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Cadmium in PDB 3omi: Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with D132A Mutation

Enzymatic activity of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with D132A Mutation

All present enzymatic activity of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with D132A 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 D132A Mutation, PDB code: 3omi 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) 35.84 / 2.15
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 125.064, 131.519, 175.674, 90.00, 90.00, 90.00
R / Rfree (%) 19.2 / 21.5

Other elements in 3omi:

The structure of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with D132A Mutation also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Iron (Fe) 4 atoms
Calcium (Ca) 2 atoms
Chlorine (Cl) 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 D132A Mutation (pdb code 3omi). 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 D132A Mutation, PDB code: 3omi:
Jump to Cadmium binding site number: 1; 2; 3; 4;

Cadmium binding site 1 out of 4 in 3omi

Go back to Cadmium Binding Sites List in 3omi
Cadmium binding site 1 out of 4 in the Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with D132A 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 D132A Mutation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd309

b:37.0
occ:1.00
 OE1 B:GLU280 2.0 33.9 1.0
NE2 B:HIS285 2.2 48.9 1.0
ND1 B:HIS283 2.3 43.0 1.0
OE2 B:GLU280 2.4 37.2 1.0
CD B:GLU280 2.6 34.9 1.0
CD2 B:HIS285 3.1 49.5 1.0
CE1 B:HIS285 3.1 49.9 1.0
CG B:HIS283 3.3 43.0 1.0
CE1 B:HIS283 3.3 43.9 1.0
CB B:HIS283 3.5 44.5 1.0
CG B:GLU280 4.1 33.8 1.0
ND1 B:HIS285 4.2 49.7 1.0
CG B:HIS285 4.2 50.4 1.0
CD2 B:HIS283 4.4 44.0 1.0
NE2 B:HIS283 4.4 43.1 1.0
C4 B:HTH306 4.8 57.2 1.0
O B:GLU280 4.8 35.3 1.0
CA B:HIS283 4.9 44.7 1.0
O B:HIS283 5.0 46.3 1.0

Cadmium binding site 2 out of 4 in 3omi

Go back to Cadmium Binding Sites List in 3omi
Cadmium binding site 2 out of 4 in the Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with D132A 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 D132A Mutation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd310

b:35.9
occ:0.50
 OE2 B:GLU101 2.0 43.7 1.0
O B:HOH482 2.2 29.3 1.0
O B:HOH430 2.2 53.7 1.0
OE1 B:GLU101 2.4 49.0 1.0
CD B:GLU101 2.5 47.1 1.0
O B:HOH483 2.5 45.5 1.0
ND1 B:HIS96 2.6 44.8 1.0
CE1 B:HIS96 3.5 44.1 1.0
CG B:HIS96 3.5 43.7 1.0
CB B:HIS96 3.8 43.5 1.0
CG B:GLU101 4.0 46.3 1.0
CA B:HIS96 4.1 43.4 1.0
O B:THR95 4.5 41.3 1.0
N B:ASN97 4.6 45.2 1.0
NE2 B:HIS96 4.6 44.4 1.0
CD2 B:HIS96 4.7 44.2 1.0
CG A:PRO315 4.9 36.7 1.0
CB B:GLU101 4.9 47.2 1.0
C B:HIS96 5.0 44.2 1.0

Cadmium binding site 3 out of 4 in 3omi

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Cadmium binding site 3 out of 4 in the Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with D132A 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 D132A Mutation within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cd307

b:36.7
occ:1.00
 OE1 D:GLU280 2.1 32.0 1.0
ND1 D:HIS283 2.2 44.2 1.0
NE2 D:HIS285 2.3 47.2 1.0
OE2 D:GLU280 2.4 35.6 1.0
CD D:GLU280 2.5 33.9 1.0
CE1 D:HIS283 3.1 45.7 1.0
CG D:HIS283 3.2 45.3 1.0
CE1 D:HIS285 3.2 46.9 1.0
CD2 D:HIS285 3.3 47.7 1.0
CB D:HIS283 3.5 45.8 1.0
CG D:GLU280 4.1 35.8 1.0
NE2 D:HIS283 4.2 45.5 1.0
CD2 D:HIS283 4.3 45.9 1.0
ND1 D:HIS285 4.4 48.4 1.0
CG D:HIS285 4.5 49.2 1.0
CA D:HIS283 4.8 46.3 1.0
O D:GLU280 4.9 37.8 1.0
O D:HIS283 5.0 47.3 1.0

Cadmium binding site 4 out of 4 in 3omi

Go back to Cadmium Binding Sites List in 3omi
Cadmium binding site 4 out of 4 in the Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with D132A 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 D132A Mutation within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cd308

b:47.7
occ:0.40
 O D:HOH501 1.9 51.5 1.0
O D:HOH502 2.2 73.6 1.0
OE2 D:GLU101 2.2 66.7 1.0
OE1 D:GLU101 2.3 64.8 1.0
ND1 D:HIS96 2.5 64.4 1.0
CD D:GLU101 2.5 66.0 1.0
CG D:HIS96 3.4 63.3 1.0
CB D:HIS96 3.5 62.1 1.0
CE1 D:HIS96 3.5 65.4 1.0
CA D:HIS96 3.9 62.0 1.0
CG D:GLU101 4.1 65.8 1.0
O D:THR95 4.3 60.0 1.0
N D:ASN97 4.5 63.3 1.0
CD2 D:HIS96 4.6 64.2 1.0
NE2 D:HIS96 4.6 65.3 1.0
C D:HIS96 4.8 62.6 1.0
CB D:GLU101 4.9 65.7 1.0
CG C:PRO315 4.9 52.5 1.0
N D:HIS96 4.9 60.9 1.0
CA C:GLY312 5.0 51.2 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: Fri Jul 19 16:19:29 2024

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