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

Protein crystallography data

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

Other elements in 4efq:

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

Potassium (K) 3 atoms

Platinum Binding Sites:

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 4efq

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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 4efq

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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 4efq

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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 4efq

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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 4efq

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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 4efq

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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

Reference:

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
Page generated: Wed Dec 16 02:04:43 2020

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