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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

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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 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

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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 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

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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 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

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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 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

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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 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: Sun Dec 13 11:22:08 2020

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