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Copper in PDB 1ocr: Bovine Heart Cytochrome C Oxidase in the Fully Reduced State

Enzymatic activity of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State

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

Protein crystallography data

The structure of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State, PDB code: 1ocr was solved by T.Tsukihara, M.Yao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 2.35
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 189.100, 210.500, 178.600, 90.00, 90.00, 90.00
R / Rfree (%) 20.3 / 24.7

Other elements in 1ocr:

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

Magnesium (Mg) 2 atoms
Zinc (Zn) 2 atoms
Iron (Fe) 4 atoms
Sodium (Na) 2 atoms

Copper Binding Sites:

The binding sites of Copper atom in the Bovine Heart Cytochrome C Oxidase in the Fully Reduced State (pdb code 1ocr). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 6 binding sites of Copper where determined in the Bovine Heart Cytochrome C Oxidase in the Fully Reduced State, PDB code: 1ocr:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 1ocr

Go back to Copper Binding Sites List in 1ocr
Copper binding site 1 out of 6 in the Bovine Heart Cytochrome C Oxidase in the Fully Reduced State


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu517

b:21.4
occ:1.00
 NE2 A:HIS291 1.9 22.1 1.0
NE2 A:HIS290 2.0 12.7 1.0
ND1 A:HIS240 2.2 21.0 1.0
CD2 A:HIS291 2.8 23.8 1.0
CE1 A:HIS290 3.0 25.8 1.0
CE1 A:HIS291 3.0 24.4 1.0
CD2 A:HIS290 3.0 19.4 1.0
CG A:HIS240 3.1 15.3 1.0
CE1 A:HIS240 3.2 19.8 1.0
CB A:HIS240 3.4 15.6 1.0
CA A:HIS240 3.9 15.5 1.0
CG A:HIS291 4.0 24.8 1.0
ND1 A:HIS291 4.1 28.5 1.0
ND1 A:HIS290 4.1 19.9 1.0
CG A:HIS290 4.2 22.4 1.0
CD2 A:HIS240 4.3 23.4 1.0
NE2 A:HIS240 4.3 27.2 1.0
C1A A:HEA516 4.7 12.3 1.0
NA A:HEA516 4.7 21.3 1.0
N A:HIS240 4.8 10.1 1.0
CG2 A:VAL243 4.8 12.3 1.0
C4A A:HEA516 4.9 16.9 1.0
C2A A:HEA516 5.0 17.1 1.0

Copper binding site 2 out of 6 in 1ocr

Go back to Copper Binding Sites List in 1ocr
Copper binding site 2 out of 6 in the Bovine Heart Cytochrome C Oxidase in the Fully Reduced State


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu228

b:24.7
occ:1.00
 ND1 B:HIS161 2.0 12.3 1.0
SG B:CYS196 2.2 23.9 1.0
SG B:CYS200 2.3 20.2 1.0
CU B:CU229 2.6 24.9 1.0
CE1 B:HIS161 2.6 7.0 1.0
SD B:MET207 2.7 27.0 1.0
CE B:MET207 3.0 20.1 1.0
CG B:HIS161 3.2 7.0 1.0
CB B:CYS200 3.3 23.6 1.0
CB B:CYS196 3.4 23.3 1.0
CG B:MET207 3.7 26.9 1.0
CB B:HIS161 3.8 14.7 1.0
NE2 B:HIS161 3.9 7.0 1.0
O B:GLU198 4.1 33.5 1.0
CD2 B:HIS161 4.2 7.0 1.0
CA B:HIS161 4.2 12.8 1.0
ND1 B:HIS204 4.5 25.6 1.0
O B:LEU160 4.6 18.6 1.0
CA B:CYS200 4.7 21.1 1.0
CA B:CYS196 4.8 21.1 1.0
CD1 B:TRP104 4.8 29.5 1.0
CA B:HIS204 4.8 20.7 1.0
O B:HIS102 4.9 8.6 1.0
N B:CYS200 4.9 21.0 1.0
CZ2 B:TRP106 4.9 34.2 1.0
O B:HIS204 5.0 24.6 1.0
CB B:MET207 5.0 16.7 1.0

Copper binding site 3 out of 6 in 1ocr

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Copper binding site 3 out of 6 in the Bovine Heart Cytochrome C Oxidase in the Fully Reduced State


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu229

b:24.9
occ:1.00
 ND1 B:HIS204 2.0 25.6 1.0
SG B:CYS200 2.2 20.2 1.0
SG B:CYS196 2.3 23.9 1.0
O B:GLU198 2.4 33.5 1.0
CU B:CU228 2.6 24.7 1.0
CE1 B:HIS204 2.9 15.1 1.0
CG B:HIS204 3.0 20.2 1.0
CB B:CYS196 3.2 23.3 1.0
CB B:HIS204 3.4 22.4 1.0
CB B:CYS200 3.4 23.6 1.0
CA B:HIS204 3.5 20.7 1.0
O B:HIS204 3.6 24.6 1.0
C B:GLU198 3.6 23.4 1.0
N B:CYS200 3.6 21.0 1.0
C B:HIS204 4.0 21.2 1.0
NE2 B:HIS204 4.1 22.0 1.0
CD2 B:HIS204 4.1 22.6 1.0
C B:ILE199 4.2 18.9 1.0
CA B:CYS200 4.2 21.1 1.0
ND1 B:HIS161 4.2 12.3 1.0
N B:GLU198 4.2 23.3 1.0
CA B:ILE199 4.2 18.5 1.0
N B:ILE199 4.3 20.0 1.0
C B:CYS196 4.3 27.4 1.0
O B:CYS196 4.4 25.6 1.0
CA B:CYS196 4.4 21.1 1.0
SD B:MET207 4.5 27.0 1.0
CA B:GLU198 4.6 19.8 1.0
CG B:MET207 4.7 26.9 1.0
N B:HIS204 4.8 27.8 1.0
N B:SER197 4.8 27.4 1.0
CE1 B:HIS161 4.8 7.0 1.0

Copper binding site 4 out of 6 in 1ocr

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Copper binding site 4 out of 6 in the Bovine Heart Cytochrome C Oxidase in the Fully Reduced State


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Cu517

b:29.0
occ:1.00
 NE2 N:HIS291 2.0 37.0 1.0
NE2 N:HIS290 2.0 16.6 1.0
ND1 N:HIS240 2.1 28.2 1.0
CD2 N:HIS291 2.9 31.8 1.0
CE1 N:HIS290 2.9 23.0 1.0
CE1 N:HIS291 3.0 36.4 1.0
CD2 N:HIS290 3.1 19.6 1.0
CG N:HIS240 3.1 25.5 1.0
CE1 N:HIS240 3.2 27.9 1.0
CB N:HIS240 3.4 22.8 1.0
CA N:HIS240 3.9 26.2 1.0
CG N:HIS291 4.1 28.0 1.0
ND1 N:HIS290 4.1 18.7 1.0
ND1 N:HIS291 4.1 32.8 1.0
CG N:HIS290 4.2 19.8 1.0
CD2 N:HIS240 4.3 28.8 1.0
NE2 N:HIS240 4.3 28.8 1.0
N N:HIS240 4.7 23.1 1.0
CG2 N:VAL243 4.8 19.0 1.0
NA N:HEA516 4.8 24.5 1.0
C1A N:HEA516 4.8 24.1 1.0
C4A N:HEA516 4.9 25.5 1.0
CG2 N:VAL287 5.0 15.1 1.0
O N:TRP288 5.0 28.0 1.0

Copper binding site 5 out of 6 in 1ocr

Go back to Copper Binding Sites List in 1ocr
Copper binding site 5 out of 6 in the Bovine Heart Cytochrome C Oxidase in the Fully Reduced State


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cu228

b:35.6
occ:1.00
 ND1 O:HIS161 2.0 27.0 1.0
SG O:CYS196 2.2 27.8 1.0
SG O:CYS200 2.2 25.4 1.0
CU O:CU229 2.3 34.1 1.0
CE1 O:HIS161 2.7 25.9 1.0
SD O:MET207 2.7 42.9 1.0
CE O:MET207 3.1 37.8 1.0
CB O:CYS200 3.2 30.9 1.0
CG O:HIS161 3.2 27.9 1.0
CB O:CYS196 3.4 35.9 1.0
CG O:MET207 3.7 36.9 1.0
CB O:HIS161 3.8 28.8 1.0
O O:GLU198 3.9 43.7 1.0
NE2 O:HIS161 4.0 26.4 1.0
CA O:HIS161 4.2 26.7 1.0
CD2 O:HIS161 4.2 23.3 1.0
ND1 O:HIS204 4.3 30.6 1.0
CA O:CYS200 4.6 32.3 1.0
O O:LEU160 4.6 32.4 1.0
CA O:CYS196 4.8 35.3 1.0
N O:CYS200 4.8 38.1 1.0
CA O:HIS204 4.8 38.9 1.0
CD1 O:TRP104 4.9 39.0 1.0
O O:HIS204 4.9 40.4 1.0
CZ2 O:TRP106 5.0 49.9 1.0

Copper binding site 6 out of 6 in 1ocr

Go back to Copper Binding Sites List in 1ocr
Copper binding site 6 out of 6 in the Bovine Heart Cytochrome C Oxidase in the Fully Reduced State


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cu229

b:34.1
occ:1.00
 ND1 O:HIS204 2.0 30.6 1.0
SG O:CYS200 2.2 25.4 1.0
SG O:CYS196 2.3 27.8 1.0
CU O:CU228 2.3 35.6 1.0
O O:GLU198 2.4 43.7 1.0
CE1 O:HIS204 3.0 32.6 1.0
CG O:HIS204 3.1 33.1 1.0
CB O:CYS196 3.2 35.9 1.0
CB O:CYS200 3.4 30.9 1.0
CB O:HIS204 3.4 36.0 1.0
CA O:HIS204 3.5 38.9 1.0
N O:CYS200 3.6 38.1 1.0
C O:GLU198 3.6 33.4 1.0
O O:HIS204 3.6 40.4 1.0
C O:HIS204 4.1 37.8 1.0
ND1 O:HIS161 4.1 27.0 1.0
CA O:CYS200 4.1 32.3 1.0
NE2 O:HIS204 4.2 31.1 1.0
C O:ILE199 4.2 34.6 1.0
CD2 O:HIS204 4.2 29.0 1.0
N O:GLU198 4.3 35.6 1.0
CA O:ILE199 4.3 31.5 1.0
SD O:MET207 4.3 42.9 1.0
N O:ILE199 4.3 31.4 1.0
O O:CYS196 4.4 39.8 1.0
C O:CYS196 4.4 39.9 1.0
CA O:CYS196 4.4 35.3 1.0
CA O:GLU198 4.6 33.4 1.0
CG O:MET207 4.6 36.9 1.0
CE1 O:HIS161 4.7 25.9 1.0
N O:HIS204 4.8 41.2 1.0
N O:SER197 4.9 41.6 1.0

Reference:

S.Yoshikawa, K.Shinzawa-Itoh, R.Nakashima, R.Yaono, E.Yamashita, N.Inoue, M.Yao, M.J.Fei, C.P.Libeu, T.Mizushima, H.Yamaguchi, T.Tomizaki, T.Tsukihara. Redox-Coupled Crystal Structural Changes in Bovine Heart Cytochrome C Oxidase. Science V. 280 1723 1998.
ISSN: ISSN 0036-8075
PubMed: 9624044
DOI: 10.1126/SCIENCE.280.5370.1723
Page generated: Sun Dec 13 11:01:04 2020

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