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Copper in PDB 1m57: Structure of Cytochrome C Oxidase From Rhodobacter Sphaeroides (Eq(I-286) Mutant))

Enzymatic activity of Structure of Cytochrome C Oxidase From Rhodobacter Sphaeroides (Eq(I-286) Mutant))

All present enzymatic activity of Structure of Cytochrome C Oxidase From Rhodobacter Sphaeroides (Eq(I-286) Mutant)):
1.9.3.1;

Protein crystallography data

The structure of Structure of Cytochrome C Oxidase From Rhodobacter Sphaeroides (Eq(I-286) Mutant)), PDB code: 1m57 was solved by M.Svensson-Ek, J.Abramson, G.Larsson, S.Tornroth, P.Brezezinski, S.Iwata, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 4.00 / 3.00
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 340.720, 340.720, 89.760, 90.00, 90.00, 120.00
R / Rfree (%) 29.3 / 32.9

Other elements in 1m57:

The structure of Structure of Cytochrome C Oxidase From Rhodobacter Sphaeroides (Eq(I-286) Mutant)) also contains other interesting chemical elements:

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

Copper Binding Sites:

The binding sites of Copper atom in the Structure of Cytochrome C Oxidase From Rhodobacter Sphaeroides (Eq(I-286) Mutant)) (pdb code 1m57). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 6 binding sites of Copper where determined in the Structure of Cytochrome C Oxidase From Rhodobacter Sphaeroides (Eq(I-286) Mutant)), PDB code: 1m57:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 1m57

Go back to Copper Binding Sites List in 1m57
Copper binding site 1 out of 6 in the Structure of Cytochrome C Oxidase From Rhodobacter Sphaeroides (Eq(I-286) Mutant))


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Structure of Cytochrome C Oxidase From Rhodobacter Sphaeroides (Eq(I-286) Mutant)) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1005

b:22.8
occ:1.00
 ND1 A:HIS284 2.1 15.2 1.0
NE2 A:HIS334 2.1 19.0 1.0
NE2 A:HIS333 2.2 17.6 1.0
CE1 A:HIS284 2.6 13.4 1.0
CD2 A:HIS334 3.0 17.2 1.0
CD2 A:HIS333 3.1 16.0 1.0
CE1 A:HIS333 3.2 11.7 1.0
CE1 A:HIS334 3.2 20.0 1.0
CG A:HIS284 3.2 13.5 1.0
NE2 A:HIS284 3.8 17.3 1.0
CB A:HIS284 3.8 12.2 1.0
CA A:HIS284 3.9 9.5 1.0
CD2 A:HIS284 4.2 15.5 1.0
CG A:HIS334 4.2 17.6 1.0
O A:GLY283 4.2 12.4 1.0
ND1 A:HIS333 4.3 13.1 1.0
CG A:HIS333 4.3 14.9 1.0
ND1 A:HIS334 4.3 20.0 1.0
NA A:HEA1002 4.4 12.7 1.0
C1A A:HEA1002 4.6 12.7 1.0
FE A:HEA1002 4.7 14.6 1.0
C4A A:HEA1002 4.7 13.0 1.0
CHA A:HEA1002 4.8 12.9 1.0
N A:HIS284 4.9 10.0 1.0
ND A:HEA1002 4.9 11.6 1.0

Copper binding site 2 out of 6 in 1m57

Go back to Copper Binding Sites List in 1m57
Copper binding site 2 out of 6 in the Structure of Cytochrome C Oxidase From Rhodobacter Sphaeroides (Eq(I-286) Mutant))


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Structure of Cytochrome C Oxidase From Rhodobacter Sphaeroides (Eq(I-286) Mutant)) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu1003

b:22.4
occ:1.00
 ND1 B:HIS260 2.1 23.0 1.0
SG B:CYS256 2.2 20.3 1.0
SG B:CYS252 2.2 20.8 1.0
CE1 B:HIS260 2.6 20.9 1.0
CU B:CU1004 2.7 19.8 1.0
O B:GLU254 2.8 18.6 1.0
CB B:CYS256 3.0 13.1 1.0
CB B:CYS252 3.1 15.4 1.0
N B:CYS256 3.3 14.0 1.0
CG B:HIS260 3.4 19.9 1.0
C B:GLU254 3.7 15.4 1.0
CA B:CYS256 3.9 14.0 1.0
NE2 B:HIS260 3.9 22.1 1.0
CB B:HIS260 3.9 14.9 1.0
CA B:HIS260 4.0 13.1 1.0
N B:GLU254 4.0 13.2 1.0
O B:HIS260 4.1 11.8 1.0
O B:CYS252 4.1 13.6 1.0
C B:CYS252 4.2 13.4 1.0
C B:LEU255 4.2 14.9 1.0
CD2 B:HIS260 4.2 21.5 1.0
N B:LEU255 4.4 14.0 1.0
ND1 B:HIS217 4.4 21.4 1.0
CA B:CYS252 4.4 14.6 1.0
CA B:LEU255 4.4 13.8 1.0
C B:HIS260 4.5 12.3 1.0
SD B:MET263 4.5 2.0 1.0
CA B:GLU254 4.5 14.7 1.0
N B:SER253 4.5 13.1 1.0
C B:CYS256 4.7 15.3 1.0
C B:SER253 4.9 12.0 1.0
CB B:HIS217 5.0 17.8 1.0

Copper binding site 3 out of 6 in 1m57

Go back to Copper Binding Sites List in 1m57
Copper binding site 3 out of 6 in the Structure of Cytochrome C Oxidase From Rhodobacter Sphaeroides (Eq(I-286) Mutant))


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Structure of Cytochrome C Oxidase From Rhodobacter Sphaeroides (Eq(I-286) Mutant)) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu1004

b:19.8
occ:1.00
 ND1 B:HIS217 2.1 21.4 1.0
SG B:CYS252 2.3 20.8 1.0
SG B:CYS256 2.3 20.3 1.0
SD B:MET263 2.6 2.0 1.0
CU B:CU1003 2.7 22.4 1.0
CE1 B:HIS217 3.0 22.0 1.0
CB B:CYS256 3.0 13.1 1.0
CG B:HIS217 3.2 19.3 1.0
CB B:HIS217 3.5 17.8 1.0
CB B:CYS252 3.5 15.4 1.0
CE B:MET263 3.9 2.0 1.0
CG B:MET263 4.0 2.0 1.0
NE2 B:HIS217 4.2 22.6 1.0
CD2 B:HIS217 4.3 19.5 1.0
CA B:HIS217 4.3 16.6 1.0
CA B:CYS256 4.5 14.0 1.0
O B:GLU254 4.6 18.6 1.0
ND1 B:HIS260 4.7 23.0 1.0
N B:CYS256 4.8 14.0 1.0
CA B:CYS252 4.9 14.6 1.0
O B:CYS256 4.9 16.7 1.0
CD1 B:TRP143 4.9 20.6 1.0

Copper binding site 4 out of 6 in 1m57

Go back to Copper Binding Sites List in 1m57
Copper binding site 4 out of 6 in the Structure of Cytochrome C Oxidase From Rhodobacter Sphaeroides (Eq(I-286) Mutant))


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Structure of Cytochrome C Oxidase From Rhodobacter Sphaeroides (Eq(I-286) Mutant)) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cu1005

b:24.2
occ:1.00
 ND1 G:HIS284 2.1 16.2 1.0
NE2 G:HIS334 2.1 19.5 1.0
NE2 G:HIS333 2.2 18.1 1.0
CD2 G:HIS334 2.7 16.9 1.0
CE1 G:HIS284 2.8 14.0 1.0
CD2 G:HIS333 2.9 16.3 1.0
CE1 G:HIS333 3.1 11.3 1.0
CG G:HIS284 3.2 15.0 1.0
CE1 G:HIS334 3.3 20.2 1.0
CB G:HIS284 3.7 12.8 1.0
NE2 G:HIS284 3.9 17.8 1.0
CG G:HIS333 4.0 15.5 1.0
CA G:HIS284 4.0 10.1 1.0
CG G:HIS334 4.0 17.6 1.0
ND1 G:HIS333 4.0 12.8 1.0
CD2 G:HIS284 4.2 16.2 1.0
ND1 G:HIS334 4.3 20.2 1.0
O G:GLY283 4.5 13.4 1.0
NA G:HEA1002 4.7 12.8 1.0
CE3 G:TRP280 4.8 6.3 1.0
C1A G:HEA1002 4.9 12.9 1.0
C4A G:HEA1002 4.9 13.1 1.0
N G:HIS284 4.9 10.2 1.0

Copper binding site 5 out of 6 in 1m57

Go back to Copper Binding Sites List in 1m57
Copper binding site 5 out of 6 in the Structure of Cytochrome C Oxidase From Rhodobacter Sphaeroides (Eq(I-286) Mutant))


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Structure of Cytochrome C Oxidase From Rhodobacter Sphaeroides (Eq(I-286) Mutant)) within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cu1003

b:25.5
occ:1.00
 ND1 H:HIS260 2.1 23.0 1.0
SG H:CYS256 2.3 21.8 1.0
SG H:CYS252 2.3 22.6 1.0
CE1 H:HIS260 2.5 20.8 1.0
CU H:CU1004 2.7 22.7 1.0
O H:GLU254 2.8 18.9 1.0
CB H:CYS252 2.9 15.9 1.0
CB H:CYS256 3.1 13.4 1.0
CG H:HIS260 3.3 19.8 1.0
N H:CYS256 3.5 15.3 1.0
O H:HIS260 3.6 12.6 1.0
CA H:HIS260 3.6 12.9 1.0
NE2 H:HIS260 3.8 22.4 1.0
C H:GLU254 3.8 15.7 1.0
CB H:HIS260 3.8 14.5 1.0
N H:GLU254 3.9 14.1 1.0
CA H:CYS256 3.9 14.7 1.0
C H:HIS260 4.1 13.2 1.0
CD2 H:HIS260 4.2 21.7 1.0
C H:CYS252 4.2 13.6 1.0
CA H:CYS252 4.3 14.8 1.0
N H:SER253 4.3 13.3 1.0
SD H:MET263 4.4 2.0 1.0
ND1 H:HIS217 4.4 21.4 1.0
C H:LEU255 4.4 15.7 1.0
O H:CYS252 4.4 13.6 1.0
CA H:GLU254 4.5 15.4 1.0
CA H:LEU255 4.6 14.2 1.0
N H:LEU255 4.6 14.1 1.0
C H:CYS256 4.7 15.5 1.0
CB H:HIS217 4.8 17.1 1.0
N H:HIS260 4.9 13.1 1.0
CG H:MET263 4.9 2.4 1.0
C H:SER253 4.9 12.7 1.0

Copper binding site 6 out of 6 in 1m57

Go back to Copper Binding Sites List in 1m57
Copper binding site 6 out of 6 in the Structure of Cytochrome C Oxidase From Rhodobacter Sphaeroides (Eq(I-286) Mutant))


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Structure of Cytochrome C Oxidase From Rhodobacter Sphaeroides (Eq(I-286) Mutant)) within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cu1004

b:22.7
occ:1.00
 ND1 H:HIS217 2.1 21.4 1.0
SG H:CYS252 2.3 22.6 1.0
SG H:CYS256 2.4 21.8 1.0
SD H:MET263 2.6 2.0 1.0
CU H:CU1003 2.7 25.5 1.0
CG H:HIS217 2.8 19.6 1.0
CB H:CYS256 2.9 13.4 1.0
CB H:HIS217 2.9 17.1 1.0
CE1 H:HIS217 3.1 21.4 1.0
CB H:CYS252 3.3 15.9 1.0
CA H:HIS217 3.9 16.5 1.0
CD2 H:HIS217 4.0 20.4 1.0
NE2 H:HIS217 4.1 23.0 1.0
CG H:MET263 4.1 2.4 1.0
CE H:MET263 4.2 2.0 1.0
O H:GLU254 4.2 18.9 1.0
CA H:CYS256 4.4 14.7 1.0
ND1 H:HIS260 4.7 23.0 1.0
CA H:CYS252 4.7 14.8 1.0
O H:CYS256 4.8 16.0 1.0
N H:SER218 4.8 16.2 1.0
N H:CYS256 4.8 15.3 1.0
O H:ILE216 4.9 20.4 1.0
C H:HIS217 4.9 16.7 1.0
N H:HIS217 4.9 16.3 1.0
C H:CYS256 5.0 15.5 1.0

Reference:

M.Svensson-Ek, J.Abramson, G.Larsson, S.Tornroth, P.Brzezinski, S.Iwata. The X-Ray Crystal Structures of Wild-Type and Eq(I-286) Mutant Cytochrome C Oxidases From Rhodobacter Sphaeroides. J.Mol.Biol. V. 321 329 2002.
ISSN: ISSN 0022-2836
PubMed: 12144789
DOI: 10.1016/S0022-2836(02)00619-8
Page generated: Mon Jul 14 00:04:50 2025

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