Cadmium in PDB 1cyj: Cytochrome C6

The structure of Cytochrome C6, PDB code: 1cyj 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 (°)	81.600, 81.600, 81.600, 90.00, 90.00, 90.00
R / Rfree (%)	18.7 / n/a

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

Iron

(Fe)

1 atom

The binding sites of Cadmium atom in the Cytochrome C6 (pdb code 1cyj). 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: 1cyj:
Jump to Cadmium binding site number: 1; 2; 3; 4;

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:20.3 occ:1.00 OE2 A:GLU71 2.4 23.3 1.0 OE1 A:GLU71 2.5 21.2 1.0 CD A:GLU71 2.7 21.3 1.0 CG A:GLU71 4.2 19.7 1.0 O A:ARG66 4.4 18.3 1.0 N A:SER68 4.4 16.2 1.0 OG A:SER68 4.6 14.6 1.0 CA A:LEU67 4.7 17.3 1.0 CB A:SER68 4.8 15.6 1.0 CD2 A:LEU67 4.9 17.3 1.0

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:25.4 occ:1.00 O A:HOH424 2.1 12.1 1.0 OD2 A:ASP2 2.3 24.7 1.0 OD1 A:ASP2 2.9 23.0 1.0 CG A:ASP2 2.9 23.8 1.0 O A:HOH463 4.3 36.5 1.0 CB A:ASP2 4.4 24.2 1.0 CB A:ALA4 4.4 20.1 1.0 N A:LEU5 4.5 18.7 1.0 CB A:LEU5 4.6 18.0 1.0

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:37.3 occ:1.00 O A:HOH403 1.9 37.9 1.0 O A:HOH419 1.9 50.1 1.0 OE2 A:GLU69 2.6 29.3 1.0 OE2 A:GLU54 2.7 26.0 1.0 OE1 A:GLU54 2.9 25.1 1.0 OE1 A:GLU69 3.0 28.6 1.0 CD A:GLU54 3.1 24.0 1.0 CD A:GLU69 3.2 27.5 1.0 O A:HOH449 4.5 36.0 1.0 O A:HOH405 4.6 29.6 1.0 CG A:GLU54 4.6 21.4 1.0 CG A:GLU69 4.6 24.9 1.0 CG2 A:ILE50 5.0 13.4 1.0 NE2 A:GLN73 5.0 29.6 1.0

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:42.9 occ:0.25 O A:HOH422 1.8 25.0 1.0 O A:HOH456 2.8 57.6 1.0 OE1 A:GLU47 3.2 24.4 1.0 O A:HOH469 3.4 46.4 1.0 CD A:GLU47 4.1 21.9 1.0 OE2 A:GLU47 4.6 22.2 1.0

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