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Zinc in PDB 1v54: Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State

Enzymatic activity of Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State:
1.9.3.1;

Protein crystallography data

The structure of Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State, PDB code: 1v54 was solved by T.Tsukihara, K.Shimokata, Y.Katayama, H.Shimada, K.Muramoto, H.Aoyama, M.Mochizuki, K.Shinzawa-Itoh, E.Yamashita, M.Yao, Y.Ishimura, S.Yoshikawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 182.590, 205.140, 178.250, 90.00, 90.00, 90.00
R / Rfree (%) 20.2 / 22.7

Other elements in 1v54:

The structure of Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Iron (Fe) 4 atoms
Copper (Cu) 6 atoms
Sodium (Na) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State (pdb code 1v54). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State, PDB code: 1v54:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 1v54

Go back to Zinc Binding Sites List in 1v54
Zinc binding site 1 out of 2 in the Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn99

b:25.6
occ:1.00
SG F:CYS82 2.2 25.4 1.0
SG F:CYS62 2.2 25.5 1.0
SG F:CYS60 2.3 26.4 1.0
SG F:CYS85 2.3 26.7 1.0
CB F:CYS82 3.2 28.0 1.0
CB F:CYS60 3.4 22.1 1.0
CB F:CYS62 3.4 23.3 1.0
CB F:CYS85 3.4 24.1 1.0
CA F:CYS62 3.5 27.9 1.0
N F:CYS85 3.7 27.5 1.0
N F:CYS62 3.9 28.1 1.0
CA F:CYS85 4.1 27.2 1.0
O F:CYS60 4.3 23.5 1.0
C F:CYS60 4.4 24.0 1.0
CB F:SER84 4.5 27.6 1.0
CA F:CYS60 4.5 22.0 1.0
OG F:SER84 4.7 30.4 1.0
O F:HOH123 4.7 43.2 1.0
CA F:CYS82 4.7 26.6 1.0
C F:SER84 4.7 27.0 1.0
C F:ILE61 4.8 27.7 1.0
C F:CYS85 4.8 28.9 1.0
CG2 F:THR87 4.8 33.3 1.0
C F:CYS62 4.9 31.3 1.0
N F:GLY86 4.9 30.3 1.0
CA F:SER84 5.0 26.5 1.0
CB F:ILE70 5.0 23.0 1.0
CG1 F:ILE70 5.0 21.7 1.0

Zinc binding site 2 out of 2 in 1v54

Go back to Zinc Binding Sites List in 1v54
Zinc binding site 2 out of 2 in the Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Bovine Heart Cytochrome C Oxidase at the Fully Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Zn99

b:25.1
occ:1.00
SG S:CYS82 2.2 24.2 1.0
SG S:CYS62 2.3 29.9 1.0
SG S:CYS60 2.3 23.8 1.0
SG S:CYS85 2.3 26.3 1.0
CB S:CYS82 3.0 25.4 1.0
CB S:CYS60 3.3 23.2 1.0
CB S:CYS62 3.4 28.0 1.0
CB S:CYS85 3.5 25.2 1.0
N S:CYS85 3.7 27.6 1.0
CA S:CYS62 3.7 27.1 1.0
N S:CYS62 4.0 28.4 1.0
CA S:CYS85 4.2 27.3 1.0
O S:CYS60 4.3 24.9 1.0
OG1 S:THR87 4.4 36.7 1.0
C S:CYS60 4.4 24.8 1.0
CA S:CYS60 4.4 23.9 1.0
CB S:SER84 4.5 27.9 1.0
CA S:CYS82 4.5 25.7 1.0
O S:HOH1319 4.7 55.2 1.0
C S:SER84 4.7 27.9 1.0
CB S:ILE70 4.9 21.7 1.0
C S:CYS85 4.9 28.6 1.0
CG1 S:ILE70 4.9 20.5 1.0
N S:GLY86 4.9 28.7 1.0
N S:SER84 4.9 28.0 1.0
C S:ILE61 4.9 28.7 1.0
CA S:SER84 4.9 27.1 1.0
CG2 S:THR87 5.0 35.3 1.0
C S:CYS82 5.0 25.0 1.0
OG S:SER84 5.0 32.8 1.0

Reference:

T.Tsukihara, K.Shimokata, Y.Katayama, H.Shimada, K.Muramoto, H.Aoyama, M.Mochizuki, K.Shinzawa-Itoh, E.Yamashita, M.Yao, Y.Ishimura, S.Yoshikawa. The Low-Spin Heme of Cytochrome C Oxidase As the Driving Element of the Proton-Pumping Process. Proc.Natl.Acad.Sci.Usa V. 100 15304 2003.
ISSN: ISSN 0027-8424
PubMed: 14673090
DOI: 10.1073/PNAS.2635097100
Page generated: Wed Dec 16 03:07:42 2020

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