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Copper in PDB 6nmf: Sfx Structure of Reduced Cytochrome C Oxidase at Room Temperature

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

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

Protein crystallography data

The structure of Sfx Structure of Reduced Cytochrome C Oxidase at Room Temperature, PDB code: 6nmf 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 / 2.80
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 (%) 17.6 / 23.2

Other elements in 6nmf:

The structure of Sfx Structure of Reduced 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 Reduced Cytochrome C Oxidase at Room Temperature (pdb code 6nmf). 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 Reduced Cytochrome C Oxidase at Room Temperature, PDB code: 6nmf:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 6nmf

Go back to Copper Binding Sites List in 6nmf
Copper binding site 1 out of 6 in the Sfx Structure of Reduced 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 Reduced Cytochrome C Oxidase at Room Temperature within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu603

b:53.5
occ:1.00
 NE2 A:HIS291 2.0 48.4 1.0
ND1 A:HIS240 2.0 49.9 1.0
NE2 A:HIS290 2.1 50.7 1.0
CD2 A:HIS291 2.9 47.9 1.0
CE1 A:HIS291 2.9 50.6 1.0
CG A:HIS240 3.0 46.6 1.0
CE1 A:HIS290 3.0 46.6 1.0
CE1 A:HIS240 3.0 51.5 1.0
CD2 A:HIS290 3.1 50.4 1.0
CB A:HIS240 3.3 44.2 1.0
ND1 A:HIS291 3.9 47.8 1.0
CG A:HIS291 4.0 45.6 1.0
CA A:HIS240 4.0 43.0 1.0
ND1 A:HIS290 4.1 44.2 1.0
CD2 A:HIS240 4.1 49.7 1.0
NE2 A:HIS240 4.1 50.2 1.0
CG A:HIS290 4.2 45.8 1.0
C1A A:HEA602 4.7 41.6 1.0
NA A:HEA602 4.8 43.1 1.0
CG2 A:VAL243 4.8 48.7 1.0
N A:HIS240 4.8 39.7 1.0
O A:TRP288 5.0 56.8 1.0
C4A A:HEA602 5.0 43.5 1.0

Copper binding site 2 out of 6 in 6nmf

Go back to Copper Binding Sites List in 6nmf
Copper binding site 2 out of 6 in the Sfx Structure of Reduced 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 Reduced Cytochrome C Oxidase at Room Temperature within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu302

b:57.1
occ:1.00
 CU1 B:CUA302 0.0 57.1 1.0
ND1 B:HIS161 2.0 47.4 1.0
SG B:CYS196 2.3 43.6 1.0
SG B:CYS200 2.3 42.4 1.0
SD B:MET207 2.4 56.5 1.0
CU2 B:CUA302 2.7 53.0 1.0
CE1 B:HIS161 3.0 43.1 1.0
CG B:HIS161 3.1 43.4 1.0
CE B:MET207 3.1 50.1 1.0
CB B:CYS200 3.1 43.4 1.0
CB B:HIS161 3.5 45.0 1.0
CG B:MET207 3.5 54.7 1.0
CB B:CYS196 3.5 48.5 1.0
O B:GLU198 4.1 68.7 1.0
NE2 B:HIS161 4.1 40.2 1.0
CA B:HIS161 4.1 45.4 1.0
CD2 B:HIS161 4.2 41.6 1.0
CA B:CYS200 4.6 46.3 1.0
CD1 B:TRP104 4.6 58.3 1.0
ND1 B:HIS204 4.6 49.3 1.0
O B:LEU160 4.8 54.6 1.0
O B:HIS102 4.8 46.7 1.0
N B:CYS200 4.9 46.4 1.0
CB B:MET207 4.9 55.6 1.0
CA B:HIS204 4.9 49.6 1.0
CA B:CYS196 4.9 49.4 1.0

Copper binding site 3 out of 6 in 6nmf

Go back to Copper Binding Sites List in 6nmf
Copper binding site 3 out of 6 in the Sfx Structure of Reduced 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 Reduced Cytochrome C Oxidase at Room Temperature within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu302

b:53.0
occ:1.00
 CU2 B:CUA302 0.0 53.0 1.0
ND1 B:HIS204 2.0 49.3 1.0
O B:GLU198 2.1 68.7 1.0
SG B:CYS200 2.3 42.4 1.0
SG B:CYS196 2.3 43.6 1.0
CU1 B:CUA302 2.7 57.1 1.0
CE1 B:HIS204 2.9 47.1 1.0
CG B:HIS204 3.1 45.8 1.0
CB B:CYS196 3.1 48.5 1.0
CB B:CYS200 3.3 43.4 1.0
C B:GLU198 3.4 45.8 1.0
CB B:HIS204 3.5 46.1 1.0
N B:CYS200 3.6 46.4 1.0
CA B:HIS204 3.7 49.6 1.0
O B:HIS204 3.9 51.6 1.0
NE2 B:HIS204 4.0 41.7 1.0
CA B:CYS200 4.1 46.3 1.0
CD2 B:HIS204 4.1 47.3 1.0
CA B:ILE199 4.2 42.9 1.0
C B:ILE199 4.2 46.1 1.0
N B:GLU198 4.2 45.0 1.0
N B:ILE199 4.2 42.0 1.0
C B:HIS204 4.2 52.0 1.0
CA B:CYS196 4.3 49.4 1.0
ND1 B:HIS161 4.3 47.4 1.0
C B:CYS196 4.3 47.1 1.0
O B:CYS196 4.4 43.4 1.0
CA B:GLU198 4.4 44.7 1.0
SD B:MET207 4.5 56.5 1.0
CG B:MET207 4.7 54.7 1.0
CA B:HIS161 4.9 45.4 1.0
N B:HIS204 4.9 51.0 1.0
N B:SER197 5.0 46.8 1.0
CB B:HIS161 5.0 45.0 1.0

Copper binding site 4 out of 6 in 6nmf

Go back to Copper Binding Sites List in 6nmf
Copper binding site 4 out of 6 in the Sfx Structure of Reduced 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 Reduced Cytochrome C Oxidase at Room Temperature within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Cu603

b:64.5
occ:1.00
 ND1 N:HIS240 2.0 57.8 1.0
NE2 N:HIS291 2.0 68.1 1.0
NE2 N:HIS290 2.0 56.5 1.0
CE1 N:HIS291 2.8 68.6 1.0
CE1 N:HIS290 2.9 56.6 1.0
CE1 N:HIS240 2.9 60.1 1.0
CG N:HIS240 3.0 54.0 1.0
CD2 N:HIS291 3.1 63.2 1.0
CD2 N:HIS290 3.1 58.9 1.0
CB N:HIS240 3.4 53.9 1.0
ND1 N:HIS291 3.9 62.5 1.0
ND1 N:HIS290 4.0 55.9 1.0
CG N:HIS291 4.1 58.9 1.0
NE2 N:HIS240 4.1 57.5 1.0
CD2 N:HIS240 4.1 54.3 1.0
CG N:HIS290 4.2 57.7 1.0
CA N:HIS240 4.2 57.2 1.0
NA N:HEA602 4.6 48.0 1.0
C1A N:HEA602 4.7 50.6 1.0
C4A N:HEA602 4.8 50.9 1.0
CG2 N:VAL243 4.8 56.9 1.0
CG2 N:VAL287 4.9 63.1 1.0

Copper binding site 5 out of 6 in 6nmf

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

b:76.7
occ:1.00
 CU1 O:CUA301 0.0 76.7 1.0
ND1 O:HIS161 2.0 73.8 1.0
SG O:CYS200 2.3 60.0 1.0
SG O:CYS196 2.3 56.2 1.0
SD O:MET207 2.4 81.9 1.0
CU2 O:CUA301 2.7 76.3 1.0
CE1 O:HIS161 3.0 71.1 1.0
CE O:MET207 3.0 75.4 1.0
CG O:HIS161 3.1 72.6 1.0
CB O:CYS200 3.3 63.5 1.0
CB O:HIS161 3.5 74.9 1.0
CG O:MET207 3.6 81.3 1.0
CB O:CYS196 3.6 67.5 1.0
O O:GLU198 4.0 93.7 1.0
NE2 O:HIS161 4.1 72.5 1.0
CA O:HIS161 4.1 68.9 1.0
CD2 O:HIS161 4.1 71.4 1.0
CD1 O:TRP104 4.6 69.2 1.0
ND1 O:HIS204 4.6 69.7 1.0
CA O:CYS200 4.7 71.5 1.0
O O:HIS102 4.8 60.0 1.0
O O:LEU160 4.8 64.2 1.0
CA O:HIS204 4.9 72.5 1.0
N O:CYS200 4.9 74.4 1.0
CB O:MET207 4.9 83.7 1.0

Copper binding site 6 out of 6 in 6nmf

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

b:76.3
occ:1.00
 CU2 O:CUA301 0.0 76.3 1.0
ND1 O:HIS204 2.0 69.7 1.0
O O:GLU198 2.0 93.7 1.0
SG O:CYS200 2.3 60.0 1.0
SG O:CYS196 2.3 56.2 1.0
CU1 O:CUA301 2.7 76.7 1.0
CE1 O:HIS204 2.9 63.0 1.0
CG O:HIS204 3.0 69.1 1.0
C O:GLU198 3.3 66.5 1.0
CB O:CYS196 3.4 67.5 1.0
CB O:HIS204 3.5 71.6 1.0
CB O:CYS200 3.7 63.5 1.0
N O:CYS200 3.7 74.4 1.0
CA O:HIS204 3.7 72.5 1.0
O O:HIS204 4.0 54.4 1.0
NE2 O:HIS204 4.0 60.0 1.0
CA O:ILE199 4.0 67.9 1.0
C O:ILE199 4.1 74.3 1.0
CD2 O:HIS204 4.1 64.3 1.0
O O:CYS196 4.1 68.5 1.0
N O:ILE199 4.1 62.6 1.0
C O:HIS204 4.2 67.3 1.0
N O:GLU198 4.2 70.6 1.0
C O:CYS196 4.3 69.9 1.0
ND1 O:HIS161 4.3 73.8 1.0
CA O:CYS200 4.3 71.5 1.0
SD O:MET207 4.4 81.9 1.0
CA O:GLU198 4.4 66.9 1.0
CA O:CYS196 4.5 67.4 1.0
CG O:MET207 4.7 81.3 1.0
O O:ILE199 4.9 77.3 1.0
N O:SER197 4.9 75.0 1.0
CA O:HIS161 5.0 68.9 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 06:40:28 2024

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