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Copper in PDB 6nkn: Time-Resolved Sfx Structure of the Pr Intermediate of Cytochrome C Oxidase at Room Temperature

Enzymatic activity of Time-Resolved Sfx Structure of the Pr Intermediate of Cytochrome C Oxidase at Room Temperature

All present enzymatic activity of Time-Resolved Sfx Structure of the Pr Intermediate of Cytochrome C Oxidase at Room Temperature:
1.9.3.1;

Protein crystallography data

The structure of Time-Resolved Sfx Structure of the Pr Intermediate of Cytochrome C Oxidase at Room Temperature, PDB code: 6nkn 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) 10.50 / 2.50
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 / 21.7

Other elements in 6nkn:

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

Copper binding site 1 out of 6 in 6nkn

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Copper binding site 1 out of 6 in the Time-Resolved Sfx Structure of the Pr Intermediate of 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 Time-Resolved Sfx Structure of the Pr Intermediate of Cytochrome C Oxidase at Room Temperature within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu601

b:46.9
occ:1.00
 O A:OH611 1.9 44.9 1.0
NE2 A:HIS290 2.0 44.9 1.0
NE2 A:HIS291 2.0 48.7 1.0
ND1 A:HIS240 2.1 45.5 1.0
CD2 A:HIS291 3.0 48.0 1.0
CE1 A:HIS290 3.0 40.2 1.0
CG A:HIS240 3.0 39.7 1.0
CD2 A:HIS290 3.1 44.4 1.0
CE1 A:HIS291 3.1 49.6 1.0
CE1 A:HIS240 3.1 41.8 1.0
O A:O610 3.2 35.2 1.0
CB A:HIS240 3.3 36.5 1.0
CA A:HIS240 4.0 35.1 1.0
ND1 A:HIS291 4.1 46.0 1.0
CG A:HIS291 4.1 43.2 1.0
ND1 A:HIS290 4.1 40.3 1.0
CG A:HIS290 4.2 44.4 1.0
CD2 A:HIS240 4.2 40.1 1.0
NE2 A:HIS240 4.2 44.6 1.0
NA A:HEA605 4.3 39.7 1.0
C1A A:HEA605 4.4 36.9 1.0
C4A A:HEA605 4.6 40.3 1.0
CG2 A:VAL243 4.8 40.2 1.0
FE A:HEA605 4.8 39.9 1.0
C2A A:HEA605 4.8 36.1 1.0
CHA A:HEA605 4.8 38.4 1.0
C3A A:HEA605 4.9 39.8 1.0
N A:HIS240 4.9 32.0 1.0
ND A:HEA605 5.0 37.4 1.0

Copper binding site 2 out of 6 in 6nkn

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Copper binding site 2 out of 6 in the Time-Resolved Sfx Structure of the Pr Intermediate of 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 Time-Resolved Sfx Structure of the Pr Intermediate of Cytochrome C Oxidase at Room Temperature within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu301

b:45.1
occ:1.00
 CU1 B:CUA301 0.0 45.1 1.0
ND1 B:HIS161 2.0 35.4 1.0
SG B:CYS196 2.3 38.2 1.0
SG B:CYS200 2.3 38.8 1.0
SD B:MET207 2.4 40.6 1.0
CU2 B:CUA301 2.6 42.6 1.0
CE1 B:HIS161 3.0 35.0 1.0
CG B:HIS161 3.1 35.1 1.0
CE B:MET207 3.1 36.1 1.0
CB B:CYS200 3.2 40.6 1.0
CB B:CYS196 3.4 40.9 1.0
CB B:HIS161 3.5 37.0 1.0
CG B:MET207 3.6 42.8 1.0
O B:GLU198 3.8 56.8 1.0
NE2 B:HIS161 4.1 35.8 1.0
CA B:HIS161 4.2 37.0 1.0
CD2 B:HIS161 4.2 35.0 1.0
ND1 B:HIS204 4.6 40.1 1.0
O B:LEU160 4.6 39.8 1.0
CA B:CYS200 4.7 40.0 1.0
CA B:HIS204 4.8 36.5 1.0
CD1 B:TRP104 4.8 47.9 1.0
CA B:CYS196 4.8 41.1 1.0
O B:HIS102 4.9 38.9 1.0
O B:HIS204 4.9 37.3 1.0
CB B:MET207 5.0 44.6 1.0

Copper binding site 3 out of 6 in 6nkn

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Copper binding site 3 out of 6 in the Time-Resolved Sfx Structure of the Pr Intermediate of 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 Time-Resolved Sfx Structure of the Pr Intermediate of Cytochrome C Oxidase at Room Temperature within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu301

b:42.6
occ:1.00
 CU2 B:CUA301 0.0 42.6 1.0
ND1 B:HIS204 2.1 40.1 1.0
O B:GLU198 2.1 56.8 1.0
SG B:CYS196 2.3 38.2 1.0
SG B:CYS200 2.3 38.8 1.0
CU1 B:CUA301 2.6 45.1 1.0
CG B:HIS204 3.1 36.6 1.0
CE1 B:HIS204 3.1 41.3 1.0
CB B:CYS196 3.2 40.9 1.0
CB B:CYS200 3.3 40.6 1.0
CB B:HIS204 3.3 35.9 1.0
C B:GLU198 3.4 41.1 1.0
CA B:HIS204 3.5 36.5 1.0
O B:HIS204 3.6 37.3 1.0
N B:CYS200 3.8 40.9 1.0
C B:HIS204 4.0 38.3 1.0
O B:CYS196 4.1 46.4 1.0
CD2 B:HIS204 4.1 42.3 1.0
CA B:CYS200 4.2 40.0 1.0
NE2 B:HIS204 4.2 45.7 1.0
C B:ILE199 4.2 39.6 1.0
N B:ILE199 4.2 38.5 1.0
N B:GLU198 4.2 38.1 1.0
CA B:ILE199 4.2 40.6 1.0
ND1 B:HIS161 4.2 35.4 1.0
C B:CYS196 4.3 42.3 1.0
SD B:MET207 4.3 40.6 1.0
CA B:CYS196 4.4 41.1 1.0
CA B:GLU198 4.4 37.3 1.0
CG B:MET207 4.7 42.8 1.0
N B:HIS204 4.8 38.8 1.0
N B:SER197 4.9 42.1 1.0
O B:ILE199 5.0 33.6 1.0

Copper binding site 4 out of 6 in 6nkn

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Copper binding site 4 out of 6 in the Time-Resolved Sfx Structure of the Pr Intermediate of 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 Time-Resolved Sfx Structure of the Pr Intermediate of Cytochrome C Oxidase at Room Temperature within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Cu602

b:58.8
occ:1.00
 O N:OH612 1.9 64.6 1.0
NE2 N:HIS290 2.0 50.2 1.0
NE2 N:HIS291 2.0 62.3 1.0
ND1 N:HIS240 2.1 54.5 1.0
CE1 N:HIS291 2.8 62.8 1.0
CE1 N:HIS290 3.0 47.8 1.0
CE1 N:HIS240 3.1 52.0 1.0
CD2 N:HIS290 3.1 50.2 1.0
CG N:HIS240 3.1 47.3 1.0
O N:O611 3.1 50.5 1.0
CD2 N:HIS291 3.2 58.1 1.0
CB N:HIS240 3.4 46.3 1.0
ND1 N:HIS291 3.9 58.0 1.0
CA N:HIS240 4.1 49.4 1.0
ND1 N:HIS290 4.1 49.1 1.0
CG N:HIS291 4.2 53.8 1.0
NA N:HEA606 4.2 43.5 1.0
CG N:HIS290 4.2 49.0 1.0
NE2 N:HIS240 4.2 51.8 1.0
CD2 N:HIS240 4.2 49.2 1.0
C1A N:HEA606 4.3 44.1 1.0
C4A N:HEA606 4.4 49.5 1.0
FE N:HEA606 4.6 51.8 1.0
CHA N:HEA606 4.8 43.0 1.0
C2A N:HEA606 4.8 46.1 1.0
CG2 N:VAL243 4.8 52.1 1.0
C3A N:HEA606 4.8 50.8 1.0
ND N:HEA606 4.9 45.6 1.0
CHB N:HEA606 5.0 47.6 1.0
O N:HOH715 5.0 67.6 1.0
C4D N:HEA606 5.0 42.2 1.0
N N:HIS240 5.0 49.8 1.0

Copper binding site 5 out of 6 in 6nkn

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Copper binding site 5 out of 6 in the Time-Resolved Sfx Structure of the Pr Intermediate of 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 Time-Resolved Sfx Structure of the Pr Intermediate of Cytochrome C Oxidase at Room Temperature within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cu301

b:61.0
occ:1.00
 CU1 O:CUA301 0.0 61.0 1.0
ND1 O:HIS161 2.0 62.2 1.0
SG O:CYS200 2.3 52.5 1.0
SG O:CYS196 2.3 51.8 1.0
SD O:MET207 2.3 64.5 1.0
CU2 O:CUA301 2.7 59.1 1.0
CE1 O:HIS161 3.0 61.4 1.0
CE O:MET207 3.0 55.6 1.0
CG O:HIS161 3.0 62.0 1.0
CB O:CYS200 3.3 54.6 1.0
CB O:HIS161 3.4 65.9 1.0
CB O:CYS196 3.6 64.5 1.0
CG O:MET207 3.7 61.2 1.0
O O:GLU198 3.8 77.4 1.0
CA O:HIS161 4.0 66.7 1.0
NE2 O:HIS161 4.1 65.8 1.0
CD2 O:HIS161 4.2 64.0 1.0
CA O:CYS200 4.7 60.7 1.0
O O:LEU160 4.7 58.9 1.0
CD1 O:TRP104 4.7 60.1 1.0
O O:HIS102 4.7 57.8 1.0
ND1 O:HIS204 4.8 58.4 1.0
N O:CYS200 4.8 67.6 1.0
CA O:HIS204 4.9 59.0 1.0
CA O:CYS196 4.9 64.6 1.0
N O:HIS161 5.0 61.9 1.0
CB O:MET207 5.0 62.0 1.0
O O:HIS204 5.0 54.2 1.0

Copper binding site 6 out of 6 in 6nkn

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

b:59.1
occ:1.00
 CU2 O:CUA301 0.0 59.1 1.0
O O:GLU198 2.0 77.4 1.0
ND1 O:HIS204 2.2 58.4 1.0
SG O:CYS200 2.3 52.5 1.0
SG O:CYS196 2.3 51.8 1.0
CU1 O:CUA301 2.7 61.0 1.0
CG O:HIS204 3.1 60.5 1.0
CB O:CYS196 3.2 64.5 1.0
CE1 O:HIS204 3.2 57.8 1.0
C O:GLU198 3.3 52.5 1.0
CB O:HIS204 3.4 59.0 1.0
CA O:HIS204 3.6 59.0 1.0
N O:CYS200 3.7 67.6 1.0
O O:HIS204 3.7 54.2 1.0
CB O:CYS200 3.8 54.6 1.0
O O:CYS196 3.8 66.4 1.0
C O:ILE199 4.0 62.6 1.0
N O:ILE199 4.0 48.8 1.0
CA O:ILE199 4.0 55.5 1.0
C O:HIS204 4.1 58.7 1.0
C O:CYS196 4.2 64.4 1.0
CD2 O:HIS204 4.2 59.6 1.0
SD O:MET207 4.3 64.5 1.0
NE2 O:HIS204 4.3 61.5 1.0
N O:GLU198 4.3 59.2 1.0
CA O:CYS196 4.3 64.6 1.0
ND1 O:HIS161 4.3 62.2 1.0
CA O:CYS200 4.4 60.7 1.0
CA O:GLU198 4.4 55.6 1.0
CG O:MET207 4.7 61.2 1.0
O O:ILE199 4.8 67.9 1.0
N O:SER197 4.9 66.0 1.0
N O:HIS204 4.9 62.5 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 06:39:58 2024

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