Zinc in PDB 1yai: 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;

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

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

Copper

(Cu)

3 atoms

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 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 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 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

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