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

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

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

Resolution Low / High (Å) 50.00 / 2.15
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 124.613, 131.472, 176.192, 90.00, 90.00, 90.00
R / Rfree (%) 19.6 / 22.1

Other elements in 3fye:

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

Cadmium binding site 1 out of 4 in 3fye

Go back to Cadmium Binding Sites List in 3fye
Cadmium binding site 1 out of 4 in the Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides 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 in the Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd8

b:44.2
occ:1.00
 OE1 B:GLU280 2.1 41.5 1.0
NE2 B:HIS285 2.2 57.4 1.0
ND1 B:HIS283 2.3 51.1 1.0
OE2 B:GLU280 2.4 41.9 1.0
CD B:GLU280 2.6 42.5 1.0
CE1 B:HIS285 3.1 57.1 1.0
CD2 B:HIS285 3.3 57.3 1.0
CG B:HIS283 3.3 51.7 1.0
CE1 B:HIS283 3.3 51.6 1.0
CB B:HIS283 3.5 52.8 1.0
CG B:GLU280 4.1 42.8 1.0
ND1 B:HIS285 4.3 56.8 1.0
CG B:HIS285 4.4 57.7 1.0
NE2 B:HIS283 4.4 50.8 1.0
CD2 B:HIS283 4.5 52.1 1.0
O B:GLU280 4.8 44.2 1.0
C4 B:HTO1 4.8 61.0 1.0
CA B:HIS283 4.9 53.2 1.0
O B:HIS283 5.0 54.5 1.0

Cadmium binding site 2 out of 4 in 3fye

Go back to Cadmium Binding Sites List in 3fye
Cadmium binding site 2 out of 4 in the Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides 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 in the Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd9

b:40.4
occ:0.50
 O B:HOH393 2.2 37.6 1.0
OE2 B:GLU101 2.3 58.1 1.0
OE1 B:GLU101 2.4 55.4 1.0
ND1 B:HIS96 2.4 54.3 1.0
CD B:GLU101 2.6 57.0 1.0
CE1 B:HIS96 3.3 54.8 1.0
CG B:HIS96 3.4 53.6 1.0
CB B:HIS96 3.7 52.8 1.0
CA B:HIS96 4.0 52.6 1.0
CG B:GLU101 4.2 56.4 1.0
O B:THR95 4.4 51.0 1.0
NE2 B:HIS96 4.4 54.4 1.0
CD2 B:HIS96 4.5 54.1 1.0
N B:ASN97 4.6 53.9 1.0
CG A:PRO315 4.8 46.4 1.0
C B:HIS96 4.9 53.2 1.0
CB B:GLU101 5.0 56.9 1.0

Cadmium binding site 3 out of 4 in 3fye

Go back to Cadmium Binding Sites List in 3fye
Cadmium binding site 3 out of 4 in the Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides 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 in the Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cd8

b:42.8
occ:1.00
 OE1 D:GLU280 2.0 37.3 1.0
NE2 D:HIS285 2.2 52.9 1.0
ND1 D:HIS283 2.4 50.7 1.0
OE2 D:GLU280 2.4 41.3 1.0
CD D:GLU280 2.5 40.5 1.0
CE1 D:HIS285 3.1 53.2 1.0
CE1 D:HIS283 3.3 51.5 1.0
CD2 D:HIS285 3.3 54.2 1.0
CG D:HIS283 3.3 51.7 1.0
CB D:HIS283 3.6 53.0 1.0
CG D:GLU280 4.1 41.5 1.0
ND1 D:HIS285 4.3 53.5 1.0
CG D:HIS285 4.4 55.2 1.0
NE2 D:HIS283 4.4 51.1 1.0
CD2 D:HIS283 4.5 52.1 1.0
O D:HIS283 4.9 54.7 1.0
CA D:HIS283 4.9 53.2 1.0
O D:GLU280 5.0 43.5 1.0

Cadmium binding site 4 out of 4 in 3fye

Go back to Cadmium Binding Sites List in 3fye
Cadmium binding site 4 out of 4 in the Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides 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 in the Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cd9

b:49.9
occ:0.40
 O D:HOH1196 1.9 46.9 1.0
O D:HOH1805 2.0 60.2 1.0
OE2 D:GLU101 2.2 70.5 1.0
OE1 D:GLU101 2.3 69.3 1.0
ND1 D:HIS96 2.3 70.8 1.0
CD D:GLU101 2.5 70.1 1.0
CE1 D:HIS96 3.2 71.6 1.0
CG D:HIS96 3.4 69.7 1.0
CB D:HIS96 3.7 68.5 1.0
CA D:HIS96 4.0 68.5 1.0
CG D:GLU101 4.0 69.8 1.0
NE2 D:HIS96 4.4 71.6 1.0
O D:THR95 4.4 66.7 1.0
CD2 D:HIS96 4.5 70.5 1.0
N D:ASN97 4.5 69.8 1.0
C D:HIS96 4.8 69.1 1.0
CG C:PRO315 4.9 59.4 1.0
CB D:GLU101 4.9 70.0 1.0
CE1 C:PHE311 4.9 57.2 1.0

Reference:

L.Qin, J.Liu, D.Mills, D.A.Proshlyakov, C.Hiser, S.Ferguson-Miller. Redox Dependent Conformational Changes in Cytochrome C Oxidase Suggest A Gating Mechanism For Proton Uptake. Biochemistry V. 48 5121 2009.
ISSN: ISSN 0006-2960
PubMed: 19397279
DOI: 10.1021/BI9001387
Page generated: Fri Jul 19 16:00:01 2024

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