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

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

All present enzymatic activity of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides in the Reduced State Bound with Cyanide:
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 Bound with Cyanide, PDB code: 3fyi 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 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 124.344, 131.877, 176.160, 90.00, 90.00, 90.00
R / Rfree (%) 19.4 / 21.9

Other elements in 3fyi:

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

Cadmium binding site 1 out of 4 in 3fyi

Go back to Cadmium Binding Sites List in 3fyi
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 Bound with Cyanide


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 Bound with Cyanide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd8

b:40.1
occ:1.00
OE1 B:GLU280 2.2 38.3 1.0
NE2 B:HIS285 2.2 53.5 1.0
ND1 B:HIS283 2.3 48.4 1.0
OE2 B:GLU280 2.4 38.0 1.0
CD B:GLU280 2.6 39.0 1.0
CE1 B:HIS285 3.2 53.5 1.0
CD2 B:HIS285 3.2 53.0 1.0
CE1 B:HIS283 3.3 48.6 1.0
CG B:HIS283 3.3 48.4 1.0
CB B:HIS283 3.6 48.9 1.0
CG B:GLU280 4.2 38.7 1.0
ND1 B:HIS285 4.3 52.6 1.0
CG B:HIS285 4.3 53.8 1.0
NE2 B:HIS283 4.4 47.9 1.0
CD2 B:HIS283 4.4 48.2 1.0
O B:HOH701 4.5 52.1 1.0
C4 B:HTO1 4.7 57.5 1.0
O B:GLU280 4.9 40.3 1.0
CA B:HIS283 4.9 49.3 1.0
O B:HIS283 4.9 50.6 1.0

Cadmium binding site 2 out of 4 in 3fyi

Go back to Cadmium Binding Sites List in 3fyi
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 Bound with Cyanide


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 Bound with Cyanide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd9

b:48.0
occ:0.40
OE1 B:GLU101 2.3 58.0 1.0
O B:HOH386 2.3 47.9 1.0
OE2 B:GLU101 2.3 60.6 1.0
CD B:GLU101 2.6 59.0 1.0
ND1 B:HIS96 2.8 56.9 1.0
CG B:HIS96 3.7 56.3 1.0
CE1 B:HIS96 3.7 57.9 1.0
CB B:HIS96 3.8 55.2 1.0
CA B:HIS96 4.0 54.8 1.0
CG B:GLU101 4.1 58.0 1.0
N B:ASN97 4.4 56.3 1.0
O B:THR95 4.6 52.6 1.0
OG B:SER98 4.7 60.6 1.0
C B:HIS96 4.8 55.5 1.0
CG A:PRO315 4.8 45.4 1.0
NE2 B:HIS96 4.9 58.0 1.0
CD2 B:HIS96 4.9 57.5 1.0
CB B:GLU101 4.9 58.1 1.0

Cadmium binding site 3 out of 4 in 3fyi

Go back to Cadmium Binding Sites List in 3fyi
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 Bound with Cyanide


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 Bound with Cyanide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cd8

b:40.9
occ:1.00
OE1 D:GLU280 2.1 37.2 1.0
NE2 D:HIS285 2.3 53.6 1.0
OE2 D:GLU280 2.3 38.9 1.0
ND1 D:HIS283 2.3 50.5 1.0
CD D:GLU280 2.6 38.1 1.0
CE1 D:HIS285 3.1 54.1 1.0
CE1 D:HIS283 3.3 51.2 1.0
CG D:HIS283 3.3 51.3 1.0
CD2 D:HIS285 3.4 53.8 1.0
CB D:HIS283 3.6 51.6 1.0
CG D:GLU280 4.1 39.6 1.0
ND1 D:HIS285 4.3 53.7 1.0
NE2 D:HIS283 4.4 51.2 1.0
CD2 D:HIS283 4.4 52.1 1.0
CG D:HIS285 4.4 54.9 1.0
O D:HIS283 4.8 53.1 1.0
CA D:HIS283 4.9 51.9 1.0
O D:GLU280 4.9 41.9 1.0

Cadmium binding site 4 out of 4 in 3fyi

Go back to Cadmium Binding Sites List in 3fyi
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 Bound with Cyanide


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 Bound with Cyanide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cd9

b:45.2
occ:0.25
OE2 D:GLU101 2.2 71.4 1.0
OE1 D:GLU101 2.5 70.3 1.0
ND1 D:HIS96 2.5 72.9 1.0
CD D:GLU101 2.7 70.6 1.0
CE1 D:HIS96 3.4 73.4 1.0
CG D:HIS96 3.5 71.1 1.0
CB D:HIS96 3.8 69.3 1.0
CA D:HIS96 4.1 68.9 1.0
CG D:GLU101 4.2 69.2 1.0
NE2 D:HIS96 4.5 73.6 1.0
N D:ASN97 4.6 69.5 1.0
CD2 D:HIS96 4.6 72.6 1.0
CG C:PRO315 4.6 61.8 1.0
O D:THR95 4.6 67.2 1.0
C D:HIS96 5.0 69.1 1.0
CB D:GLU101 5.0 68.7 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: Sat Dec 12 08:21:32 2020

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