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Tin in PDB 3wj4: Crystal Structure of Ppargamma Ligand Binding Domain in Complex with Tributyltin

Protein crystallography data

The structure of Crystal Structure of Ppargamma Ligand Binding Domain in Complex with Tributyltin, PDB code: 3wj4 was solved by S.Harada, Y.Hiromori, S.Fukakusa, K.Kawahara, S.Nakamura, M.Noda, S.Uchiyama, K.Fukui, J.Nishikawa, H.Nagase, Y.Kobayashi, T.Ohkubo, T.Yoshida, T.Nakanishi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.44 / 1.95
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 56.338, 88.286, 57.509, 90.00, 90.68, 90.00
R / Rfree (%) 19.4 / 24.1

Tin Binding Sites:

The binding sites of Tin atom in the Crystal Structure of Ppargamma Ligand Binding Domain in Complex with Tributyltin (pdb code 3wj4). This binding sites where shown within 5.0 Angstroms radius around Tin atom.
In total 3 binding sites of Tin where determined in the Crystal Structure of Ppargamma Ligand Binding Domain in Complex with Tributyltin, PDB code: 3wj4:
Jump to Tin binding site number: 1; 2; 3;

Tin binding site 1 out of 3 in 3wj4

Go back to Tin Binding Sites List in 3wj4
Tin binding site 1 out of 3 in the Crystal Structure of Ppargamma Ligand Binding Domain in Complex with Tributyltin


Mono view


Stereo pair view

A full contact list of Tin with other atoms in the Sn binding site number 1 of Crystal Structure of Ppargamma Ligand Binding Domain in Complex with Tributyltin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sn501

b:42.6
occ:1.00
SN1 A:TBY501 0.0 42.6 1.0
C6 A:TBY501 1.8 44.2 1.0
C2 A:TBY501 1.8 42.6 1.0
C10 A:TBY501 1.8 46.1 1.0
SG A:CYS285 2.6 40.3 1.0
C3 A:TBY501 2.8 41.2 1.0
C11 A:TBY501 2.8 45.3 1.0
C7 A:TBY501 2.9 44.3 1.0
CB A:CYS285 3.4 35.1 1.0
C8 A:TBY501 3.6 44.7 1.0
C4 A:TBY501 3.7 41.4 1.0
SD A:MET364 3.8 49.5 1.0
CG A:MET364 4.1 44.3 1.0
C9 A:TBY501 4.1 45.1 1.0
C12 A:TBY501 4.2 45.8 1.0
CA A:CYS285 4.7 34.6 1.0
CE A:MET364 4.9 45.1 1.0
C5 A:TBY501 4.9 41.3 1.0

Tin binding site 2 out of 3 in 3wj4

Go back to Tin Binding Sites List in 3wj4
Tin binding site 2 out of 3 in the Crystal Structure of Ppargamma Ligand Binding Domain in Complex with Tributyltin


Mono view


Stereo pair view

A full contact list of Tin with other atoms in the Sn binding site number 2 of Crystal Structure of Ppargamma Ligand Binding Domain in Complex with Tributyltin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Sn501

b:27.1
occ:0.50
SN1 B:TBY501 0.0 27.1 0.5
C2 B:TBY501 1.8 21.2 0.5
C6 B:TBY501 1.8 25.2 0.5
C10 B:TBY501 1.8 24.8 0.5
SG B:CYS285 2.1 20.0 0.5
SN1 B:TBY501 2.4 28.2 0.3
C6 B:TBY501 2.6 22.9 0.3
SG B:CYS285 2.6 22.9 0.5
C3 B:TBY501 2.7 17.7 0.5
C11 B:TBY501 2.7 22.8 0.5
C7 B:TBY501 2.7 27.7 0.5
C12 B:TBY501 2.8 23.3 0.3
C11 B:TBY501 2.9 24.9 0.3
C13 B:TBY501 2.9 21.5 0.3
C8 B:TBY501 3.1 27.6 0.5
CB B:CYS285 3.1 19.8 0.5
C10 B:TBY501 3.2 24.3 0.3
C4 B:TBY501 3.2 7.0 0.5
CB B:CYS285 3.2 20.3 0.5
C12 B:TBY501 3.2 18.6 0.5
C5 B:TBY501 3.8 15.2 0.5
SD B:MET364 3.9 34.3 1.0
C2 B:TBY501 4.0 21.5 0.3
C7 B:TBY501 4.0 20.7 0.3
CA B:CYS285 4.3 20.0 0.5
CA B:CYS285 4.3 20.4 0.5
CG B:MET364 4.4 30.4 1.0
C3 B:TBY501 4.6 16.1 0.3
C9 B:TBY501 4.6 29.9 0.5
C13 B:TBY501 4.6 18.1 0.5
CE B:MET364 4.8 31.4 1.0
C4 B:TBY501 5.0 7.8 0.3
OH B:TYR327 5.0 28.7 1.0
C8 B:TBY501 5.0 18.4 0.3

Tin binding site 3 out of 3 in 3wj4

Go back to Tin Binding Sites List in 3wj4
Tin binding site 3 out of 3 in the Crystal Structure of Ppargamma Ligand Binding Domain in Complex with Tributyltin


Mono view


Stereo pair view

A full contact list of Tin with other atoms in the Sn binding site number 3 of Crystal Structure of Ppargamma Ligand Binding Domain in Complex with Tributyltin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Sn501

b:28.2
occ:0.35
SN1 B:TBY501 0.0 28.2 0.3
C2 B:TBY501 1.1 21.2 0.5
C10 B:TBY501 1.8 24.3 0.3
C2 B:TBY501 1.8 21.5 0.3
C6 B:TBY501 1.8 22.9 0.3
C3 B:TBY501 2.1 17.7 0.5
SN1 B:TBY501 2.4 27.1 0.5
SG B:CYS285 2.5 20.0 0.5
C7 B:TBY501 2.6 20.7 0.3
C11 B:TBY501 2.7 24.9 0.3
C3 B:TBY501 2.8 16.1 0.3
C10 B:TBY501 2.9 24.8 0.5
C13 B:TBY501 3.0 21.5 0.3
SG B:CYS285 3.2 22.9 0.5
C12 B:TBY501 3.3 23.3 0.3
C4 B:TBY501 3.4 7.8 0.3
C4 B:TBY501 3.4 7.0 0.5
CB B:CYS285 3.6 19.8 0.5
CB B:CYS285 3.7 20.3 0.5
C6 B:TBY501 3.8 25.2 0.5
CA B:CYS285 4.0 20.0 0.5
CA B:CYS285 4.0 20.4 0.5
C8 B:TBY501 4.0 18.4 0.3
C11 B:TBY501 4.3 22.8 0.5
C5 B:TBY501 4.4 15.2 0.5
C5 B:TBY501 4.6 5.1 0.3
O B:HOH682 4.7 31.9 1.0
C7 B:TBY501 4.7 27.7 0.5
N B:CYS285 4.8 19.5 1.0
C12 B:TBY501 4.8 18.6 0.5

Reference:

S.Harada, Y.Hiromori, S.Fukakusa, K.Kawahara, S.Nakamura, M.Noda, S.Uchiyama, K.Fukui, J.Nishikawa, H.Nagase, Y.Kobayashi, T.Ohkubo, T.Yoshida, T.Nakanishi. Structural Basis For Ppargamma Transactivation By Endocrine Disrupting Organotin Compounds To Be Published.
Page generated: Wed Dec 16 02:10:17 2020

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