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Copper in PDB 2gsm: Catalytic Core (Subunits I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides

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

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

Protein crystallography data

The structure of Catalytic Core (Subunits I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides, PDB code: 2gsm was solved by L.Qin, C.Hiser, A.Mulichak, R.M.Garavito, S.Ferguson-Miller, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 125.020, 131.639, 176.802, 90.00, 90.00, 90.00
R / Rfree (%) 21.4 / 23.2

Other elements in 2gsm:

The structure of Catalytic Core (Subunits I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Cadmium (Cd) 4 atoms
Iron (Fe) 4 atoms
Calcium (Ca) 2 atoms

Copper Binding Sites:

The binding sites of Copper atom in the Catalytic Core (Subunits I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides (pdb code 2gsm). 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, PDB code: 2gsm:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 2gsm

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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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu3005

b:27.2
occ:1.00
 ND1 A:HIS284 2.1 26.6 1.0
NE2 A:HIS333 2.1 28.2 1.0
NE2 A:HIS334 2.1 28.5 1.0
O A:OH6501 2.1 26.7 1.0
CE1 A:HIS333 2.9 31.6 1.0
O A:HOH6506 3.0 24.5 1.0
CE1 A:HIS334 3.0 27.7 1.0
CG A:HIS284 3.0 27.1 1.0
CD2 A:HIS334 3.0 28.7 1.0
CE1 A:HIS284 3.1 26.5 1.0
CD2 A:HIS333 3.1 26.5 1.0
CB A:HIS284 3.3 26.2 1.0
CA A:HIS284 3.9 26.3 1.0
ND1 A:HIS334 4.0 26.1 1.0
ND1 A:HIS333 4.1 28.5 1.0
CG A:HIS334 4.1 27.5 1.0
CD2 A:HIS284 4.2 27.8 1.0
NE2 A:HIS284 4.2 27.3 1.0
CG A:HIS333 4.2 27.5 1.0
NA A:HEA2002 4.5 25.6 1.0
N A:HIS284 4.6 26.7 1.0
C1A A:HEA2002 4.7 25.2 1.0
C4A A:HEA2002 4.7 26.0 1.0
O A:HOH6601 4.8 34.2 1.0
FE A:HEA2002 4.9 24.2 1.0
C2A A:HEA2002 4.9 26.4 1.0
C3A A:HEA2002 4.9 26.6 1.0

Copper binding site 2 out of 6 in 2gsm

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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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu3003

b:25.0
occ:1.00
 ND1 B:HIS260 2.1 21.2 1.0
SG B:CYS256 2.3 23.2 1.0
SG B:CYS252 2.4 22.4 1.0
O B:GLU254 2.6 22.9 1.0
CU B:CU3004 2.6 24.8 1.0
CE1 B:HIS260 3.0 23.6 1.0
CG B:HIS260 3.2 21.4 1.0
CB B:CYS252 3.4 22.5 1.0
CB B:CYS256 3.4 22.9 1.0
C B:GLU254 3.5 22.9 1.0
CA B:HIS260 3.6 21.8 1.0
CB B:HIS260 3.6 20.9 1.0
N B:CYS256 3.7 23.0 1.0
O B:HIS260 3.9 21.7 1.0
N B:GLU254 4.1 23.3 1.0
NE2 B:HIS260 4.1 22.8 1.0
O B:CYS252 4.2 21.8 1.0
C B:CYS252 4.2 22.8 1.0
C B:HIS260 4.2 22.2 1.0
CA B:LEU255 4.2 23.1 1.0
CA B:CYS256 4.2 23.0 1.0
C B:LEU255 4.2 23.2 1.0
CD2 B:HIS260 4.2 20.5 1.0
N B:LEU255 4.2 23.3 1.0
ND1 B:HIS217 4.3 20.1 1.0
CA B:CYS252 4.4 22.6 1.0
CA B:GLU254 4.5 23.3 1.0
SD B:MET263 4.5 21.9 1.0
N B:SER253 4.6 22.2 1.0
CG B:MET263 4.7 19.6 1.0
N B:HIS260 4.8 21.3 1.0
CA B:HIS217 5.0 22.8 1.0

Copper binding site 3 out of 6 in 2gsm

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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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu3004

b:24.8
occ:1.00
 ND1 B:HIS217 2.1 20.1 1.0
SG B:CYS252 2.3 22.4 1.0
SD B:MET263 2.4 21.9 1.0
SG B:CYS256 2.4 23.2 1.0
CU B:CU3003 2.6 25.0 1.0
CE1 B:HIS217 3.0 19.8 1.0
CE B:MET263 3.0 18.9 1.0
CG B:HIS217 3.2 21.2 1.0
CB B:CYS256 3.4 22.9 1.0
CG B:MET263 3.4 19.6 1.0
CB B:CYS252 3.5 22.5 1.0
CB B:HIS217 3.6 21.7 1.0
NE2 B:HIS217 4.2 23.0 1.0
CA B:HIS217 4.3 22.8 1.0
CD2 B:HIS217 4.3 19.8 1.0
O B:GLU254 4.3 22.9 1.0
CD1 B:TRP143 4.4 23.4 1.0
ND1 B:HIS260 4.6 21.2 1.0
O B:TYR141 4.7 23.2 1.0
CA B:HIS260 4.7 21.8 1.0
CA B:CYS256 4.8 23.0 1.0
CB B:MET263 4.9 22.2 1.0
CA B:CYS252 4.9 22.6 1.0

Copper binding site 4 out of 6 in 2gsm

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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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu4005

b:33.8
occ:1.00
 O C:OH7501 2.0 35.4 1.0
NE2 C:HIS333 2.0 31.2 1.0
ND1 C:HIS284 2.1 33.9 1.0
NE2 C:HIS334 2.1 33.2 1.0
CE1 C:HIS333 2.9 30.8 1.0
CE1 C:HIS334 3.0 31.6 1.0
O C:HOH1006 3.0 27.8 1.0
CE1 C:HIS284 3.0 32.9 1.0
CG C:HIS284 3.0 33.7 1.0
CD2 C:HIS334 3.1 30.7 1.0
CD2 C:HIS333 3.1 30.2 1.0
CB C:HIS284 3.3 33.5 1.0
CA C:HIS284 3.9 33.4 1.0
ND1 C:HIS334 4.1 31.5 1.0
ND1 C:HIS333 4.1 30.5 1.0
CG C:HIS334 4.1 30.9 1.0
NE2 C:HIS284 4.2 33.8 1.0
CD2 C:HIS284 4.2 34.2 1.0
CG C:HIS333 4.2 31.5 1.0
NA C:HEA3002 4.5 28.7 1.0
C1A C:HEA3002 4.6 29.8 1.0
C4A C:HEA3002 4.7 30.7 1.0
N C:HIS284 4.7 33.7 1.0
C2A C:HEA3002 4.8 29.9 1.0
FE C:HEA3002 4.9 28.0 1.0
C3A C:HEA3002 4.9 29.6 1.0

Copper binding site 5 out of 6 in 2gsm

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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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu4003

b:27.8
occ:1.00
 ND1 D:HIS260 2.0 29.7 1.0
SG D:CYS256 2.3 27.2 1.0
SG D:CYS252 2.3 26.1 1.0
CU D:CU4004 2.6 29.2 1.0
O D:GLU254 2.7 27.9 1.0
CE1 D:HIS260 2.9 29.8 1.0
CG D:HIS260 3.1 28.5 1.0
CB D:CYS252 3.3 25.9 1.0
CB D:CYS256 3.4 27.4 1.0
CA D:HIS260 3.5 28.6 1.0
CB D:HIS260 3.5 28.8 1.0
C D:GLU254 3.6 28.0 1.0
N D:CYS256 3.7 27.7 1.0
O D:HIS260 3.8 28.3 1.0
NE2 D:HIS260 4.1 29.0 1.0
C D:HIS260 4.1 28.6 1.0
N D:GLU254 4.1 28.1 1.0
C D:CYS252 4.1 26.4 1.0
CD2 D:HIS260 4.2 28.9 1.0
O D:CYS252 4.2 25.7 1.0
CA D:CYS256 4.2 27.7 1.0
CA D:LEU255 4.3 27.9 1.0
ND1 D:HIS217 4.3 26.2 1.0
C D:LEU255 4.3 27.9 1.0
N D:LEU255 4.3 28.2 1.0
CA D:CYS252 4.3 26.7 1.0
SD D:MET263 4.5 28.9 1.0
N D:SER253 4.5 27.2 1.0
CA D:GLU254 4.5 28.3 1.0
CG D:MET263 4.7 26.9 1.0
N D:HIS260 4.7 28.2 1.0
CA D:HIS217 4.9 28.4 1.0

Copper binding site 6 out of 6 in 2gsm

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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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu4004

b:29.2
occ:1.00
 ND1 D:HIS217 2.1 26.2 1.0
SG D:CYS256 2.4 27.2 1.0
SG D:CYS252 2.4 26.1 1.0
SD D:MET263 2.4 28.9 1.0
CU D:CU4003 2.6 27.8 1.0
CE1 D:HIS217 3.0 28.1 1.0
CE D:MET263 3.1 28.0 1.0
CG D:HIS217 3.2 27.8 1.0
CB D:CYS256 3.3 27.4 1.0
CB D:CYS252 3.5 25.9 1.0
CG D:MET263 3.5 26.9 1.0
CB D:HIS217 3.5 28.0 1.0
CA D:HIS217 4.2 28.4 1.0
NE2 D:HIS217 4.2 27.2 1.0
CD2 D:HIS217 4.3 26.3 1.0
O D:GLU254 4.3 27.9 1.0
CD1 D:TRP143 4.4 32.6 1.0
ND1 D:HIS260 4.5 29.7 1.0
CA D:HIS260 4.7 28.6 1.0
O D:TYR141 4.7 31.0 1.0
CA D:CYS256 4.7 27.7 1.0
CA D:CYS252 4.9 26.7 1.0
CB D:MET263 4.9 28.0 1.0
O D:HIS260 5.0 28.3 1.0

Reference:

L.Qin, C.Hiser, A.Mulichak, R.M.Garavito, S.Ferguson-Miller. Identification of Conserved Lipid/Detergent-Binding Sites in A High-Resolution Structure of the Membrane Protein Cytochrome C Oxidase. Proc.Natl.Acad.Sci.Usa V. 103 16117 2006.
ISSN: ISSN 0027-8424
PubMed: 17050688
DOI: 10.1073/PNAS.0606149103
Page generated: Tue Jul 30 23:38:32 2024

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