynitrite-Modified Bovine Cu,Zn Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn808

b:12.7
occ:1.00
ND1 B:HIS61 1.8 9.1 1.0
ND1 B:HIS78 1.8 5.0 1.0
OD1 B:ASP81 1.9 3.5 1.0
ND1 B:HIS69 2.1 10.7 1.0
CE1 B:HIS61 2.6 9.9 1.0
CE1 B:HIS78 2.7 5.8 1.0
CG B:ASP81 2.7 8.0 1.0
OD2 B:ASP81 2.8 9.8 1.0
CG B:HIS61 2.9 8.1 1.0
CG B:HIS78 2.9 5.8 1.0
CE1 B:HIS69 3.0 10.2 1.0
CG B:HIS69 3.2 10.4 1.0
CB B:HIS61 3.4 9.1 1.0
CB B:HIS78 3.5 4.8 1.0
CB B:HIS69 3.6 9.7 1.0
O B:LYS134 3.8 11.5 1.0
NE2 B:HIS61 3.8 9.8 1.0
NE2 B:HIS78 3.9 6.0 1.0
CD2 B:HIS61 3.9 8.6 1.0
CD2 B:HIS78 4.0 4.1 1.0
CA B:HIS69 4.2 8.5 1.0
CB B:ASP81 4.2 7.5 1.0
NE2 B:HIS69 4.2 10.9 1.0
CD2 B:HIS69 4.3 10.0 1.0
CA B:HIS78 4.7 3.0 1.0
N B:HIS78 4.7 2.5 1.0
CA B:ASP81 4.8 8.5 1.0
C B:LYS134 4.9 9.3 1.0
N B:GLY70 4.9 8.4 1.0
CA B:HIS61 5.0 9.0 1.0
N B:ASP81 5.0 6.8 1.0

Zinc binding site 4 out of 4 in 1sda

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Zinc binding site 4 out of 4 in the Crystal Structure of Peroxynitrite-Modified Bovine Cu,Zn Superoxide Dismutase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Peroxynitrite-Modified Bovine Cu,Zn Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn811

b:16.3
occ:1.00
ND1 G:HIS61 1.8 14.4 1.0
ND1 G:HIS78 2.0 11.0 1.0
ND1 G:HIS69 2.0 4.7 1.0
OD1 G:ASP81 2.1 11.3 1.0
CE1 G:HIS78 2.7 10.8 1.0
CE1 G:HIS61 2.7 14.5 1.0
CE1 G:HIS69 2.8 4.2 1.0
CG G:HIS61 2.9 11.8 1.0
CG G:ASP81 2.9 9.7 1.0
OD2 G:ASP81 3.0 8.6 1.0
CG G:HIS69 3.2 4.5 1.0
CG G:HIS78 3.2 10.2 1.0
CB G:HIS61 3.4 10.1 1.0
CB G:HIS69 3.6 4.5 1.0
O G:LYS134 3.7 16.6 1.0
CB G:HIS78 3.8 9.9 1.0
NE2 G:HIS61 3.8 14.2 1.0
CD2 G:HIS61 3.9 13.3 1.0
NE2 G:HIS78 3.9 11.8 1.0
NE2 G:HIS69 4.0 2.0 1.0
CA G:HIS69 4.1 9.7 1.0
CD2 G:HIS78 4.2 7.0 1.0
CD2 G:HIS69 4.2 3.0 1.0
CB G:ASP81 4.3 7.9 1.0
C G:LYS134 4.8 15.3 1.0
CA G:HIS61 4.9 8.7 1.0
CA G:THR135 4.9 12.0 1.0
CA G:ASP81 4.9 7.1 1.0
CD2 G:HIS44 4.9 8.7 1.0
N G:HIS78 4.9 11.4 1.0
CA G:HIS78 5.0 10.4 1.0
N G:GLY70 5.0 12.3 1.0

Reference:

C.D.Smith, M.Carson, M.Van Der Woerd, J.Chen, H.Ischiropoulos, J.S.Beckman. Crystal Structure of Peroxynitrite-Modified Bovine Cu,Zn Superoxide Dismutase. Arch.Biochem.Biophys. V. 299 350 1992.
ISSN: ISSN 0003-9861
PubMed: 1444476
DOI: 10.1016/0003-9861(92)90286-6
Page generated: Wed Oct 16 18:47:25 2024

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