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Copper in PDB 3omi: Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with D132A Mutation

Enzymatic activity of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with D132A Mutation

All present enzymatic activity of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with D132A Mutation:
1.9.3.1;

Protein crystallography data

The structure of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with D132A Mutation, PDB code: 3omi was solved by J.Liu, L.Qin, S.Ferguson-Miller, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.84 / 2.15
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 125.064, 131.519, 175.674, 90.00, 90.00, 90.00
R / Rfree (%) 19.2 / 21.5

Copper Binding Sites:

The binding sites of Copper atom in the Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with D132A Mutation (pdb code 3omi). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 6 binding sites of Copper where determined in the Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with D132A Mutation, PDB code: 3omi:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 3omi

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Copper binding site 1 out of 6 in the Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with D132A Mutation


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with D132A Mutation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu611

b:28.2
occ:1.00
NE2 A:HIS333 2.0 30.0 1.0
NE2 A:HIS334 2.1 28.2 1.0
ND1 A:HIS284 2.2 25.5 1.0
O A:OH601 2.4 17.9 1.0
O A:HOH744 2.8 18.4 1.0
CE1 A:HIS333 2.9 31.5 1.0
CE1 A:HIS334 2.9 26.0 1.0
CD2 A:HIS334 3.1 26.1 1.0
CD2 A:HIS333 3.1 28.1 1.0
CG A:HIS284 3.2 25.1 1.0
CE1 A:HIS284 3.2 25.5 1.0
CB A:HIS284 3.4 24.6 1.0
CA A:HIS284 4.0 24.6 1.0
ND1 A:HIS334 4.0 25.9 1.0
ND1 A:HIS333 4.1 29.3 1.0
CG A:HIS334 4.1 26.2 1.0
CG A:HIS333 4.2 27.9 1.0
CD2 A:HIS284 4.3 26.4 1.0
NE2 A:HIS284 4.3 25.9 1.0
NA A:HEA608 4.4 24.4 1.0
C1A A:HEA608 4.5 24.2 1.0
C4A A:HEA608 4.5 24.3 1.0
N A:HIS284 4.8 24.4 1.0
FE A:HEA608 4.8 24.3 1.0
C2A A:HEA608 4.8 24.7 1.0
C3A A:HEA608 4.8 26.1 1.0
CHA A:HEA608 5.0 21.8 1.0

Copper binding site 2 out of 6 in 3omi

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Copper binding site 2 out of 6 in the Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with D132A Mutation


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with D132A Mutation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu307

b:21.7
occ:1.00
ND1 B:HIS260 2.1 16.7 1.0
SG B:CYS252 2.3 20.5 1.0
SG B:CYS256 2.3 19.9 1.0
O B:GLU254 2.6 21.4 1.0
CU B:CU1308 2.6 21.0 1.0
CE1 B:HIS260 3.0 17.0 1.0
CG B:HIS260 3.1 18.1 1.0
CB B:CYS252 3.3 19.8 1.0
CB B:CYS256 3.5 20.5 1.0
C B:GLU254 3.5 21.6 1.0
CB B:HIS260 3.5 16.9 1.0
CA B:HIS260 3.6 18.4 1.0
N B:CYS256 3.7 20.4 1.0
O B:HIS260 3.9 18.2 1.0
N B:GLU254 4.1 22.5 1.0
NE2 B:HIS260 4.1 18.8 1.0
C B:CYS252 4.2 20.8 1.0
C B:HIS260 4.2 18.3 1.0
CA B:LEU255 4.2 20.7 1.0
O B:CYS252 4.2 19.6 1.0
CD2 B:HIS260 4.2 16.5 1.0
C B:LEU255 4.2 20.6 1.0
CA B:CYS256 4.2 20.2 1.0
N B:LEU255 4.2 20.8 1.0
ND1 B:HIS217 4.3 18.4 1.0
CA B:CYS252 4.3 20.1 1.0
SD B:MET263 4.5 19.0 1.0
CA B:GLU254 4.5 22.3 1.0
N B:SER253 4.6 21.7 1.0
CG B:MET263 4.7 18.0 1.0
N B:HIS260 4.8 18.4 1.0
CA B:HIS217 4.9 19.6 1.0

Copper binding site 3 out of 6 in 3omi

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Copper binding site 3 out of 6 in the Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with D132A Mutation


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with D132A Mutation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu308

b:21.0
occ:1.00
ND1 B:HIS217 2.1 18.4 1.0
SG B:CYS252 2.3 20.5 1.0
SG B:CYS256 2.4 19.9 1.0
SD B:MET263 2.4 19.0 1.0
CU B:CU307 2.6 21.7 1.0
CE1 B:HIS217 3.0 19.8 1.0
CE B:MET263 3.0 16.5 1.0
CG B:HIS217 3.2 19.8 1.0
CB B:CYS256 3.4 20.5 1.0
CB B:CYS252 3.5 19.8 1.0
CG B:MET263 3.5 18.0 1.0
CB B:HIS217 3.6 18.9 1.0
NE2 B:HIS217 4.1 19.4 1.0
CA B:HIS217 4.2 19.6 1.0
O B:GLU254 4.3 21.4 1.0
CD2 B:HIS217 4.3 19.9 1.0
CD1 B:TRP143 4.4 21.0 1.0
ND1 B:HIS260 4.6 16.7 1.0
O B:TYR141 4.7 21.7 1.0
CA B:HIS260 4.7 18.4 1.0
CA B:CYS256 4.8 20.2 1.0
CA B:CYS252 4.8 20.1 1.0
CB B:MET263 4.9 19.2 1.0

Copper binding site 4 out of 6 in 3omi

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Copper binding site 4 out of 6 in the Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with D132A Mutation


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with D132A Mutation within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu608

b:35.5
occ:1.00
NE2 C:HIS333 2.1 32.1 1.0
NE2 C:HIS334 2.1 34.6 1.0
ND1 C:HIS284 2.2 35.2 1.0
O C:OH601 2.3 27.1 1.0
O C:HOH795 2.8 25.4 1.0
CE1 C:HIS333 3.0 31.8 1.0
CD2 C:HIS334 3.0 30.9 1.0
CE1 C:HIS334 3.0 31.7 1.0
CE1 C:HIS284 3.1 35.9 1.0
CG C:HIS284 3.2 36.2 1.0
CD2 C:HIS333 3.2 31.8 1.0
CB C:HIS284 3.4 35.0 1.0
CA C:HIS284 4.0 35.1 1.0
ND1 C:HIS334 4.1 31.4 1.0
CG C:HIS334 4.1 31.2 1.0
ND1 C:HIS333 4.1 31.6 1.0
CD2 C:HIS284 4.3 36.8 1.0
CG C:HIS333 4.3 32.1 1.0
NE2 C:HIS284 4.3 36.4 1.0
NA C:HEA606 4.5 30.5 1.0
C1A C:HEA606 4.5 29.8 1.0
C4A C:HEA606 4.6 32.1 1.0
FE C:HEA606 4.8 29.0 1.0
C2A C:HEA606 4.8 30.5 1.0
N C:HIS284 4.8 35.0 1.0
C3A C:HEA606 4.8 30.3 1.0
CG2 C:VAL287 5.0 34.0 1.0
CHA C:HEA606 5.0 29.9 1.0

Copper binding site 5 out of 6 in 3omi

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Copper binding site 5 out of 6 in the Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with D132A Mutation


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with D132A Mutation within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu305

b:27.3
occ:1.00
ND1 D:HIS260 2.1 27.0 1.0
SG D:CYS252 2.3 24.1 1.0
SG D:CYS256 2.3 25.7 1.0
CU D:CU1306 2.6 26.9 1.0
O D:GLU254 2.6 27.7 1.0
CE1 D:HIS260 2.9 26.3 1.0
CG D:HIS260 3.2 26.5 1.0
CB D:CYS252 3.2 23.8 1.0
CB D:CYS256 3.4 27.3 1.0
C D:GLU254 3.6 27.7 1.0
CA D:HIS260 3.6 26.7 1.0
CB D:HIS260 3.6 26.7 1.0
N D:CYS256 3.7 27.4 1.0
O D:HIS260 3.9 26.1 1.0
NE2 D:HIS260 4.0 26.5 1.0
N D:GLU254 4.1 27.4 1.0
C D:CYS252 4.1 25.0 1.0
CA D:CYS256 4.2 27.1 1.0
CD2 D:HIS260 4.2 26.4 1.0
ND1 D:HIS217 4.2 25.5 1.0
C D:HIS260 4.2 26.6 1.0
O D:CYS252 4.3 24.2 1.0
CA D:LEU255 4.3 27.8 1.0
C D:LEU255 4.3 27.5 1.0
CA D:CYS252 4.3 24.5 1.0
N D:LEU255 4.3 27.6 1.0
SD D:MET263 4.4 27.2 1.0
CA D:GLU254 4.5 27.9 1.0
N D:SER253 4.5 25.8 1.0
CG D:MET263 4.6 26.3 1.0
N D:HIS260 4.8 27.6 1.0
CA D:HIS217 4.9 26.8 1.0
CB D:HIS217 5.0 27.1 1.0

Copper binding site 6 out of 6 in 3omi

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Copper binding site 6 out of 6 in the Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with D132A Mutation


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with D132A Mutation within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu306

b:26.9
occ:1.00
ND1 D:HIS217 2.1 25.5 1.0
SG D:CYS252 2.3 24.1 1.0
SG D:CYS256 2.4 25.7 1.0
SD D:MET263 2.4 27.2 1.0
CU D:CU305 2.6 27.3 1.0
CE1 D:HIS217 3.0 25.7 1.0
CE D:MET263 3.0 26.8 1.0
CG D:HIS217 3.1 25.5 1.0
CB D:CYS256 3.3 27.3 1.0
CG D:MET263 3.4 26.3 1.0
CB D:CYS252 3.4 23.8 1.0
CB D:HIS217 3.5 27.1 1.0
NE2 D:HIS217 4.1 24.3 1.0
CA D:HIS217 4.2 26.8 1.0
CD2 D:HIS217 4.2 23.9 1.0
O D:GLU254 4.3 27.7 1.0
CD1 D:TRP143 4.4 31.4 1.0
ND1 D:HIS260 4.5 27.0 1.0
CA D:CYS256 4.7 27.1 1.0
O D:TYR141 4.7 29.1 1.0
CA D:HIS260 4.8 26.7 1.0
CB D:MET263 4.8 27.4 1.0
CA D:CYS252 4.8 24.5 1.0
CZ2 D:TRP145 5.0 29.0 1.0

Reference:

J.Liu, L.Qin, S.Ferguson-Miller. Crystallographic and Online Spectral Evidence For Role of Conformational Change and Conserved Water in Cytochrome Oxidase Proton Pump. Proc.Natl.Acad.Sci.Usa V. 108 1284 2011.
ISSN: ISSN 0027-8424
PubMed: 21205904
DOI: 10.1073/PNAS.1012846108
Page generated: Fri Sep 4 08:12:52 2020
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