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

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

All present enzymatic activity of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with D132A Mutation in the Reduced State:
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 in the Reduced State, PDB code: 3omn 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) 42.70 / 2.15
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 124.670, 132.033, 176.286, 90.00, 90.00, 90.00
R / Rfree (%) 19.8 / 21.9

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 in the Reduced State (pdb code 3omn). 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 in the Reduced State, PDB code: 3omn:
Jump to Cadmium binding site number: 1; 2; 3; 4;

Cadmium binding site 1 out of 4 in 3omn

Go back to Cadmium Binding Sites List in 3omn
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 in the Reduced State


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 in the Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd8

b:41.1
occ:1.00
OE1 B:GLU280 2.1 38.8 1.0
NE2 B:HIS285 2.2 55.1 1.0
ND1 B:HIS283 2.3 48.1 1.0
OE2 B:GLU280 2.4 39.3 1.0
CD B:GLU280 2.5 39.1 1.0
CE1 B:HIS285 3.2 55.3 1.0
CD2 B:HIS285 3.2 54.8 1.0
CG B:HIS283 3.3 48.4 1.0
CE1 B:HIS283 3.3 48.0 1.0
CB B:HIS283 3.5 49.4 1.0
CG B:GLU280 4.1 39.3 1.0
ND1 B:HIS285 4.3 54.8 1.0
CG B:HIS285 4.3 55.3 1.0
NE2 B:HIS283 4.4 47.4 1.0
CD2 B:HIS283 4.4 48.5 1.0
C4 B:HTH286 4.8 60.1 1.0
O B:GLU280 4.8 40.6 1.0
CA B:HIS283 4.9 49.7 1.0

Cadmium binding site 2 out of 4 in 3omn

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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 in the Reduced State


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 in the Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd9

b:39.8
occ:0.35
OE2 B:GLU101 2.1 57.8 1.0
O B:HOH733 2.2 66.9 1.0
O B:HOH769 2.3 52.9 1.0
O B:HOH768 2.5 40.5 1.0
OE1 B:GLU101 2.5 59.5 1.0
CD B:GLU101 2.6 58.5 1.0
ND1 B:HIS96 2.6 55.5 1.0
CE1 B:HIS96 3.5 56.0 1.0
CG B:HIS96 3.7 54.7 1.0
CB B:HIS96 3.9 53.8 1.0
CA B:HIS96 4.0 53.5 1.0
CG B:GLU101 4.1 57.8 1.0
N B:ASN97 4.4 55.1 1.0
O B:THR95 4.6 51.0 1.0
NE2 B:HIS96 4.7 55.9 1.0
CD2 B:HIS96 4.8 55.0 1.0
CG A:PRO315 4.8 44.8 1.0
C B:HIS96 4.8 54.3 1.0
OG B:SER98 4.9 60.0 1.0
CB B:GLU101 4.9 58.2 1.0

Cadmium binding site 3 out of 4 in 3omn

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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 in the Reduced State


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 in the Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cd288

b:40.6
occ:1.00
OE1 D:GLU280 2.1 35.6 1.0
NE2 D:HIS285 2.2 52.8 1.0
ND1 D:HIS283 2.2 50.1 1.0
OE2 D:GLU280 2.4 41.2 1.0
CD D:GLU280 2.6 39.1 1.0
CE1 D:HIS285 3.1 53.3 1.0
CE1 D:HIS283 3.2 51.0 1.0
CG D:HIS283 3.2 50.1 1.0
CD2 D:HIS285 3.3 53.0 1.0
CB D:HIS283 3.5 50.3 1.0
CG D:GLU280 4.1 40.5 1.0
ND1 D:HIS285 4.3 53.1 1.0
NE2 D:HIS283 4.3 51.0 1.0
CD2 D:HIS283 4.4 51.3 1.0
CG D:HIS285 4.4 53.7 1.0
CA D:HIS283 4.9 50.4 1.0
O D:GLU280 5.0 42.0 1.0

Cadmium binding site 4 out of 4 in 3omn

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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 in the Reduced State


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 in the Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cd9

b:63.1
occ:0.35
O D:HOH378 2.2 72.0 1.0
OE2 D:GLU101 2.2 71.2 1.0
O D:HOH377 2.2 65.4 1.0
OE1 D:GLU101 2.4 70.5 1.0
CD D:GLU101 2.6 70.5 1.0
ND1 D:HIS96 2.7 71.8 1.0
CG D:HIS96 3.5 70.4 1.0
CB D:HIS96 3.6 69.0 1.0
CE1 D:HIS96 3.7 72.5 1.0
CA D:HIS96 3.9 68.8 1.0
CG D:GLU101 4.1 70.5 1.0
N D:ASN97 4.4 69.7 1.0
O D:THR95 4.4 66.9 1.0
CD2 D:HIS96 4.7 71.4 1.0
C D:HIS96 4.7 69.1 1.0
NE2 D:HIS96 4.8 72.5 1.0
CA C:GLY312 4.8 58.7 1.0
CG C:PRO315 4.8 61.4 1.0
CB D:GLU101 4.9 70.3 1.0
CE1 C:PHE311 5.0 56.8 1.0
N D:HIS96 5.0 67.7 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: Fri Aug 28 13:52:54 2020
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