Cadmium in PDB 4efp: Bombyx Mori Lipoprotein 7 Isolated From Its Natural Source at 1.33 A Resolution

The structure of Bombyx Mori Lipoprotein 7 Isolated From Its Natural Source at 1.33 A Resolution, PDB code: 4efp was solved by A.J.Pietrzyk, S.Panjikar, A.Bujacz, J.Mueller-Dieckmann, M.Jaskolski, G.Bujacz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	23.00 / 1.33
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	42.211, 49.993, 55.244, 93.41, 94.70, 102.78
R / Rfree (%)	18.4 / 23.1

The structure of Bombyx Mori Lipoprotein 7 Isolated From Its Natural Source at 1.33 A Resolution also contains other interesting chemical elements:

Potassium

(K)

2 atoms

The binding sites of Cadmium atom in the Bombyx Mori Lipoprotein 7 Isolated From Its Natural Source at 1.33 A Resolution (pdb code 4efp). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 2 binding sites of Cadmium where determined in the Bombyx Mori Lipoprotein 7 Isolated From Its Natural Source at 1.33 A Resolution, PDB code: 4efp:
Jump to Cadmium binding site number: 1; 2;

Cadmium binding site 1 out of 2 in the Bombyx Mori Lipoprotein 7 Isolated From Its Natural Source at 1.33 A Resolution


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Bombyx Mori Lipoprotein 7 Isolated From Its Natural Source at 1.33 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd302 b:10.3 occ:1.00 N A:SCN301 2.3 11.0 1.0 O A:HOH600 2.3 19.3 1.0 OE2 A:GLU40 2.4 10.8 1.0 O A:LYS37 2.4 10.4 1.0 OE1 A:GLU40 2.5 11.0 1.0 CD A:GLU40 2.8 10.7 1.0 C A:SCN301 3.1 11.2 1.0 C A:LYS37 3.4 10.6 1.0 O A:HOH501 4.1 24.6 1.0 N A:LYS38 4.2 10.2 1.0 CA A:LYS37 4.2 10.6 1.0 CB A:LYS37 4.3 11.5 1.0 CA A:LYS38 4.3 11.0 1.0 CG A:GLU40 4.3 10.1 1.0 N A:SER39 4.5 10.5 1.0 S A:SCN301 4.6 14.1 1.0 C A:LYS38 4.8 10.8 1.0 N A:GLU40 4.9 9.2 1.0

Cadmium binding site 2 out of 2 in the Bombyx Mori Lipoprotein 7 Isolated From Its Natural Source at 1.33 A Resolution


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Bombyx Mori Lipoprotein 7 Isolated From Its Natural Source at 1.33 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd302 b:10.8 occ:1.00 N B:SCN301 2.3 10.6 1.0 OE2 B:GLU40 2.4 10.7 1.0 O B:LYS37 2.4 12.4 1.0 OE1 B:GLU40 2.5 11.0 1.0 O B:HOH553 2.5 16.1 1.0 CD B:GLU40 2.8 9.8 1.0 C B:SCN301 3.1 11.8 1.0 C B:LYS37 3.4 11.3 1.0 N B:LYS38 4.2 11.4 1.0 CA B:LYS37 4.3 11.6 1.0 CB B:LYS37 4.3 10.8 1.0 CG B:GLU40 4.3 10.9 1.0 CA B:LYS38 4.3 12.0 1.0 N B:SER39 4.4 11.3 1.0 S B:SCN301 4.6 14.5 1.0 O B:HOH474 4.7 22.2 1.0 C B:LYS38 4.8 11.5 1.0 N B:GLU40 4.9 9.7 1.0

A.J.Pietrzyk, S.Panjikar, A.Bujacz, J.Mueller-Dieckmann, M.Lochynska, M.Jaskolski, G.Bujacz. High-Resolution Structure of Bombyx Mori Lipoprotein 7: Crystallographic Determination of the Identity of the Protein and Its Potential Role in Detoxification. Acta Crystallogr.,Sect.D V. 68 1140 2012.
ISSN: ISSN 0907-4449
PubMed: 22948915
DOI: 10.1107/S0907444912021555