Platinum in PDB 4efq: Bombyx Mori Lipoprotein 7 - Platinum Derivative at 1.94 A Resolution

The structure of Bombyx Mori Lipoprotein 7 - Platinum Derivative at 1.94 A Resolution, PDB code: 4efq 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)	54.60 / 1.94
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	41.806, 49.785, 54.958, 93.17, 94.87, 102.86
R / Rfree (%)	18.5 / 22.7

The structure of Bombyx Mori Lipoprotein 7 - Platinum Derivative at 1.94 A Resolution also contains other interesting chemical elements:

Potassium

(K)

3 atoms

The binding sites of Platinum atom in the Bombyx Mori Lipoprotein 7 - Platinum Derivative at 1.94 A Resolution (pdb code 4efq). This binding sites where shown within 5.0 Angstroms radius around Platinum atom.
In total 6 binding sites of Platinum where determined in the Bombyx Mori Lipoprotein 7 - Platinum Derivative at 1.94 A Resolution, PDB code: 4efq:
Jump to Platinum binding site number: 1; 2; 3; 4; 5; 6;

Platinum binding site 1 out of 6 in the Bombyx Mori Lipoprotein 7 - Platinum Derivative at 1.94 A Resolution


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 1 of Bombyx Mori Lipoprotein 7 - Platinum Derivative at 1.94 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Pt304 b:29.1 occ:0.50 SD A:MET217 2.4 17.4 0.5 O A:HOH504 2.4 9.4 1.0 O A:HOH466 2.7 18.8 1.0 SD A:MET217 3.3 21.6 0.5 CG A:MET217 3.4 15.4 0.5 CG A:MET217 3.5 17.0 0.5 CE A:MET217 3.6 16.8 0.5 CG A:GLU211 4.2 21.2 1.0 O A:HOH505 4.2 20.8 1.0 CD A:GLU211 4.3 21.9 1.0 OE2 A:GLU211 4.4 23.4 1.0 O A:HOH463 4.7 9.5 1.0 OE1 A:GLU211 4.7 22.6 1.0 CD1 A:LEU114 4.8 28.1 1.0 CE A:MET217 4.8 22.8 0.5 CB A:MET217 4.9 16.7 0.5 CB A:MET217 4.9 17.1 0.5

Platinum binding site 2 out of 6 in the Bombyx Mori Lipoprotein 7 - Platinum Derivative at 1.94 A Resolution


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 2 of Bombyx Mori Lipoprotein 7 - Platinum Derivative at 1.94 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Pt305 b:22.1 occ:1.00 OE2 A:GLU40 2.1 14.2 0.5 O A:HOH444 2.2 12.5 1.0 N A:SCN301 2.3 19.1 1.0 O A:LYS37 2.4 15.4 1.0 OE1 A:GLU40 2.4 8.6 0.5 OE2 A:GLU40 2.5 9.3 0.5 OE1 A:GLU40 2.6 11.7 0.5 CD A:GLU40 2.7 14.1 0.5 CD A:GLU40 2.8 12.3 0.5 C A:SCN301 3.1 18.9 1.0 C A:LYS37 3.3 15.7 1.0 CB A:LYS37 4.1 15.3 1.0 CA A:LYS37 4.1 15.7 1.0 CG A:GLU40 4.1 16.1 0.5 N A:LYS38 4.2 17.1 1.0 CA A:LYS38 4.3 16.9 1.0 CG A:GLU40 4.3 14.3 0.5 N A:SER39 4.5 17.4 1.0 S A:SCN301 4.6 21.0 1.0 C A:LYS38 4.8 16.5 1.0 N A:GLU40 4.9 16.4 1.0

Platinum binding site 3 out of 6 in the Bombyx Mori Lipoprotein 7 - Platinum Derivative at 1.94 A Resolution


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 3 of Bombyx Mori Lipoprotein 7 - Platinum Derivative at 1.94 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Pt306 b:31.0 occ:0.60 O A:HOH496 2.3 16.5 1.0 CG A:HIS108 2.9 43.5 1.0 ND1 A:HIS108 3.0 47.1 1.0 CD2 A:HIS108 3.1 45.4 1.0 CE1 A:HIS108 3.3 48.8 1.0 CA A:HIS108 3.3 42.0 1.0 NE2 A:HIS108 3.4 46.4 1.0 CB A:HIS108 3.5 41.1 1.0 C A:HIS108 3.9 45.7 1.0 N A:GLY109 4.4 48.1 1.0 O A:VAL107 4.4 36.7 1.0 O A:HIS108 4.5 47.6 1.0 N A:HIS108 4.6 38.4 1.0 C A:VAL107 4.9 36.3 1.0

Platinum binding site 4 out of 6 in the Bombyx Mori Lipoprotein 7 - Platinum Derivative at 1.94 A Resolution


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 4 of Bombyx Mori Lipoprotein 7 - Platinum Derivative at 1.94 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Pt303 b:29.5 occ:0.40 SD B:MET217 2.6 19.2 0.5 SD B:MET217 3.2 20.6 0.5 CD1 B:LEU114 3.3 27.8 1.0 CG B:MET217 3.3 16.7 0.5 CG B:MET217 3.4 16.8 0.5 CE B:MET217 4.3 21.3 0.5 CE B:MET217 4.3 17.6 0.5 CG B:GLU211 4.4 17.0 1.0 CD B:GLU211 4.4 16.5 1.0 OE1 B:GLU211 4.6 17.5 1.0 CG B:LEU114 4.6 24.0 1.0 CD2 B:LEU114 4.7 28.2 1.0 CB B:MET217 4.8 16.2 0.5 CB B:MET217 4.8 16.3 0.5 OE2 B:GLU211 4.8 19.2 1.0

Platinum binding site 5 out of 6 in the Bombyx Mori Lipoprotein 7 - Platinum Derivative at 1.94 A Resolution


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 5 of Bombyx Mori Lipoprotein 7 - Platinum Derivative at 1.94 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Pt304 b:22.3 occ:1.00 N B:SCN301 2.2 18.6 1.0 OE2 B:GLU40 2.3 12.1 1.0 O B:LYS37 2.4 15.8 1.0 O B:HOH502 2.4 8.9 1.0 OE1 B:GLU40 2.7 20.6 1.0 CD B:GLU40 2.8 20.2 1.0 C B:SCN301 3.0 17.2 1.0 C B:LYS37 3.3 17.9 1.0 N B:LYS38 4.1 18.8 1.0 CA B:LYS37 4.2 18.0 1.0 CB B:LYS37 4.2 18.6 1.0 CA B:LYS38 4.3 18.0 1.0 CG B:GLU40 4.4 18.4 1.0 O B:HOH411 4.4 11.3 1.0 O B:HOH473 4.4 18.4 1.0 N B:SER39 4.4 16.6 1.0 S B:SCN301 4.5 18.7 1.0 C B:LYS38 4.8 17.5 1.0 N B:GLU40 4.9 16.0 1.0

Platinum binding site 6 out of 6 in the Bombyx Mori Lipoprotein 7 - Platinum Derivative at 1.94 A Resolution


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 6 of Bombyx Mori Lipoprotein 7 - Platinum Derivative at 1.94 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Pt305 b:30.8 occ:0.50 C B:HIS108 2.8 39.3 1.0 N B:GLY109 2.9 42.1 1.0 O B:HIS108 3.1 40.5 1.0 CA B:HIS108 3.4 34.7 1.0 CA B:GLY109 3.5 46.8 1.0 CB B:HIS108 4.2 33.3 1.0 N B:HIS108 4.6 31.8 1.0 O B:VAL107 4.6 32.3 1.0 C B:GLY109 4.9 47.5 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