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Copper 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:

Zinc (Zn) 3 atoms

Copper Binding Sites:

The binding sites of Copper 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 Copper atom.
In total 3 binding sites of Copper where determined in the X-Ray Structure of A Bacterial Copper,Zinc Superoxide Dismutase, PDB code: 1yai:
Jump to Copper binding site number: 1; 2; 3;

Copper binding site 1 out of 3 in 1yai

Go back to Copper Binding Sites List in 1yai
Copper 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 Copper with other atoms in the Cu 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:Cu152

b:24.1
occ:1.00
ND1 A:HIS45 2.0 12.3 1.0
NE2 A:HIS125 2.1 18.2 1.0
NE2 A:HIS47 2.2 16.9 1.0
NE2 A:HIS70 2.8 26.4 1.0
CE1 A:HIS125 2.9 17.3 1.0
O A:HOH154 2.9 27.9 1.0
CE1 A:HIS45 3.0 13.7 1.0
CG A:HIS45 3.0 12.0 1.0
CE1 A:HIS47 3.1 13.8 1.0
CD2 A:HIS125 3.1 17.4 1.0
CD2 A:HIS47 3.2 16.0 1.0
CD2 A:HIS70 3.3 24.8 1.0
CB A:HIS45 3.3 12.0 1.0
CE1 A:HIS70 3.8 25.9 1.0
ND1 A:HIS125 4.0 17.9 1.0
NE2 A:HIS45 4.1 11.4 1.0
CD2 A:HIS45 4.1 11.1 1.0
CG A:HIS125 4.2 17.9 1.0
O A:HOH172 4.2 26.1 1.0
ND1 A:HIS47 4.2 19.1 1.0
CG A:HIS47 4.3 16.2 1.0
CB A:MET123 4.4 11.7 1.0
CG A:HIS70 4.4 24.1 1.0
CG A:MET123 4.5 14.0 1.0
CA A:HIS45 4.5 15.4 1.0
N A:HIS45 4.6 16.8 1.0
O A:HOH214 4.7 51.4 1.0
ND1 A:HIS70 4.7 23.0 1.0
O A:HIS45 5.0 16.1 1.0
C A:HIS45 5.0 17.6 1.0

Copper binding site 2 out of 3 in 1yai

Go back to Copper Binding Sites List in 1yai
Copper 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 Copper with other atoms in the Cu 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:Cu152

b:24.1
occ:1.00
ND1 B:HIS45 2.0 16.2 1.0
NE2 B:HIS125 2.1 18.7 1.0
NE2 B:HIS47 2.1 20.8 1.0
NE2 B:HIS70 2.8 24.9 1.0
CG B:HIS45 3.0 12.3 1.0
CD2 B:HIS125 3.0 16.3 1.0
CE1 B:HIS45 3.0 18.2 1.0
CE1 B:HIS47 3.0 18.7 1.0
CE1 B:HIS125 3.1 17.7 1.0
CD2 B:HIS47 3.2 19.6 1.0
O B:HOH154 3.2 35.9 1.0
CB B:HIS45 3.2 11.1 1.0
CD2 B:HIS70 3.3 20.3 1.0
CE1 B:HIS70 3.9 23.1 1.0
CD2 B:HIS45 4.1 16.5 1.0
CB B:MET123 4.1 15.9 1.0
NE2 B:HIS45 4.1 20.6 1.0
O B:HOH187 4.2 35.5 1.0
CG B:HIS125 4.2 20.5 1.0
ND1 B:HIS125 4.2 18.0 1.0
ND1 B:HIS47 4.2 19.1 1.0
CG B:HIS47 4.3 17.2 1.0
CG B:MET123 4.4 16.7 1.0
CA B:HIS45 4.4 16.0 1.0
CG B:HIS70 4.5 22.7 1.0
N B:HIS45 4.5 17.2 1.0
O B:HIS45 4.7 15.7 1.0
C B:HIS45 4.8 14.1 1.0
ND1 B:HIS70 4.8 20.3 1.0
O B:MET123 4.9 13.1 1.0

Copper binding site 3 out of 3 in 1yai

Go back to Copper Binding Sites List in 1yai
Copper 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 Copper with other atoms in the Cu 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:Cu152

b:26.9
occ:1.00
ND1 C:HIS45 2.0 21.3 1.0
NE2 C:HIS125 2.1 20.2 1.0
NE2 C:HIS47 2.1 17.3 1.0
O C:HOH154 2.5 36.1 1.0
NE2 C:HIS70 2.6 19.3 1.0
CE1 C:HIS125 3.0 19.3 1.0
CE1 C:HIS45 3.0 18.4 1.0
CE1 C:HIS47 3.0 14.7 1.0
CG C:HIS45 3.0 20.2 1.0
CD2 C:HIS70 3.1 19.6 1.0
CD2 C:HIS125 3.1 18.0 1.0
CD2 C:HIS47 3.2 14.8 1.0
CB C:HIS45 3.3 16.0 1.0
CE1 C:HIS70 3.7 18.2 1.0
NE2 C:HIS45 4.1 19.5 1.0
ND1 C:HIS125 4.1 20.0 1.0
CD2 C:HIS45 4.1 19.8 1.0
ND1 C:HIS47 4.2 17.4 1.0
CG C:HIS125 4.2 19.4 1.0
CG C:HIS47 4.3 19.2 1.0
O C:HOH177 4.3 30.7 1.0
CG C:HIS70 4.4 22.5 1.0
CB C:MET123 4.4 14.9 1.0
CA C:HIS45 4.5 18.1 1.0
ND1 C:HIS70 4.6 20.7 1.0
N C:HIS45 4.6 17.6 1.0
CG C:MET123 4.7 15.7 1.0
O C:HIS45 4.9 19.3 1.0
C C:HIS45 5.0 17.8 1.0
O C:HOH161 5.0 35.0 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 Oct 28 14:18:13 2020
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