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Cadmium in PDB 1cyi: Cytochrome C6

Protein crystallography data

The structure of Cytochrome C6, PDB code: 1cyi was solved by C.A.Kerfeld, T.O.Yeates, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 1.90
Space group I 2 3
Cell size a, b, c (Å), α, β, γ (°) 82.600, 82.600, 82.600, 90.00, 90.00, 90.00
R / Rfree (%) 19.7 / n/a

Other elements in 1cyi:

The structure of Cytochrome C6 also contains other interesting chemical elements:

Iron (Fe) 1 atom

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Cytochrome C6 (pdb code 1cyi). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 4 binding sites of Cadmium where determined in the Cytochrome C6, PDB code: 1cyi:
Jump to Cadmium binding site number: 1; 2; 3; 4;

Cadmium binding site 1 out of 4 in 1cyi

Go back to Cadmium Binding Sites List in 1cyi
Cadmium binding site 1 out of 4 in the Cytochrome C6


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Cytochrome C6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd300

b:31.3
occ:1.00
O A:HOH435 1.8 28.5 1.0
O A:HOH425 1.9 12.5 1.0
OE2 A:GLU71 2.3 22.9 1.0
OE1 A:GLU71 2.8 21.5 1.0
CD A:GLU71 2.9 22.9 1.0
CG A:GLU71 4.4 17.8 1.0
N A:SER68 4.5 20.2 1.0
O A:ARG66 4.6 24.5 1.0
OG A:SER68 4.7 17.9 1.0
CA A:LEU67 4.7 21.1 1.0
CB A:SER68 5.0 18.7 1.0

Cadmium binding site 2 out of 4 in 1cyi

Go back to Cadmium Binding Sites List in 1cyi
Cadmium binding site 2 out of 4 in the Cytochrome C6


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Cytochrome C6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd301

b:28.9
occ:0.40
OE2 A:GLU54 2.4 36.6 1.0
O A:HOH402 2.7 48.2 1.0
OE1 A:GLU54 3.1 37.9 1.0
CD A:GLU54 3.1 33.7 1.0
CG A:GLU69 4.0 31.0 1.0
CD A:CD302 4.3 25.0 0.3
CD A:GLU69 4.4 37.2 1.0
CG A:GLU54 4.5 30.3 1.0
OE2 A:GLU69 4.6 38.2 1.0
O A:HOH463 4.8 51.8 0.5
OE1 A:GLU69 5.0 36.8 1.0

Cadmium binding site 3 out of 4 in 1cyi

Go back to Cadmium Binding Sites List in 1cyi
Cadmium binding site 3 out of 4 in the Cytochrome C6


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Cytochrome C6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd302

b:25.0
occ:0.28
O A:HOH463 1.8 51.8 0.5
O A:HOH402 1.8 48.2 1.0
OE1 A:GLU69 2.4 36.8 1.0
CD A:GLU69 3.1 37.2 1.0
OE2 A:GLU69 3.5 38.2 1.0
CG A:GLU69 4.0 31.0 1.0
CD A:CD301 4.3 28.9 0.4
CB A:GLU69 5.0 22.0 1.0

Cadmium binding site 4 out of 4 in 1cyi

Go back to Cadmium Binding Sites List in 1cyi
Cadmium binding site 4 out of 4 in the Cytochrome C6


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Cytochrome C6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd303

b:26.9
occ:0.28
O A:HOH409 1.9 47.8 1.0
OH A:TYR39 4.2 24.7 1.0
OE1 A:GLU28 4.2 39.8 1.0
CB A:GLU28 4.9 31.6 1.0

Reference:

C.A.Kerfeld, H.P.Anwar, R.Interrante, S.Merchant, T.O.Yeates. The Structure of Chloroplast Cytochrome C6 at 1.9 A Resolution: Evidence For Functional Oligomerization. J.Mol.Biol. V. 250 627 1995.
ISSN: ISSN 0022-2836
PubMed: 7623381
DOI: 10.1006/JMBI.1995.0404
Page generated: Sun Jan 24 09:41:28 2021

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