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Cadmium in PDB 3oma: Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with K362M Mutation

Enzymatic activity of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with K362M Mutation

All present enzymatic activity of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with K362M 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 K362M Mutation, PDB code: 3oma was solved by J.Liu, L.Qin, S.Ferguson-Miller, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 125.019, 131.579, 176.626, 90.00, 90.00, 90.00
R / Rfree (%) 19.1 / 21.9

Other elements in 3oma:

The structure of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with K362M Mutation also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Iron (Fe) 4 atoms
Calcium (Ca) 2 atoms
Copper (Cu) 6 atoms

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with K362M Mutation (pdb code 3oma). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 4 binding sites of Cadmium where determined in the Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with K362M Mutation, PDB code: 3oma:
Jump to Cadmium binding site number: 1; 2; 3; 4;

Cadmium binding site 1 out of 4 in 3oma

Go back to Cadmium Binding Sites List in 3oma
Cadmium binding site 1 out of 4 in the Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with K362M Mutation


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with K362M Mutation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd8

b:45.0
occ:1.00
 OE1 B:GLU280 2.2 42.1 1.0
NE2 B:HIS285 2.2 56.4 1.0
ND1 B:HIS283 2.3 51.2 1.0
OE2 B:GLU280 2.4 43.8 1.0
CD B:GLU280 2.6 43.2 1.0
CD2 B:HIS285 3.1 56.9 1.0
CE1 B:HIS285 3.2 56.8 1.0
CG B:HIS283 3.2 51.4 1.0
CE1 B:HIS283 3.2 51.6 1.0
CB B:HIS283 3.5 52.5 1.0
CG B:GLU280 4.1 43.6 1.0
ND1 B:HIS285 4.2 57.1 1.0
CG B:HIS285 4.3 57.7 1.0
NE2 B:HIS283 4.3 51.1 1.0
CD2 B:HIS283 4.3 52.4 1.0
C4 B:HTH286 4.7 75.0 1.0
O B:GLU280 4.8 44.7 1.0
CA B:HIS283 4.9 53.0 1.0

Cadmium binding site 2 out of 4 in 3oma

Go back to Cadmium Binding Sites List in 3oma
Cadmium binding site 2 out of 4 in the Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with K362M Mutation


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with K362M Mutation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd9

b:53.8
occ:0.40
 OE1 B:GLU101 2.1 63.8 1.0
O B:HOH714 2.1 75.3 1.0
O B:HOH802 2.2 62.5 1.0
OE2 B:GLU101 2.3 66.2 1.0
O B:HOH801 2.5 46.8 1.0
CD B:GLU101 2.5 65.1 1.0
ND1 B:HIS96 2.8 59.9 1.0
CG B:HIS96 3.7 59.2 1.0
CB B:HIS96 3.7 58.1 1.0
CE1 B:HIS96 3.9 60.8 1.0
CA B:HIS96 4.0 58.0 1.0
CG B:GLU101 4.0 64.4 1.0
N B:ASN97 4.4 59.4 1.0
O B:THR95 4.6 56.3 1.0
OG B:SER98 4.7 64.1 1.0
CG A:PRO315 4.7 51.3 1.0
C B:HIS96 4.8 58.5 1.0
CB B:GLU101 4.8 64.7 1.0
CD2 B:HIS96 4.9 59.8 1.0
NE2 B:HIS96 5.0 60.3 1.0

Cadmium binding site 3 out of 4 in 3oma

Go back to Cadmium Binding Sites List in 3oma
Cadmium binding site 3 out of 4 in the Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with K362M Mutation


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with K362M Mutation within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cd288

b:43.9
occ:1.00
 OE1 D:GLU280 2.2 38.6 1.0
ND1 D:HIS283 2.2 51.0 1.0
NE2 D:HIS285 2.3 56.5 1.0
OE2 D:GLU280 2.4 42.0 1.0
CD D:GLU280 2.6 42.1 1.0
CE1 D:HIS283 3.1 52.0 1.0
CE1 D:HIS285 3.2 56.3 1.0
CG D:HIS283 3.3 53.0 1.0
CD2 D:HIS285 3.3 56.6 1.0
CB D:HIS283 3.6 53.8 1.0
CG D:GLU280 4.1 43.4 1.0
NE2 D:HIS283 4.3 52.2 1.0
ND1 D:HIS285 4.3 56.4 1.0
CD2 D:HIS283 4.4 53.2 1.0
CG D:HIS285 4.4 58.0 1.0
CA D:HIS283 4.9 54.4 1.0
O D:HIS283 5.0 55.7 1.0

Cadmium binding site 4 out of 4 in 3oma

Go back to Cadmium Binding Sites List in 3oma
Cadmium binding site 4 out of 4 in the Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with K362M Mutation


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with K362M Mutation within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cd9

b:64.2
occ:0.30
 OE2 D:GLU101 2.2 77.0 1.0
O D:HOH376 2.3 65.4 1.0
OE1 D:GLU101 2.4 76.3 1.0
CD D:GLU101 2.6 76.0 1.0
O D:HOH375 2.8 67.7 1.0
CD2 D:HIS96 3.0 76.0 1.0
CG D:HIS96 3.6 74.7 1.0
CB D:HIS96 3.7 73.4 1.0
CA D:HIS96 4.0 73.3 1.0
NE2 D:HIS96 4.0 77.0 1.0
CG D:GLU101 4.2 75.8 1.0
O D:THR95 4.5 71.0 1.0
N D:ASN97 4.5 74.7 1.0
CG C:PRO315 4.6 61.5 1.0
ND1 D:HIS96 4.8 76.0 1.0
CA C:GLY312 4.8 58.4 1.0
C D:HIS96 4.8 73.9 1.0
CB D:GLU101 4.9 75.3 1.0
CD C:PRO315 5.0 61.2 1.0
CE1 D:HIS96 5.0 76.7 1.0

Reference:

J.Liu, L.Qin, S.Ferguson-Miller. Crystallographic and Online Spectral Evidence For Role of Conformational Change and Conserved Water in Cytochrome Oxidase Proton Pump. Proc.Natl.Acad.Sci.Usa V. 108 1284 2011.
ISSN: ISSN 0027-8424
PubMed: 21205904
DOI: 10.1073/PNAS.1012846108
Page generated: Sat Dec 12 08:22:44 2020

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