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Copper in PDB 1m56: Structure of Cytochrome C Oxidase From Rhodobactor Sphaeroides (Wild Type)

Enzymatic activity of Structure of Cytochrome C Oxidase From Rhodobactor Sphaeroides (Wild Type)

All present enzymatic activity of Structure of Cytochrome C Oxidase From Rhodobactor Sphaeroides (Wild Type):
1.9.3.1;

Protein crystallography data

The structure of Structure of Cytochrome C Oxidase From Rhodobactor Sphaeroides (Wild Type), PDB code: 1m56 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) 40.00 / 2.30
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 340.360, 340.360, 89.668, 90.00, 90.00, 120.00
R / Rfree (%) 23.6 / 27.5

Other elements in 1m56:

The structure of Structure of Cytochrome C Oxidase From Rhodobactor Sphaeroides (Wild Type) 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 Rhodobactor Sphaeroides (Wild Type) (pdb code 1m56). 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 Rhodobactor Sphaeroides (Wild Type), PDB code: 1m56:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 1m56

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Copper binding site 1 out of 6 in the Structure of Cytochrome C Oxidase From Rhodobactor Sphaeroides (Wild Type)


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 Rhodobactor Sphaeroides (Wild Type) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1005

b:26.9
occ:1.00
ND1 A:HIS284 2.1 24.4 1.0
NE2 A:HIS333 2.1 18.0 1.0
NE2 A:HIS334 2.1 20.7 1.0
CE1 A:HIS284 2.6 23.0 1.0
CD2 A:HIS334 2.8 15.0 1.0
CE1 A:HIS333 2.9 16.4 1.0
CD2 A:HIS333 2.9 16.4 1.0
CG A:HIS284 3.3 21.8 1.0
CE1 A:HIS334 3.3 18.4 1.0
NE2 A:HIS284 3.8 26.1 1.0
CB A:HIS284 3.8 15.5 1.0
ND1 A:HIS333 4.0 16.7 1.0
CG A:HIS333 4.0 15.4 1.0
CA A:HIS284 4.0 12.9 1.0
CG A:HIS334 4.0 18.7 1.0
CD2 A:HIS284 4.2 23.7 1.0
ND1 A:HIS334 4.3 18.2 1.0
NA A:HEA1002 4.5 14.9 1.0
C1A A:HEA1002 4.6 14.9 1.0
C4A A:HEA1002 4.7 15.8 1.0
N A:HIS284 4.8 13.8 1.0
FE A:HEA1002 4.8 20.6 1.0
CG2 A:VAL287 4.9 2.0 1.0
CHA A:HEA1002 5.0 14.7 1.0
C2A A:HEA1002 5.0 12.9 1.0
C3A A:HEA1002 5.0 14.4 1.0

Copper binding site 2 out of 6 in 1m56

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Copper binding site 2 out of 6 in the Structure of Cytochrome C Oxidase From Rhodobactor Sphaeroides (Wild Type)


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 Rhodobactor Sphaeroides (Wild Type) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu1003

b:25.3
occ:1.00
ND1 B:HIS260 2.2 20.2 1.0
SG B:CYS252 2.2 25.8 1.0
SG B:CYS256 2.3 23.9 1.0
CU B:CU1004 2.6 25.8 1.0
O B:GLU254 2.7 19.8 1.0
CE1 B:HIS260 2.8 18.9 1.0
CB B:CYS256 3.2 16.8 1.0
N B:CYS256 3.2 14.8 1.0
CG B:HIS260 3.4 17.3 1.0
CB B:CYS252 3.4 17.4 1.0
C B:GLU254 3.6 16.3 1.0
CA B:CYS256 3.7 16.5 1.0
CA B:HIS260 3.8 16.6 1.0
CB B:HIS260 3.9 16.4 1.0
N B:GLU254 4.0 16.0 1.0
C B:LEU255 4.0 15.4 1.0
NE2 B:HIS260 4.1 18.4 1.0
ND1 B:HIS217 4.2 15.2 1.0
O B:HIS260 4.3 14.4 1.0
CA B:LEU255 4.3 15.5 1.0
N B:LEU255 4.3 16.2 1.0
CD2 B:HIS260 4.3 15.6 1.0
CA B:GLU254 4.4 16.0 1.0
SD B:MET263 4.4 2.0 1.0
C B:HIS260 4.5 15.2 1.0
C B:CYS256 4.7 16.9 1.0
CA B:CYS252 4.7 16.4 1.0
C B:CYS252 4.9 16.5 1.0
O B:ILE216 4.9 19.1 1.0
CE1 B:HIS217 4.9 11.0 1.0
N B:SER253 4.9 15.9 1.0
N B:GLY257 5.0 19.0 1.0
N B:HIS260 5.0 18.9 1.0
CA B:HIS217 5.0 17.4 1.0
O B:LEU255 5.0 14.8 1.0

Copper binding site 3 out of 6 in 1m56

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Copper binding site 3 out of 6 in the Structure of Cytochrome C Oxidase From Rhodobactor Sphaeroides (Wild Type)


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 Rhodobactor Sphaeroides (Wild Type) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu1004

b:25.8
occ:1.00
ND1 B:HIS217 2.1 15.2 1.0
SG B:CYS256 2.2 23.9 1.0
SG B:CYS252 2.3 25.8 1.0
SD B:MET263 2.5 2.0 1.0
CU B:CU1003 2.6 25.3 1.0
CE1 B:HIS217 2.7 11.0 1.0
CB B:CYS256 3.2 16.8 1.0
CG B:HIS217 3.2 15.7 1.0
CB B:CYS252 3.8 17.4 1.0
CG B:MET263 3.8 9.2 1.0
CE B:MET263 3.8 8.3 1.0
CB B:HIS217 3.8 17.1 1.0
NE2 B:HIS217 4.0 11.3 1.0
CD2 B:HIS217 4.2 12.5 1.0
CA B:HIS217 4.3 17.4 1.0
CA B:CYS256 4.5 16.5 1.0
O B:GLU254 4.6 19.8 1.0
ND1 B:HIS260 4.6 20.2 1.0
O B:ILE216 4.7 19.1 1.0
CD1 B:TRP143 4.8 21.0 1.0
N B:CYS256 4.8 14.8 1.0

Copper binding site 4 out of 6 in 1m56

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Copper binding site 4 out of 6 in the Structure of Cytochrome C Oxidase From Rhodobactor Sphaeroides (Wild Type)


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 Rhodobactor Sphaeroides (Wild Type) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cu1005

b:28.5
occ:1.00
NE2 G:HIS334 2.1 21.2 1.0
NE2 G:HIS333 2.2 18.2 1.0
ND1 G:HIS284 2.2 25.2 1.0
CE1 G:HIS284 2.8 22.9 1.0
CD2 G:HIS334 2.9 15.9 1.0
CD2 G:HIS333 2.9 16.9 1.0
CE1 G:HIS334 3.1 18.6 1.0
CE1 G:HIS333 3.2 15.1 1.0
CG G:HIS284 3.4 22.0 1.0
CB G:HIS284 3.8 17.0 1.0
NE2 G:HIS284 4.0 25.4 1.0
CG G:HIS334 4.0 18.5 1.0
CA G:HIS284 4.1 12.5 1.0
CG G:HIS333 4.1 16.5 1.0
ND1 G:HIS334 4.2 18.2 1.0
ND1 G:HIS333 4.2 16.3 1.0
NA G:HEA1002 4.3 15.3 1.0
CD2 G:HIS284 4.4 22.1 1.0
C1A G:HEA1002 4.4 14.6 1.0
C4A G:HEA1002 4.5 15.6 1.0
FE G:HEA1002 4.6 20.2 1.0
CHA G:HEA1002 4.7 14.1 1.0
CG2 G:VAL287 4.7 2.0 1.0
C2A G:HEA1002 4.8 13.0 1.0
ND G:HEA1002 4.8 14.2 1.0
C3A G:HEA1002 4.9 13.6 1.0
C4D G:HEA1002 4.9 14.7 1.0
N G:HIS284 5.0 14.6 1.0

Copper binding site 5 out of 6 in 1m56

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Copper binding site 5 out of 6 in the Structure of Cytochrome C Oxidase From Rhodobactor Sphaeroides (Wild Type)


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 Rhodobactor Sphaeroides (Wild Type) within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cu1003

b:28.6
occ:1.00
ND1 H:HIS260 2.1 19.4 1.0
SG H:CYS252 2.3 26.6 1.0
SG H:CYS256 2.3 26.0 1.0
CU H:CU1004 2.6 28.6 1.0
CE1 H:HIS260 2.8 18.7 1.0
O H:GLU254 2.9 20.6 1.0
CB H:CYS256 3.2 17.7 1.0
CB H:CYS252 3.2 18.1 1.0
CG H:HIS260 3.2 17.7 1.0
N H:CYS256 3.4 15.9 1.0
CA H:HIS260 3.5 17.4 1.0
O H:HIS260 3.6 15.6 1.0
CB H:HIS260 3.7 17.0 1.0
C H:GLU254 3.9 16.7 1.0
CA H:CYS256 3.9 16.4 1.0
NE2 H:HIS260 4.0 17.8 1.0
C H:HIS260 4.1 15.8 1.0
N H:GLU254 4.1 16.4 1.0
CD2 H:HIS260 4.2 15.9 1.0
C H:LEU255 4.3 15.1 1.0
ND1 H:HIS217 4.4 14.8 1.0
SD H:MET263 4.4 2.0 1.0
CA H:LEU255 4.4 14.5 1.0
N H:LEU255 4.4 16.8 1.0
CA H:CYS252 4.6 16.5 1.0
CA H:GLU254 4.6 16.2 1.0
C H:CYS252 4.7 16.9 1.0
C H:CYS256 4.7 17.3 1.0
N H:SER253 4.7 16.9 1.0
N H:GLY257 4.8 18.2 1.0
N H:HIS260 4.8 19.0 1.0
CG H:MET263 4.8 9.5 1.0

Copper binding site 6 out of 6 in 1m56

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Copper binding site 6 out of 6 in the Structure of Cytochrome C Oxidase From Rhodobactor Sphaeroides (Wild Type)


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 Rhodobactor Sphaeroides (Wild Type) within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cu1004

b:28.6
occ:1.00
ND1 H:HIS217 2.1 14.8 1.0
SG H:CYS256 2.2 26.0 1.0
SG H:CYS252 2.3 26.6 1.0
SD H:MET263 2.6 2.0 1.0
CU H:CU1003 2.6 28.6 1.0
CE1 H:HIS217 3.0 10.8 1.0
CB H:CYS256 3.1 17.7 1.0
CG H:HIS217 3.2 15.3 1.0
CB H:CYS252 3.4 18.1 1.0
CB H:HIS217 3.6 17.3 1.0
CG H:MET263 3.8 9.5 1.0
CE H:MET263 4.0 8.1 1.0
NE2 H:HIS217 4.2 10.8 1.0
CA H:HIS217 4.2 17.6 1.0
CD2 H:HIS217 4.3 11.6 1.0
O H:GLU254 4.3 20.6 1.0
CA H:CYS256 4.5 16.4 1.0
ND1 H:HIS260 4.6 19.4 1.0
O H:ILE216 4.6 19.3 1.0
CA H:CYS252 4.8 16.5 1.0
N H:CYS256 4.8 15.9 1.0
CD1 H:TRP143 4.9 21.9 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: Wed Oct 28 14:15:43 2020
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