Atomistry » Copper » PDB 5zpp-6fja » 6ci0
Atomistry »
  Copper »
    PDB 5zpp-6fja »
      6ci0 »

Copper in PDB 6ci0: Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with E101A (II) Mutation

Enzymatic activity of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with E101A (II) Mutation

All present enzymatic activity of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with E101A (II) 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 E101A (II) Mutation, PDB code: 6ci0 was solved by J.Liu, C.Hiser, S.Ferguson-Miller, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.09 / 2.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 124.916, 130.969, 177.788, 90.00, 90.00, 90.00
R / Rfree (%) 19.9 / 23.4

Other elements in 6ci0:

The structure of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with E101A (II) Mutation also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Potassium (K) 1 atom
Cadmium (Cd) 2 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 with E101A (II) Mutation (pdb code 6ci0). 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 E101A (II) Mutation, PDB code: 6ci0:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 6ci0

Go back to Copper Binding Sites List in 6ci0
Copper binding site 1 out of 6 in the Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with E101A (II) 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 E101A (II) Mutation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu614

b:51.4
occ:1.00
 NE2 A:HIS333 2.0 55.9 1.0
NE2 A:HIS334 2.2 55.7 1.0
ND1 A:HIS284 2.2 55.1 1.0
O A:HOH770 2.7 47.0 1.0
CE1 A:HIS333 2.9 52.0 1.0
CE1 A:HIS334 3.0 51.3 1.0
CG A:HIS284 3.0 47.0 1.0
CD2 A:HIS334 3.1 50.0 1.0
CD2 A:HIS333 3.1 58.0 1.0
CE1 A:HIS284 3.2 49.9 1.0
CB A:HIS284 3.2 42.8 1.0
CA A:HIS284 3.9 54.8 1.0
ND1 A:HIS333 4.1 62.7 1.0
ND1 A:HIS334 4.1 51.3 1.0
CG A:HIS334 4.2 55.1 1.0
CD2 A:HIS284 4.2 46.6 1.0
CG A:HIS333 4.2 55.9 1.0
NE2 A:HIS284 4.3 58.0 1.0
NA A:HEA618 4.4 57.6 1.0
C1A A:HEA618 4.6 42.8 1.0
C4A A:HEA618 4.7 44.0 1.0
N A:HIS284 4.7 46.7 1.0
FE A:HEA618 4.8 46.5 1.0
C2A A:HEA618 4.8 52.6 1.0
C3A A:HEA618 4.8 53.8 1.0

Copper binding site 2 out of 6 in 6ci0

Go back to Copper Binding Sites List in 6ci0
Copper binding site 2 out of 6 in the Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with E101A (II) 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 E101A (II) Mutation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu306

b:43.0
occ:1.00
 ND1 B:HIS260 2.1 41.6 1.0
SG B:CYS252 2.3 41.7 1.0
SG B:CYS256 2.3 40.7 1.0
O B:GLU254 2.5 41.7 1.0
CU B:CU307 2.5 41.9 1.0
CE1 B:HIS260 2.9 34.7 1.0
CG B:HIS260 3.1 40.1 1.0
CB B:CYS252 3.3 34.4 1.0
CB B:CYS256 3.4 34.4 1.0
C B:GLU254 3.5 40.9 1.0
CB B:HIS260 3.6 37.1 1.0
CA B:HIS260 3.6 40.7 1.0
N B:CYS256 3.7 41.4 1.0
O B:HIS260 3.8 41.3 1.0
NE2 B:HIS260 4.1 41.7 1.0
N B:GLU254 4.1 43.5 1.0
CA B:CYS256 4.2 38.8 1.0
C B:HIS260 4.2 41.2 1.0
O B:CYS252 4.2 38.0 1.0
CD2 B:HIS260 4.2 33.4 1.0
C B:CYS252 4.2 39.6 1.0
C B:LEU255 4.2 38.7 1.0
CA B:LEU255 4.2 39.9 1.0
N B:LEU255 4.3 39.5 1.0
ND1 B:HIS217 4.3 40.4 1.0
CA B:CYS252 4.4 37.7 1.0
SD B:MET263 4.4 42.1 1.0
CA B:GLU254 4.5 39.8 1.0
N B:SER253 4.7 40.4 1.0
CG B:MET263 4.7 45.1 1.0
N B:HIS260 4.9 43.6 1.0
CA B:HIS217 5.0 42.5 1.0

Copper binding site 3 out of 6 in 6ci0

Go back to Copper Binding Sites List in 6ci0
Copper binding site 3 out of 6 in the Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with E101A (II) 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 E101A (II) Mutation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu307

b:41.9
occ:1.00
 ND1 B:HIS217 2.2 40.4 1.0
SG B:CYS256 2.3 40.7 1.0
SG B:CYS252 2.3 41.7 1.0
SD B:MET263 2.4 42.1 1.0
CU B:CU306 2.5 43.0 1.0
CE B:MET263 3.1 32.5 1.0
CE1 B:HIS217 3.1 36.2 1.0
CG B:HIS217 3.2 40.6 1.0
CB B:CYS256 3.3 34.4 1.0
CB B:CYS252 3.5 34.4 1.0
CG B:MET263 3.6 45.1 1.0
CB B:HIS217 3.6 39.1 1.0
O B:GLU254 4.2 41.7 1.0
NE2 B:HIS217 4.3 42.3 1.0
CA B:HIS217 4.3 42.5 1.0
CD2 B:HIS217 4.3 41.4 1.0
ND1 B:HIS260 4.5 41.6 1.0
CD1 B:TRP143 4.5 36.5 1.0
O B:TYR141 4.6 42.0 1.0
CA B:CYS256 4.7 38.8 1.0
CA B:HIS260 4.8 40.7 1.0
CA B:CYS252 4.9 37.7 1.0
CB B:MET263 4.9 38.6 1.0
O B:HIS260 5.0 41.3 1.0
N B:CYS256 5.0 41.4 1.0

Copper binding site 4 out of 6 in 6ci0

Go back to Copper Binding Sites List in 6ci0
Copper binding site 4 out of 6 in the Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with E101A (II) 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 E101A (II) Mutation within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu604

b:62.1
occ:1.00
 NE2 C:HIS334 2.1 69.6 1.0
NE2 C:HIS333 2.2 66.4 1.0
ND1 C:HIS284 2.3 67.3 1.0
O C:HOH730 2.4 51.4 1.0
CE1 C:HIS333 3.0 63.5 1.0
CD2 C:HIS334 3.0 59.3 1.0
CE1 C:HIS334 3.0 56.3 1.0
CG C:HIS284 3.1 61.3 1.0
CB C:HIS284 3.2 60.6 1.0
CD2 C:HIS333 3.3 56.0 1.0
CE1 C:HIS284 3.4 71.8 1.0
CA C:HIS284 3.8 68.9 1.0
ND1 C:HIS334 4.1 59.7 1.0
CG C:HIS334 4.1 60.3 1.0
ND1 C:HIS333 4.2 61.1 1.0
CD2 C:HIS284 4.3 71.7 1.0
CG C:HIS333 4.3 58.8 1.0
NE2 C:HIS284 4.4 81.2 1.0
N C:HIS284 4.6 60.4 1.0
C1A C:HEA606 4.7 57.3 1.0
FE C:HEA606 4.7 57.5 1.0
C4A C:HEA606 4.8 56.9 1.0
C2A C:HEA606 4.8 63.1 1.0
NA C:HEA606 4.8 71.3 1.0
C3A C:HEA606 4.9 57.9 1.0
CG1 C:VAL287 4.9 67.1 1.0

Copper binding site 5 out of 6 in 6ci0

Go back to Copper Binding Sites List in 6ci0
Copper binding site 5 out of 6 in the Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with E101A (II) 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 E101A (II) Mutation within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu307

b:51.9
occ:1.00
 ND1 D:HIS217 2.1 46.8 1.0
SG D:CYS252 2.3 48.6 1.0
SG D:CYS256 2.4 46.6 1.0
SD D:MET263 2.5 57.2 1.0
CU D:CU308 2.6 53.5 1.0
CE D:MET263 3.0 44.0 1.0
CE1 D:HIS217 3.0 49.8 1.0
CG D:HIS217 3.2 48.9 1.0
CB D:CYS256 3.4 41.0 1.0
CB D:CYS252 3.5 47.6 1.0
CB D:HIS217 3.6 52.5 1.0
CG D:MET263 3.6 50.0 1.0
NE2 D:HIS217 4.1 47.2 1.0
CD2 D:HIS217 4.2 45.5 1.0
O D:GLU254 4.3 61.1 1.0
CA D:HIS217 4.3 52.6 1.0
ND1 D:HIS260 4.4 59.1 1.0
CD1 D:TRP143 4.5 56.4 1.0
O D:TYR141 4.7 50.0 1.0
CA D:CYS256 4.8 51.3 1.0
CA D:HIS260 4.8 47.8 1.0
CA D:CYS252 4.9 50.6 1.0
CB D:MET263 4.9 48.2 1.0
O D:HIS260 4.9 49.3 1.0
CZ2 D:TRP145 5.0 49.9 1.0

Copper binding site 6 out of 6 in 6ci0

Go back to Copper Binding Sites List in 6ci0
Copper binding site 6 out of 6 in the Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with E101A (II) 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 E101A (II) Mutation within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu308

b:53.5
occ:1.00
 ND1 D:HIS260 2.0 59.1 1.0
SG D:CYS252 2.3 48.6 1.0
SG D:CYS256 2.3 46.6 1.0
CU D:CU307 2.6 51.9 1.0
O D:GLU254 2.6 61.1 1.0
CE1 D:HIS260 2.8 51.9 1.0
CG D:HIS260 3.1 55.5 1.0
CB D:CYS252 3.3 47.6 1.0
CB D:CYS256 3.4 41.0 1.0
CB D:HIS260 3.6 54.1 1.0
C D:GLU254 3.6 55.4 1.0
CA D:HIS260 3.6 47.8 1.0
O D:HIS260 3.7 49.3 1.0
N D:CYS256 3.7 50.4 1.0
NE2 D:HIS260 3.9 54.9 1.0
CD2 D:HIS260 4.1 48.8 1.0
C D:HIS260 4.1 52.2 1.0
N D:GLU254 4.1 58.6 1.0
CA D:CYS256 4.2 51.3 1.0
C D:CYS252 4.2 50.6 1.0
ND1 D:HIS217 4.2 46.8 1.0
C D:LEU255 4.3 46.3 1.0
CA D:LEU255 4.3 47.7 1.0
N D:LEU255 4.3 48.4 1.0
O D:CYS252 4.3 48.6 1.0
CA D:CYS252 4.4 50.6 1.0
SD D:MET263 4.5 57.2 1.0
CA D:GLU254 4.5 50.5 1.0
N D:SER253 4.6 53.3 1.0
CG D:MET263 4.7 50.0 1.0
N D:HIS260 4.9 58.0 1.0

Reference:

C.Hiser, J.Liu, S.Ferguson-Miller. The K-Path Entrance in Cytochrome C Oxidase Is Defined By Mutation of E101 and Controlled By An Adjacent Ligand Binding Domain. Biochim. Biophys. Acta V.1859 725 2018.
ISSN: ISSN 0006-3002
PubMed: 29626419
DOI: 10.1016/J.BBABIO.2018.03.017
Page generated: Wed Jul 31 05:49:14 2024

Last articles

Ca in 2OVZ
Ca in 2OVX
Ca in 2OW4
Ca in 2OW0
Ca in 2OW1
Ca in 2OS9
Ca in 2OVU
Ca in 2OT4
Ca in 2OTV
Ca in 2OTM
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy