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Zinc in PDB 1yai: X-Ray Structure of A Bacterial Copper,Zinc Superoxide Dismutase

Enzymatic activity of X-Ray Structure of A Bacterial Copper,Zinc Superoxide Dismutase

All present enzymatic activity of X-Ray Structure of A Bacterial Copper,Zinc Superoxide Dismutase:
1.15.1.1;

Protein crystallography data

The structure of X-Ray Structure of A Bacterial Copper,Zinc Superoxide Dismutase, PDB code: 1yai was solved by Y.Bourne, S.M.Redford, T.P.Lo, J.A.Tainer, E.D.Getzoff, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.90
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 120.700, 87.000, 43.500, 90.00, 90.60, 90.00
R / Rfree (%) 14.9 / 21.5

Other elements in 1yai:

The structure of X-Ray Structure of A Bacterial Copper,Zinc Superoxide Dismutase also contains other interesting chemical elements:

Copper (Cu) 3 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the X-Ray Structure of A Bacterial Copper,Zinc Superoxide Dismutase (pdb code 1yai). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the X-Ray Structure of A Bacterial Copper,Zinc Superoxide Dismutase, PDB code: 1yai:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 1yai

Go back to Zinc Binding Sites List in 1yai
Zinc binding site 1 out of 3 in the X-Ray Structure of A Bacterial 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 X-Ray Structure of A Bacterial Copper,Zinc Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn153

b:17.4
occ:1.00
ND1 A:HIS70 1.8 23.0 1.0
OD1 A:ASP91 1.9 16.0 1.0
ND1 A:HIS79 2.1 13.1 1.0
ND1 A:HIS88 2.1 16.0 1.0
CE1 A:HIS70 2.6 25.9 1.0
CG A:ASP91 2.7 13.8 1.0
CE1 A:HIS79 2.9 13.5 1.0
OD2 A:ASP91 3.0 12.8 1.0
CG A:HIS70 3.0 24.1 1.0
CG A:HIS88 3.1 16.9 1.0
CE1 A:HIS88 3.1 14.8 1.0
CG A:HIS79 3.2 14.2 1.0
CB A:HIS88 3.4 15.2 1.0
CB A:HIS70 3.5 18.2 1.0
CB A:HIS79 3.6 13.9 1.0
CA A:HIS79 3.7 13.7 1.0
NE2 A:HIS70 3.8 26.4 1.0
CD2 A:HIS70 4.0 24.8 1.0
NE2 A:HIS79 4.1 13.2 1.0
CB A:ASP91 4.2 10.1 1.0
NE2 A:HIS88 4.2 17.4 1.0
CD2 A:HIS88 4.2 16.6 1.0
CD2 A:HIS79 4.3 11.2 1.0
N A:GLY80 4.6 13.4 1.0
CD2 A:LEU138 4.6 22.4 1.0
N A:HIS79 4.7 12.1 1.0
CA A:HIS88 4.7 15.3 1.0
C A:HIS79 4.7 14.9 1.0
CA A:ASP91 4.7 11.3 1.0
O A:LYS78 4.7 15.9 1.0
N A:ASP91 4.9 13.4 1.0
N A:HIS88 4.9 17.2 1.0
CD2 A:HIS45 5.0 11.1 1.0

Zinc binding site 2 out of 3 in 1yai

Go back to Zinc Binding Sites List in 1yai
Zinc binding site 2 out of 3 in the X-Ray Structure of A Bacterial 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 X-Ray Structure of A Bacterial Copper,Zinc Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn153

b:19.9
occ:1.00
OD1 B:ASP91 1.8 19.1 1.0
ND1 B:HIS79 1.9 19.1 1.0
ND1 B:HIS70 2.0 20.3 1.0
ND1 B:HIS88 2.1 19.2 1.0
CG B:ASP91 2.6 21.6 1.0
CE1 B:HIS79 2.7 19.3 1.0
CE1 B:HIS70 2.8 23.1 1.0
OD2 B:ASP91 3.0 18.3 1.0
CG B:HIS88 3.1 16.9 1.0
CG B:HIS79 3.1 17.8 1.0
CE1 B:HIS88 3.1 20.8 1.0
CG B:HIS70 3.1 22.7 1.0
CB B:HIS88 3.3 16.1 1.0
CB B:HIS70 3.6 21.1 1.0
CB B:HIS79 3.6 16.5 1.0
CA B:HIS79 3.8 16.0 1.0
NE2 B:HIS79 3.9 18.1 1.0
NE2 B:HIS70 4.0 24.9 1.0
CB B:ASP91 4.1 14.9 1.0
CD2 B:HIS79 4.1 20.7 1.0
CD2 B:HIS70 4.2 20.3 1.0
NE2 B:HIS88 4.2 19.9 1.0
CD2 B:HIS88 4.2 17.4 1.0
CD2 B:LEU138 4.3 24.8 1.0
N B:GLY80 4.6 15.5 1.0
CA B:ASP91 4.7 16.7 1.0
CA B:HIS88 4.7 17.7 1.0
C B:HIS79 4.7 18.4 1.0
O B:LYS78 4.7 17.6 1.0
N B:HIS79 4.8 15.5 1.0
N B:ASP91 4.8 14.3 1.0
N B:HIS88 4.9 15.5 1.0
CD2 B:HIS45 5.0 16.5 1.0

Zinc binding site 3 out of 3 in 1yai

Go back to Zinc Binding Sites List in 1yai
Zinc binding site 3 out of 3 in the X-Ray Structure of A Bacterial 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 X-Ray Structure of A Bacterial Copper,Zinc Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn153

b:19.9
occ:1.00
ND1 C:HIS70 1.8 20.7 1.0
OD1 C:ASP91 1.9 18.8 1.0
ND1 C:HIS79 2.0 14.1 1.0
ND1 C:HIS88 2.0 17.8 1.0
CE1 C:HIS70 2.5 18.2 1.0
CG C:ASP91 2.7 15.3 1.0
CE1 C:HIS79 2.8 14.6 1.0
OD2 C:ASP91 2.9 16.8 1.0
CG C:HIS88 3.0 17.2 1.0
CG C:HIS70 3.0 22.5 1.0
CE1 C:HIS88 3.0 15.3 1.0
CG C:HIS79 3.1 17.3 1.0
CB C:HIS88 3.3 15.8 1.0
CB C:HIS70 3.6 19.5 1.0
CB C:HIS79 3.6 16.9 1.0
NE2 C:HIS70 3.7 19.3 1.0
CA C:HIS79 3.8 19.1 1.0
NE2 C:HIS79 4.0 15.5 1.0
CD2 C:HIS70 4.0 19.6 1.0
CB C:ASP91 4.1 17.4 1.0
CD2 C:HIS88 4.1 19.6 1.0
NE2 C:HIS88 4.2 15.6 1.0
CD2 C:HIS79 4.2 12.7 1.0
CD2 C:LEU138 4.6 25.6 1.0
CA C:HIS88 4.6 17.1 1.0
O C:LYS78 4.6 17.9 1.0
CA C:ASP91 4.7 19.2 1.0
N C:GLY80 4.8 13.2 1.0
N C:HIS79 4.8 20.9 1.0
N C:HIS88 4.8 20.3 1.0
C C:HIS79 4.8 19.9 1.0
N C:ASP91 4.8 15.6 1.0
CD2 C:HIS45 5.0 19.8 1.0

Reference:

Y.Bourne, S.M.Redford, H.M.Steinman, J.R.Lepock, J.A.Tainer, E.D.Getzoff. Novel Dimeric Interface and Electrostatic Recognition in Bacterial Cu,Zn Superoxide Dismutase. Proc.Natl.Acad.Sci.Usa V. 93 12774 1996.
ISSN: ISSN 0027-8424
PubMed: 8917495
DOI: 10.1073/PNAS.93.23.12774
Page generated: Wed Dec 16 03:13:55 2020

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