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Copper in PDB 5w97: Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Serial Femtosecond X-Ray Crystallography at Room Temperature

Enzymatic activity of Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Serial Femtosecond X-Ray Crystallography at Room Temperature

All present enzymatic activity of Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Serial Femtosecond X-Ray Crystallography at Room Temperature:
1.9.3.1;

Protein crystallography data

The structure of Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Serial Femtosecond X-Ray Crystallography at Room Temperature, PDB code: 5w97 was solved by D.L.Rousseau, S.-R.Yeh, I.Ishigami, N.A.Zatsepin, T.D.Grant, P.Fromme, R.Fromme, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.86 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 178.300, 189.000, 209.000, 90.00, 90.00, 90.00
R / Rfree (%) 20.8 / 25.2

Other elements in 5w97:

The structure of Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Serial Femtosecond X-Ray Crystallography at Room Temperature 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 Serial Femtosecond X-Ray Crystallography at Room Temperature (pdb code 5w97). 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 Serial Femtosecond X-Ray Crystallography at Room Temperature, PDB code: 5w97:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 5w97

Go back to Copper Binding Sites List in 5w97
Copper binding site 1 out of 6 in the Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Serial Femtosecond X-Ray Crystallography at Room Temperature


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 Serial Femtosecond X-Ray Crystallography at Room Temperature within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu603

b:28.4
occ:1.00
NE2 A:HIS291 2.0 29.4 1.0
ND1 A:HIS240 2.0 27.6 1.0
NE2 A:HIS290 2.1 24.1 1.0
O A:CMO609 2.7 24.4 1.0
CD2 A:HIS291 2.8 28.6 1.0
CG A:HIS240 3.0 23.5 1.0
CD2 A:HIS290 3.0 24.5 1.0
CE1 A:HIS240 3.0 27.3 1.0
CE1 A:HIS291 3.1 28.4 1.0
CE1 A:HIS290 3.1 25.4 1.0
CB A:HIS240 3.3 21.6 1.0
C A:CMO609 3.5 23.5 1.0
CA A:HIS240 3.9 21.6 1.0
CG A:HIS291 4.0 26.9 1.0
ND1 A:HIS291 4.1 27.5 1.0
CD2 A:HIS240 4.1 25.6 1.0
NE2 A:HIS240 4.1 28.9 1.0
CG A:HIS290 4.2 24.1 1.0
ND1 A:HIS290 4.2 23.4 1.0
N A:HIS240 4.7 21.4 1.0
CG2 A:VAL243 4.8 28.6 1.0
O A:VAL287 4.9 22.9 1.0
CG2 A:VAL287 4.9 23.6 1.0

Copper binding site 2 out of 6 in 5w97

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Copper binding site 2 out of 6 in the Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Serial Femtosecond X-Ray Crystallography at Room Temperature


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 Serial Femtosecond X-Ray Crystallography at Room Temperature within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu301

b:31.7
occ:1.00
CU1 B:CUA301 0.0 31.7 1.0
ND1 B:HIS161 2.0 25.4 1.0
SG B:CYS196 2.3 25.8 1.0
SG B:CYS200 2.4 26.3 1.0
SD B:MET207 2.4 28.2 1.0
CU2 B:CUA301 2.6 29.4 1.0
CE1 B:HIS161 2.9 21.7 1.0
CE B:MET207 3.0 26.1 1.0
CG B:HIS161 3.2 22.4 1.0
CB B:CYS200 3.2 27.4 1.0
CB B:CYS196 3.4 27.9 1.0
CG B:MET207 3.5 28.7 1.0
CB B:HIS161 3.6 23.9 1.0
O B:GLU198 3.8 31.9 1.0
NE2 B:HIS161 4.1 21.2 1.0
CA B:HIS161 4.2 23.6 1.0
CD2 B:HIS161 4.2 20.9 1.0
ND1 B:HIS204 4.6 28.0 1.0
CD1 B:TRP104 4.6 29.5 1.0
CA B:CYS200 4.6 28.0 1.0
O B:LEU160 4.7 23.6 1.0
O B:HIS102 4.7 24.3 1.0
CA B:HIS204 4.8 27.7 1.0
CA B:CYS196 4.8 26.8 1.0
CB B:MET207 4.9 27.2 1.0
N B:CYS200 4.9 26.8 1.0
CZ2 B:TRP106 4.9 32.1 1.0

Copper binding site 3 out of 6 in 5w97

Go back to Copper Binding Sites List in 5w97
Copper binding site 3 out of 6 in the Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Serial Femtosecond X-Ray Crystallography at Room Temperature


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 Serial Femtosecond X-Ray Crystallography at Room Temperature within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu301

b:29.4
occ:1.00
CU2 B:CUA301 0.0 29.4 1.0
ND1 B:HIS204 2.0 28.0 1.0
O B:GLU198 2.1 31.9 1.0
SG B:CYS200 2.3 26.3 1.0
SG B:CYS196 2.3 25.8 1.0
CU1 B:CUA301 2.6 31.7 1.0
CE1 B:HIS204 2.9 28.0 1.0
CG B:HIS204 3.1 25.7 1.0
CB B:CYS200 3.3 27.4 1.0
CB B:CYS196 3.4 27.9 1.0
C B:GLU198 3.4 25.2 1.0
CA B:HIS204 3.5 27.7 1.0
CB B:HIS204 3.5 27.2 1.0
N B:CYS200 3.5 26.8 1.0
O B:HIS204 3.8 23.8 1.0
NE2 B:HIS204 4.1 28.8 1.0
CA B:CYS200 4.1 28.0 1.0
CA B:ILE199 4.1 24.8 1.0
C B:HIS204 4.1 27.4 1.0
N B:ILE199 4.1 25.5 1.0
C B:ILE199 4.1 25.7 1.0
CD2 B:HIS204 4.2 26.8 1.0
N B:GLU198 4.2 27.5 1.0
ND1 B:HIS161 4.2 25.4 1.0
C B:CYS196 4.3 27.1 1.0
SD B:MET207 4.3 28.2 1.0
CA B:GLU198 4.4 25.0 1.0
CA B:CYS196 4.5 26.8 1.0
O B:CYS196 4.5 26.6 1.0
CG B:MET207 4.6 28.7 1.0
N B:SER197 4.7 25.7 1.0
N B:HIS204 4.7 30.5 1.0
C B:CYS200 5.0 29.8 1.0

Copper binding site 4 out of 6 in 5w97

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Copper binding site 4 out of 6 in the Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Serial Femtosecond X-Ray Crystallography at Room Temperature


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 Serial Femtosecond X-Ray Crystallography at Room Temperature within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Cu603

b:39.8
occ:1.00
NE2 a:HIS290 2.0 31.1 1.0
NE2 a:HIS291 2.0 41.5 1.0
ND1 a:HIS240 2.0 35.2 1.0
CE1 a:HIS291 2.8 41.2 1.0
O a:CMO608 2.9 33.9 1.0
CE1 a:HIS290 2.9 30.4 1.0
CE1 a:HIS240 3.0 34.4 1.0
CG a:HIS240 3.0 34.1 1.0
CD2 a:HIS290 3.0 30.3 1.0
CD2 a:HIS291 3.1 42.2 1.0
C a:CMO608 3.3 36.6 1.0
CB a:HIS240 3.3 33.9 1.0
ND1 a:HIS291 3.9 38.4 1.0
CA a:HIS240 4.0 33.9 1.0
ND1 a:HIS290 4.1 28.2 1.0
CG a:HIS291 4.1 41.2 1.0
NE2 a:HIS240 4.1 36.6 1.0
CD2 a:HIS240 4.1 33.9 1.0
CG a:HIS290 4.1 28.5 1.0
CG2 a:VAL287 4.7 33.6 1.0
N a:HIS240 4.8 34.6 1.0
CG2 a:VAL243 4.8 34.2 1.0

Copper binding site 5 out of 6 in 5w97

Go back to Copper Binding Sites List in 5w97
Copper binding site 5 out of 6 in the Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Serial Femtosecond X-Ray Crystallography at Room Temperature


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 Serial Femtosecond X-Ray Crystallography at Room Temperature within 5.0Å range:
probe atom residue distance (Å) B Occ
b:Cu302

b:46.6
occ:1.00
CU1 b:CUA302 0.0 46.6 1.0
ND1 b:HIS161 2.0 50.6 1.0
SG b:CYS200 2.3 41.1 1.0
SG b:CYS196 2.3 41.0 1.0
SD b:MET207 2.4 47.1 1.0
CU2 b:CUA302 2.7 47.1 1.0
CE1 b:HIS161 2.9 47.9 1.0
CE b:MET207 3.0 44.6 1.0
CG b:HIS161 3.1 48.3 1.0
CB b:CYS200 3.3 46.8 1.0
CB b:HIS161 3.5 50.2 1.0
CB b:CYS196 3.6 49.7 1.0
CG b:MET207 3.6 48.2 1.0
O b:GLU198 3.9 65.8 1.0
NE2 b:HIS161 4.0 48.0 1.0
CD2 b:HIS161 4.1 49.4 1.0
CA b:HIS161 4.1 46.5 1.0
ND1 b:HIS204 4.6 46.0 1.0
CA b:CYS200 4.6 45.1 1.0
CD1 b:TRP104 4.7 41.0 1.0
O b:LEU160 4.7 40.6 1.0
O b:HIS102 4.7 40.6 1.0
N b:CYS200 4.8 50.2 1.0
CB b:MET207 4.8 51.8 1.0
CZ2 b:TRP106 4.9 58.5 1.0
CA b:HIS204 5.0 45.2 1.0
CA b:CYS196 5.0 48.2 1.0

Copper binding site 6 out of 6 in 5w97

Go back to Copper Binding Sites List in 5w97
Copper binding site 6 out of 6 in the Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Serial Femtosecond X-Ray Crystallography at Room Temperature


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 Serial Femtosecond X-Ray Crystallography at Room Temperature within 5.0Å range:
probe atom residue distance (Å) B Occ
b:Cu302

b:47.1
occ:1.00
CU2 b:CUA302 0.0 47.1 1.0
ND1 b:HIS204 2.0 46.0 1.0
O b:GLU198 2.1 65.8 1.0
SG b:CYS196 2.3 41.0 1.0
SG b:CYS200 2.3 41.1 1.0
CU1 b:CUA302 2.7 46.6 1.0
CE1 b:HIS204 2.8 40.8 1.0
CG b:HIS204 3.1 45.5 1.0
C b:GLU198 3.4 43.3 1.0
CB b:CYS196 3.5 49.7 1.0
CB b:HIS204 3.5 46.3 1.0
CA b:HIS204 3.6 45.2 1.0
CB b:CYS200 3.6 46.8 1.0
N b:CYS200 3.6 50.2 1.0
O b:HIS204 3.8 40.9 1.0
O b:CYS196 3.9 41.2 1.0
NE2 b:HIS204 4.0 50.3 1.0
C b:CYS196 4.1 47.2 1.0
CD2 b:HIS204 4.1 45.5 1.0
C b:HIS204 4.1 42.5 1.0
N b:GLU198 4.2 44.8 1.0
N b:ILE199 4.2 40.8 1.0
CA b:CYS200 4.2 45.1 1.0
CA b:ILE199 4.2 42.7 1.0
ND1 b:HIS161 4.3 50.6 1.0
SD b:MET207 4.3 47.1 1.0
C b:ILE199 4.4 50.9 1.0
CA b:CYS196 4.4 48.2 1.0
CA b:GLU198 4.4 40.8 1.0
CG b:MET207 4.6 48.2 1.0
N b:SER197 4.6 49.0 1.0
N b:HIS204 4.9 49.1 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: Sun Dec 13 11:20:04 2020

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