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Copper in PDB 6nmp: Sfx Structure of Oxidized Cytochrome C Oxidase at Room Temperature

Enzymatic activity of Sfx Structure of Oxidized Cytochrome C Oxidase at Room Temperature

All present enzymatic activity of Sfx Structure of Oxidized Cytochrome C Oxidase at Room Temperature:
1.9.3.1;

Protein crystallography data

The structure of Sfx Structure of Oxidized Cytochrome C Oxidase at Room Temperature, PDB code: 6nmp was solved by D.L.Rousseau, S.-R.Yeh, I.Ishigami, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 2.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 178.700, 189.800, 211.300, 90.00, 90.00, 90.00
R / Rfree (%) 19.2 / 24.4

Other elements in 6nmp:

The structure of Sfx Structure of Oxidized Cytochrome C Oxidase 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 Sfx Structure of Oxidized Cytochrome C Oxidase at Room Temperature (pdb code 6nmp). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 6 binding sites of Copper where determined in the Sfx Structure of Oxidized Cytochrome C Oxidase at Room Temperature, PDB code: 6nmp:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 6nmp

Go back to Copper Binding Sites List in 6nmp
Copper binding site 1 out of 6 in the Sfx Structure of Oxidized Cytochrome C Oxidase 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 Sfx Structure of Oxidized Cytochrome C Oxidase at Room Temperature within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu601

b:44.3
occ:1.00
 O1 A:PER609 1.9 38.6 1.0
NE2 A:HIS290 2.0 43.4 1.0
NE2 A:HIS291 2.0 47.4 1.0
ND1 A:HIS240 2.1 42.2 1.0
CE1 A:HIS290 2.8 41.9 1.0
CD2 A:HIS291 3.0 45.7 1.0
CE1 A:HIS291 3.0 47.4 1.0
CE1 A:HIS240 3.0 43.9 1.0
CG A:HIS240 3.1 38.3 1.0
O2 A:PER609 3.1 38.4 1.0
CD2 A:HIS290 3.2 43.4 1.0
CB A:HIS240 3.4 35.8 1.0
ND1 A:HIS290 4.0 41.7 1.0
ND1 A:HIS291 4.0 44.9 1.0
CG A:HIS291 4.0 43.3 1.0
CA A:HIS240 4.1 33.7 1.0
NE2 A:HIS240 4.2 42.4 1.0
CG A:HIS290 4.2 41.7 1.0
CD2 A:HIS240 4.2 39.8 1.0
NA A:HEA605 4.4 33.9 1.0
C1A A:HEA605 4.5 33.9 1.0
C4A A:HEA605 4.7 34.2 1.0
CG2 A:VAL243 4.7 38.5 1.0
C2A A:HEA605 4.9 32.9 1.0
CHA A:HEA605 4.9 35.3 1.0
FE A:HEA605 4.9 35.5 1.0
N A:HIS240 4.9 31.4 1.0
C3A A:HEA605 5.0 34.3 1.0

Copper binding site 2 out of 6 in 6nmp

Go back to Copper Binding Sites List in 6nmp
Copper binding site 2 out of 6 in the Sfx Structure of Oxidized Cytochrome C Oxidase 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 Sfx Structure of Oxidized Cytochrome C Oxidase at Room Temperature within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu301

b:42.2
occ:1.00
 CU1 B:CUA301 0.0 42.2 1.0
ND1 B:HIS161 2.0 44.4 1.0
SG B:CYS196 2.3 34.9 1.0
SG B:CYS200 2.3 36.3 1.0
SD B:MET207 2.4 41.1 1.0
CU2 B:CUA301 2.7 43.5 1.0
CE1 B:HIS161 3.0 42.7 1.0
CG B:HIS161 3.0 41.5 1.0
CE B:MET207 3.1 38.2 1.0
CB B:CYS200 3.2 38.9 1.0
CB B:HIS161 3.4 39.7 1.0
CB B:CYS196 3.4 39.1 1.0
CG B:MET207 3.6 42.4 1.0
O B:GLU198 4.0 49.4 1.0
NE2 B:HIS161 4.1 40.6 1.0
CA B:HIS161 4.1 39.1 1.0
CD2 B:HIS161 4.2 41.8 1.0
ND1 B:HIS204 4.6 38.9 1.0
CA B:CYS200 4.7 38.7 1.0
CD1 B:TRP104 4.7 40.8 1.0
O B:LEU160 4.8 46.6 1.0
O B:HIS102 4.8 33.2 1.0
CA B:CYS196 4.9 40.4 1.0
CA B:HIS204 4.9 39.4 1.0
N B:CYS200 4.9 37.1 1.0
O B:HIS204 5.0 43.3 1.0
CB B:MET207 5.0 43.8 1.0

Copper binding site 3 out of 6 in 6nmp

Go back to Copper Binding Sites List in 6nmp
Copper binding site 3 out of 6 in the Sfx Structure of Oxidized Cytochrome C Oxidase 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 Sfx Structure of Oxidized Cytochrome C Oxidase at Room Temperature within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu301

b:43.5
occ:1.00
 CU2 B:CUA301 0.0 43.5 1.0
ND1 B:HIS204 2.0 38.9 1.0
O B:GLU198 2.0 49.4 1.0
SG B:CYS200 2.3 36.3 1.0
SG B:CYS196 2.3 34.9 1.0
CU1 B:CUA301 2.7 42.2 1.0
CE1 B:HIS204 2.9 39.0 1.0
CG B:HIS204 3.1 38.9 1.0
C B:GLU198 3.3 39.5 1.0
CB B:CYS196 3.4 39.1 1.0
CB B:CYS200 3.4 38.9 1.0
CB B:HIS204 3.5 38.9 1.0
N B:CYS200 3.6 37.1 1.0
CA B:HIS204 3.8 39.4 1.0
O B:HIS204 3.8 43.3 1.0
C B:ILE199 4.0 38.4 1.0
NE2 B:HIS204 4.0 37.8 1.0
CA B:ILE199 4.1 38.2 1.0
N B:ILE199 4.1 37.7 1.0
CD2 B:HIS204 4.1 40.6 1.0
CA B:CYS200 4.1 38.7 1.0
N B:GLU198 4.1 37.9 1.0
O B:CYS196 4.2 37.5 1.0
C B:HIS204 4.2 41.9 1.0
ND1 B:HIS161 4.3 44.4 1.0
C B:CYS196 4.3 40.3 1.0
CA B:GLU198 4.3 39.1 1.0
SD B:MET207 4.4 41.1 1.0
CA B:CYS196 4.5 40.4 1.0
O B:ILE199 4.8 38.1 1.0
CG B:MET207 4.8 42.4 1.0
CA B:HIS161 4.9 39.1 1.0
CB B:HIS161 4.9 39.7 1.0
N B:SER197 5.0 39.9 1.0

Copper binding site 4 out of 6 in 6nmp

Go back to Copper Binding Sites List in 6nmp
Copper binding site 4 out of 6 in the Sfx Structure of Oxidized Cytochrome C Oxidase 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 Sfx Structure of Oxidized Cytochrome C Oxidase at Room Temperature within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Cu601

b:58.2
occ:1.00
 O2 N:PER607 2.0 50.1 1.0
NE2 N:HIS291 2.0 62.9 1.0
ND1 N:HIS240 2.0 53.6 1.0
NE2 N:HIS290 2.0 51.4 1.0
CE1 N:HIS291 2.7 62.3 1.0
CE1 N:HIS290 2.9 49.9 1.0
CE1 N:HIS240 3.0 55.4 1.0
O1 N:PER607 3.0 53.4 1.0
CG N:HIS240 3.1 48.6 1.0
CD2 N:HIS290 3.2 51.1 1.0
CD2 N:HIS291 3.2 62.5 1.0
CB N:HIS240 3.5 46.9 1.0
ND1 N:HIS291 3.9 58.9 1.0
ND1 N:HIS290 4.0 48.7 1.0
CA N:HIS240 4.1 46.9 1.0
NE2 N:HIS240 4.1 52.9 1.0
CG N:HIS291 4.1 57.6 1.0
CD2 N:HIS240 4.2 49.6 1.0
CG N:HIS290 4.2 50.0 1.0
NA N:HEA605 4.4 43.0 1.0
C1A N:HEA605 4.6 42.9 1.0
C4A N:HEA605 4.6 42.9 1.0
CG2 N:VAL243 4.8 50.7 1.0
FE N:HEA605 4.8 47.5 1.0
N N:HIS240 4.9 47.4 1.0
C3A N:HEA605 5.0 43.4 1.0
CE2 N:TYR244 5.0 46.2 1.0

Copper binding site 5 out of 6 in 6nmp

Go back to Copper Binding Sites List in 6nmp
Copper binding site 5 out of 6 in the Sfx Structure of Oxidized Cytochrome C Oxidase 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 Sfx Structure of Oxidized Cytochrome C Oxidase at Room Temperature within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cu301

b:62.7
occ:1.00
 CU1 O:CUA301 0.0 62.7 1.0
ND1 O:HIS161 2.0 65.8 1.0
SG O:CYS196 2.3 49.2 1.0
SG O:CYS200 2.3 52.1 1.0
SD O:MET207 2.3 72.6 1.0
CU2 O:CUA301 2.7 62.2 1.0
CE O:MET207 2.9 68.7 1.0
CE1 O:HIS161 2.9 66.2 1.0
CG O:HIS161 3.1 62.0 1.0
CB O:HIS161 3.5 60.8 1.0
CB O:CYS200 3.5 58.7 1.0
CB O:CYS196 3.5 56.1 1.0
CG O:MET207 3.7 73.4 1.0
O O:GLU198 4.0 72.0 1.0
NE2 O:HIS161 4.0 65.8 1.0
CD2 O:HIS161 4.1 63.9 1.0
CA O:HIS161 4.1 57.7 1.0
ND1 O:HIS204 4.6 66.9 1.0
O O:LEU160 4.6 53.3 1.0
O O:HIS102 4.7 51.7 1.0
CD1 O:TRP104 4.8 62.6 1.0
CA O:CYS200 4.8 63.9 1.0
CA O:CYS196 4.9 57.4 1.0
N O:CYS200 4.9 70.3 1.0
CA O:HIS204 5.0 63.2 1.0
CB O:MET207 5.0 74.7 1.0
O O:HIS204 5.0 60.9 1.0

Copper binding site 6 out of 6 in 6nmp

Go back to Copper Binding Sites List in 6nmp
Copper binding site 6 out of 6 in the Sfx Structure of Oxidized Cytochrome C Oxidase 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 Sfx Structure of Oxidized Cytochrome C Oxidase at Room Temperature within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cu301

b:62.2
occ:1.00
 CU2 O:CUA301 0.0 62.2 1.0
O O:GLU198 2.0 72.0 1.0
ND1 O:HIS204 2.0 66.9 1.0
SG O:CYS200 2.3 52.1 1.0
SG O:CYS196 2.3 49.2 1.0
CU1 O:CUA301 2.7 62.7 1.0
CE1 O:HIS204 2.8 66.8 1.0
CG O:HIS204 3.0 65.2 1.0
C O:GLU198 3.2 60.3 1.0
CB O:CYS196 3.5 56.1 1.0
CB O:HIS204 3.5 62.3 1.0
N O:CYS200 3.6 70.3 1.0
CB O:CYS200 3.8 58.7 1.0
CA O:HIS204 3.8 63.2 1.0
O O:HIS204 3.8 60.9 1.0
NE2 O:HIS204 3.9 66.6 1.0
CD2 O:HIS204 4.0 66.2 1.0
C O:ILE199 4.0 67.4 1.0
CA O:ILE199 4.0 60.6 1.0
N O:ILE199 4.1 58.4 1.0
O O:CYS196 4.1 56.8 1.0
C O:HIS204 4.2 63.2 1.0
N O:GLU198 4.2 62.4 1.0
ND1 O:HIS161 4.3 65.8 1.0
C O:CYS196 4.3 58.0 1.0
SD O:MET207 4.3 72.6 1.0
CA O:CYS200 4.4 63.9 1.0
CA O:GLU198 4.4 60.1 1.0
CA O:CYS196 4.5 57.4 1.0
O O:ILE199 4.8 68.9 1.0
CG O:MET207 4.8 73.4 1.0
N O:SER197 4.9 57.7 1.0

Reference:

I.Ishigami, A.Lewis-Ballester, A.Echelmeier, G.Brehm, N.A.Zatsepin, T.D.Grant, J.D.Coe, S.Lisova, G.Nelson, S.Zhang, Z.F.Dobson, S.Boutet, R.G.Sierra, A.Batyuk, P.Fromme, R.Fromme, J.C.H.Spence, A.Ros, S.R.Yeh, D.L.Rousseau. Snapshot of An Oxygen Intermediate in the Catalytic Reaction of Cytochromecoxidase. Proc. Natl. Acad. Sci. V. 116 3572 2019U.S.A..
ISSN: ESSN 1091-6490
PubMed: 30808749
DOI: 10.1073/PNAS.1814526116
Page generated: Wed Jul 31 06:41:20 2024

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