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Cadmium in PDB 3om3: Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with K362M Mutation in the Reduced State

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

All present enzymatic activity of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with K362M 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 K362M Mutation in the Reduced State, PDB code: 3om3 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) 40.46 / 2.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 124.650, 132.365, 178.006, 90.00, 90.00, 90.00
R / Rfree (%) 19.8 / 22.9

Other elements in 3om3:

The structure of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with K362M Mutation in the Reduced State 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 in the Reduced State (pdb code 3om3). 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 in the Reduced State, PDB code: 3om3:
Jump to Cadmium binding site number: 1; 2; 3; 4;

Cadmium binding site 1 out of 4 in 3om3

Go back to Cadmium Binding Sites List in 3om3
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 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 K362M Mutation in the Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd8

b:52.7
occ:1.00
NE2 B:HIS285 2.2 58.8 1.0
OE1 B:GLU280 2.2 46.1 1.0
ND1 B:HIS283 2.3 59.1 1.0
OE2 B:GLU280 2.3 49.4 1.0
CD B:GLU280 2.6 49.4 1.0
CE1 B:HIS285 3.1 58.5 1.0
CD2 B:HIS285 3.2 59.6 1.0
CG B:HIS283 3.2 58.7 1.0
CE1 B:HIS283 3.3 59.1 1.0
CB B:HIS283 3.5 58.7 1.0
CG B:GLU280 4.2 50.1 1.0
ND1 B:HIS285 4.2 59.4 1.0
CG B:HIS285 4.3 60.3 1.0
NE2 B:HIS283 4.4 58.6 1.0
CD2 B:HIS283 4.4 58.9 1.0
C4 B:HTH286 4.7 66.2 1.0
O B:GLU280 4.8 52.0 1.0
CA B:HIS283 4.9 59.0 1.0
O B:HIS283 4.9 60.0 1.0

Cadmium binding site 2 out of 4 in 3om3

Go back to Cadmium Binding Sites List in 3om3
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 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 K362M Mutation in the Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd9

b:79.5
occ:0.55
OE2 B:GLU101 2.3 76.1 1.0
O B:HOH708 2.4 81.1 1.0
O B:HOH742 2.4 66.7 1.0
O B:HOH741 2.6 51.3 1.0
OE1 B:GLU101 2.7 77.2 1.0
ND1 B:HIS96 2.8 72.4 1.0
CD B:GLU101 2.8 75.7 1.0
CE1 B:HIS96 3.7 73.2 1.0
CG B:HIS96 3.8 71.0 1.0
CB B:HIS96 3.9 69.9 1.0
CA B:HIS96 4.1 69.5 1.0
N B:ASN97 4.2 70.1 1.0
CG B:GLU101 4.3 74.0 1.0
OG B:SER98 4.6 73.3 1.0
N B:SER98 4.7 71.8 1.0
C B:HIS96 4.7 69.7 1.0
O B:THR95 4.8 68.3 1.0
NE2 B:HIS96 4.9 72.7 1.0
CB B:GLU101 4.9 73.4 1.0
CD2 B:HIS96 4.9 71.9 1.0
CA B:SER98 4.9 72.4 1.0
CG A:PRO315 5.0 61.6 1.0

Cadmium binding site 3 out of 4 in 3om3

Go back to Cadmium Binding Sites List in 3om3
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 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 K362M Mutation in the Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cd287

b:54.1
occ:1.00
NE2 D:HIS285 2.1 63.9 1.0
OE1 D:GLU280 2.2 46.5 1.0
ND1 D:HIS283 2.3 64.2 1.0
OE2 D:GLU280 2.3 49.5 1.0
CD D:GLU280 2.6 50.3 1.0
CE1 D:HIS285 3.1 63.7 1.0
CD2 D:HIS285 3.2 64.4 1.0
CE1 D:HIS283 3.2 64.2 1.0
CG D:HIS283 3.3 63.9 1.0
CB D:HIS283 3.6 63.8 1.0
CG D:GLU280 4.1 52.4 1.0
ND1 D:HIS285 4.2 64.4 1.0
CG D:HIS285 4.3 65.5 1.0
NE2 D:HIS283 4.4 64.2 1.0
CD2 D:HIS283 4.5 64.0 1.0
O D:HIS283 4.7 64.9 1.0
CA D:HIS283 4.9 64.0 1.0
O D:GLU280 4.9 55.4 1.0
C D:HIS283 5.0 64.6 1.0

Cadmium binding site 4 out of 4 in 3om3

Go back to Cadmium Binding Sites List in 3om3
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 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 K362M Mutation in the Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cd9

b:95.5
occ:0.40
OE2 D:GLU101 2.3 89.5 1.0
OE1 D:GLU101 2.6 90.0 1.0
CD D:GLU101 2.7 89.0 1.0
ND1 D:HIS96 2.7 89.8 1.0
CB D:HIS96 3.5 86.7 1.0
CG D:HIS96 3.5 88.3 1.0
CA D:HIS96 3.8 86.5 1.0
CE1 D:HIS96 3.8 90.7 1.0
N D:ASN97 4.1 86.9 1.0
CG D:GLU101 4.1 87.7 1.0
C D:HIS96 4.5 86.7 1.0
O D:THR95 4.5 84.7 1.0
CD2 D:HIS96 4.8 89.9 1.0
NE2 D:HIS96 4.9 90.8 1.0
CB D:GLU101 4.9 86.6 1.0
N D:HIS96 4.9 85.6 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 08:22:45 2020

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