Atomistry » Copper » PDB 1jxd-1mfm » 1m57
Atomistry »
  Copper »
    PDB 1jxd-1mfm »
      1m57 »

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: Sun Dec 13 11:00:22 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy