Atomistry » Copper » PDB 6l8s-6pvy » 6nmf
Atomistry »
  Copper »
    PDB 6l8s-6pvy »
      6nmf »

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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy