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Copper in PDB 5wau: Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Synchrotron X-Ray Crystallography at 100 K

Enzymatic activity of Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Synchrotron X-Ray Crystallography at 100 K

All present enzymatic activity of Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Synchrotron X-Ray Crystallography at 100 K:
1.9.3.1;

Protein crystallography data

The structure of Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Synchrotron X-Ray Crystallography at 100 K, PDB code: 5wau was solved by R.Fromme, I.Ishigami, S.Y.Yeh, N.Zatsepin, T.Grant, P.Fromme, D.Rousseau, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.00 / 1.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 177.923, 182.555, 208.450, 90.00, 90.00, 90.00
R / Rfree (%) 21.7 / 24.4

Other elements in 5wau:

The structure of Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Synchrotron X-Ray Crystallography at 100 K 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 Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Synchrotron X-Ray Crystallography at 100 K (pdb code 5wau). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 6 binding sites of Copper where determined in the Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Synchrotron X-Ray Crystallography at 100 K, PDB code: 5wau:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 5wau

Go back to Copper Binding Sites List in 5wau
Copper binding site 1 out of 6 in the Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Synchrotron X-Ray Crystallography at 100 K


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Synchrotron X-Ray Crystallography at 100 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu603

b:25.7
occ:1.00
NE2 A:HIS290 2.0 24.9 1.0
NE2 A:HIS291 2.1 24.4 1.0
ND1 A:HIS240 2.1 24.1 1.0
O A:CMO610 2.2 46.3 1.0
C A:CMO610 2.6 46.1 1.0
CE1 A:HIS291 3.0 22.4 1.0
CE1 A:HIS240 3.0 24.4 1.0
CD2 A:HIS290 3.0 23.7 1.0
CE1 A:HIS290 3.0 25.5 1.0
CD2 A:HIS291 3.0 22.0 1.0
CG A:HIS240 3.1 22.5 1.0
CB A:HIS240 3.5 21.1 1.0
ND1 A:HIS291 4.0 22.3 1.0
CA A:HIS240 4.1 22.5 1.0
CG A:HIS291 4.1 22.3 1.0
ND1 A:HIS290 4.1 24.5 1.0
CG A:HIS290 4.2 24.6 1.0
NE2 A:HIS240 4.2 25.5 1.0
CD2 A:HIS240 4.2 24.1 1.0
C1A A:HEA602 4.5 23.1 1.0
C4A A:HEA602 4.7 23.0 1.0
NA A:HEA602 4.7 25.4 1.0
C2A A:HEA602 4.7 24.2 1.0
CG2 A:VAL243 4.8 23.7 1.0
C3A A:HEA602 4.8 23.5 1.0
FE A:HEA602 4.9 25.3 1.0
N A:HIS240 5.0 21.3 1.0

Copper binding site 2 out of 6 in 5wau

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Copper binding site 2 out of 6 in the Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Synchrotron X-Ray Crystallography at 100 K


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Synchrotron X-Ray Crystallography at 100 K within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu302

b:24.6
occ:1.00
CU1 B:CUA302 0.0 24.6 1.0
ND1 B:HIS204 2.0 23.7 1.0
O B:GLU198 2.1 30.3 1.0
SG B:CYS200 2.2 24.5 1.0
SG B:CYS196 2.3 24.0 1.0
CU2 B:CUA302 2.6 24.4 1.0
CE1 B:HIS204 2.9 24.9 1.0
CG B:HIS204 3.2 24.4 1.0
CE B:MET207 3.2 37.0 1.0
CB B:CYS196 3.3 23.0 1.0
C B:GLU198 3.3 28.3 1.0
CB B:CYS200 3.4 24.4 1.0
CA B:HIS204 3.6 23.9 1.0
CB B:HIS204 3.7 24.0 1.0
N B:CYS200 3.7 22.7 1.0
O B:HIS204 3.8 23.1 1.0
NE2 B:HIS204 4.0 23.6 1.0
N B:GLU198 4.1 26.7 1.0
C B:HIS204 4.1 23.0 1.0
C B:CYS196 4.2 23.6 1.0
N B:ILE199 4.2 26.5 1.0
O B:CYS196 4.2 22.3 1.0
CD2 B:HIS204 4.2 24.1 1.0
CA B:CYS200 4.2 24.4 1.0
CA B:ILE199 4.2 24.8 1.0
ND1 B:HIS161 4.3 23.9 1.0
C B:ILE199 4.3 25.0 1.0
CA B:CYS196 4.3 23.3 1.0
CA B:GLU198 4.4 27.3 1.0
SD B:MET207 4.4 26.9 1.0
N B:SER197 4.6 25.0 1.0
N B:HIS204 4.8 25.6 1.0
CG B:MET207 4.8 27.6 1.0
CA B:HIS161 4.9 22.8 1.0

Copper binding site 3 out of 6 in 5wau

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Copper binding site 3 out of 6 in the Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Synchrotron X-Ray Crystallography at 100 K


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Synchrotron X-Ray Crystallography at 100 K within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu302

b:24.4
occ:1.00
CU2 B:CUA302 0.0 24.4 1.0
ND1 B:HIS161 2.0 23.9 1.0
CE B:MET207 2.1 37.0 1.0
SG B:CYS196 2.3 24.0 1.0
SG B:CYS200 2.4 24.5 1.0
SD B:MET207 2.4 26.9 1.0
CU1 B:CUA302 2.6 24.6 1.0
CE1 B:HIS161 2.9 23.7 1.0
CG B:HIS161 3.1 23.1 1.0
CB B:CYS200 3.3 24.4 1.0
CB B:CYS196 3.5 23.0 1.0
CG B:MET207 3.6 27.6 1.0
CB B:HIS161 3.6 24.2 1.0
O B:GLU198 3.9 30.3 1.0
NE2 B:HIS161 4.1 23.1 1.0
CA B:HIS161 4.2 22.8 1.0
CD2 B:HIS161 4.2 22.8 1.0
O B:HIS102 4.6 23.9 1.0
ND1 B:HIS204 4.6 23.7 1.0
CD1 B:TRP104 4.6 26.6 1.0
O B:LEU160 4.7 24.1 1.0
CA B:CYS200 4.7 24.4 1.0
CA B:HIS204 4.9 23.9 1.0
CA B:CYS196 4.9 23.3 1.0
CB B:MET207 5.0 25.9 1.0
CZ2 B:TRP106 5.0 26.6 1.0

Copper binding site 4 out of 6 in 5wau

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Copper binding site 4 out of 6 in the Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Synchrotron X-Ray Crystallography at 100 K


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Synchrotron X-Ray Crystallography at 100 K within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Cu603

b:34.7
occ:1.00
ND1 a:HIS240 2.0 32.4 1.0
NE2 a:HIS290 2.0 29.7 1.0
NE2 a:HIS291 2.1 34.8 1.0
O a:CMO608 2.6 69.0 1.0
C a:CMO608 2.7 65.8 1.0
CE1 a:HIS291 2.9 33.8 1.0
CE1 a:HIS290 2.9 29.0 1.0
CE1 a:HIS240 3.0 33.1 1.0
CG a:HIS240 3.0 33.7 1.0
CD2 a:HIS291 3.1 33.9 1.0
CD2 a:HIS290 3.1 29.7 1.0
CB a:HIS240 3.4 32.5 1.0
ND1 a:HIS291 4.0 33.1 1.0
CG a:HIS291 4.1 33.2 1.0
ND1 a:HIS290 4.1 29.5 1.0
CA a:HIS240 4.1 32.3 1.0
NE2 a:HIS240 4.1 32.6 1.0
CD2 a:HIS240 4.1 34.4 1.0
CG a:HIS290 4.2 29.4 1.0
C1A a:HEA602 4.5 32.2 1.0
C4A a:HEA602 4.7 31.5 1.0
C2A a:HEA602 4.7 33.3 1.0
NA a:HEA602 4.7 32.2 1.0
C3A a:HEA602 4.8 32.4 1.0
CG2 a:VAL243 4.9 35.7 1.0
FE a:HEA602 4.9 34.5 1.0
N a:HIS240 5.0 33.2 1.0

Copper binding site 5 out of 6 in 5wau

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Copper binding site 5 out of 6 in the Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Synchrotron X-Ray Crystallography at 100 K


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Synchrotron X-Ray Crystallography at 100 K within 5.0Å range:
probe atom residue distance (Å) B Occ
b:Cu301

b:38.4
occ:1.00
CU1 b:CUA301 0.0 38.4 1.0
ND1 b:HIS161 2.0 44.6 1.0
SG b:CYS200 2.3 35.2 1.0
SG b:CYS196 2.3 37.7 1.0
SD b:MET207 2.4 38.4 1.0
CU2 b:CUA301 2.7 37.0 1.0
CE1 b:HIS161 2.9 45.2 1.0
CG b:HIS161 3.1 40.7 1.0
CE b:MET207 3.1 40.7 1.0
CB b:CYS200 3.3 37.6 1.0
CB b:CYS196 3.5 42.1 1.0
CB b:HIS161 3.5 38.5 1.0
CG b:MET207 3.6 43.7 1.0
O b:GLU198 3.9 43.0 1.0
NE2 b:HIS161 4.1 44.0 1.0
CA b:HIS161 4.2 38.9 1.0
CD2 b:HIS161 4.2 41.0 1.0
O b:HIS102 4.5 37.4 1.0
CD1 b:TRP104 4.6 42.3 1.0
ND1 b:HIS204 4.6 35.3 1.0
CA b:CYS200 4.7 37.5 1.0
O b:LEU160 4.8 34.3 1.0
CA b:HIS204 4.9 38.9 1.0
CA b:CYS196 4.9 40.5 1.0
CB b:MET207 4.9 42.5 1.0
N b:CYS200 4.9 38.5 1.0
CZ2 b:TRP106 4.9 42.2 1.0

Copper binding site 6 out of 6 in 5wau

Go back to Copper Binding Sites List in 5wau
Copper binding site 6 out of 6 in the Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Synchrotron X-Ray Crystallography at 100 K


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Synchrotron X-Ray Crystallography at 100 K within 5.0Å range:
probe atom residue distance (Å) B Occ
b:Cu301

b:37.0
occ:1.00
CU2 b:CUA301 0.0 37.0 1.0
ND1 b:HIS204 2.0 35.3 1.0
O b:GLU198 2.1 43.0 1.0
SG b:CYS196 2.3 37.7 1.0
SG b:CYS200 2.3 35.2 1.0
CU1 b:CUA301 2.7 38.4 1.0
CE1 b:HIS204 2.9 36.1 1.0
CG b:HIS204 3.1 39.1 1.0
C b:GLU198 3.3 39.5 1.0
CB b:CYS196 3.4 42.1 1.0
CB b:CYS200 3.5 37.6 1.0
CA b:HIS204 3.5 38.9 1.0
CB b:HIS204 3.6 39.4 1.0
N b:CYS200 3.6 38.5 1.0
O b:HIS204 3.9 39.1 1.0
NE2 b:HIS204 4.0 35.7 1.0
O b:CYS196 4.1 39.1 1.0
N b:GLU198 4.1 40.6 1.0
N b:ILE199 4.1 39.0 1.0
CD2 b:HIS204 4.1 36.8 1.0
C b:CYS196 4.2 39.0 1.0
C b:HIS204 4.2 38.4 1.0
CA b:ILE199 4.2 39.0 1.0
CA b:CYS200 4.2 37.5 1.0
C b:ILE199 4.3 40.6 1.0
CA b:GLU198 4.3 40.6 1.0
ND1 b:HIS161 4.4 44.6 1.0
CA b:CYS196 4.4 40.5 1.0
SD b:MET207 4.4 38.4 1.0
N b:SER197 4.6 39.0 1.0
N b:HIS204 4.7 41.6 1.0
CG b:MET207 4.8 43.7 1.0
CA b:HIS161 5.0 38.9 1.0

Reference:

I.Ishigami, N.A.Zatsepin, M.Hikita, C.E.Conrad, G.Nelson, J.D.Coe, S.Basu, T.D.Grant, M.H.Seaberg, R.G.Sierra, M.S.Hunter, P.Fromme, R.Fromme, S.R.Yeh, D.L.Rousseau. Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Serial Femtosecond X-Ray Crystallography at Room Temperature. Proc. Natl. Acad. Sci. V. 114 8011 2017U.S.A..
ISSN: ESSN 1091-6490
PubMed: 28698372
DOI: 10.1073/PNAS.1705628114
Page generated: Mon Jul 14 05:30:07 2025

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