Atomistry » Zinc » PDB 1y8f-1yj6 » 1yai
Atomistry »
  Zinc »
    PDB 1y8f-1yj6 »
      1yai »

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

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy