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Silicon in PDB 2zy0: Crystal Structure of the Human Rxr Alpha Ligand Binding Domain Bound to A Synthetic Agonist Compound and A Coactivator Peptide

Protein crystallography data

The structure of Crystal Structure of the Human Rxr Alpha Ligand Binding Domain Bound to A Synthetic Agonist Compound and A Coactivator Peptide, PDB code: 2zy0 was solved by Y.Sato, P.Antony, N.Rochel, D.Moras, Structural Genomics Consortium Forresearch On Gene Expression (Sgcges), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 2.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 64.975, 66.850, 110.793, 90.00, 90.00, 90.00
R / Rfree (%) 21.7 / 28.9

Silicon Binding Sites:

The binding sites of Silicon atom in the Crystal Structure of the Human Rxr Alpha Ligand Binding Domain Bound to A Synthetic Agonist Compound and A Coactivator Peptide (pdb code 2zy0). This binding sites where shown within 5.0 Angstroms radius around Silicon atom.
In total 4 binding sites of Silicon where determined in the Crystal Structure of the Human Rxr Alpha Ligand Binding Domain Bound to A Synthetic Agonist Compound and A Coactivator Peptide, PDB code: 2zy0:
Jump to Silicon binding site number: 1; 2; 3; 4;

Silicon binding site 1 out of 4 in 2zy0

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Silicon binding site 1 out of 4 in the Crystal Structure of the Human Rxr Alpha Ligand Binding Domain Bound to A Synthetic Agonist Compound and A Coactivator Peptide


Mono view


Stereo pair view

A full contact list of Silicon with other atoms in the Si binding site number 1 of Crystal Structure of the Human Rxr Alpha Ligand Binding Domain Bound to A Synthetic Agonist Compound and A Coactivator Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Si1

b:40.8
occ:1.00
SI1 A:21P1 0.0 40.8 1.0
C2 A:21P1 1.9 40.5 1.0
C1 A:21P1 1.9 40.8 1.0
C8 A:21P1 1.9 41.2 1.0
C3 A:21P1 1.9 40.7 1.0
C7 A:21P1 2.8 41.1 1.0
C9 A:21P1 2.9 42.0 1.0
SI2 A:21P1 3.0 40.8 1.0
C12 A:21P1 4.1 41.5 1.0
C10 A:21P1 4.2 42.9 1.0
C5 A:21P1 4.3 40.7 1.0
C6 A:21P1 4.3 41.2 1.0
SG A:CYS432 4.4 46.9 1.0
CZ A:PHE313 4.5 39.1 1.0
CG2 A:ILE268 4.6 47.4 1.0
C11 A:21P1 4.6 42.5 1.0
CG2 A:ILE345 4.8 40.8 1.0
CD1 A:PHE346 4.8 39.0 1.0

Silicon binding site 2 out of 4 in 2zy0

Go back to Silicon Binding Sites List in 2zy0
Silicon binding site 2 out of 4 in the Crystal Structure of the Human Rxr Alpha Ligand Binding Domain Bound to A Synthetic Agonist Compound and A Coactivator Peptide


Mono view


Stereo pair view

A full contact list of Silicon with other atoms in the Si binding site number 2 of Crystal Structure of the Human Rxr Alpha Ligand Binding Domain Bound to A Synthetic Agonist Compound and A Coactivator Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Si1

b:40.8
occ:1.00
SI2 A:21P1 0.0 40.8 1.0
C7 A:21P1 1.9 41.1 1.0
C5 A:21P1 1.9 40.7 1.0
C6 A:21P1 1.9 41.2 1.0
C3 A:21P1 1.9 40.7 1.0
C8 A:21P1 2.7 41.2 1.0
C12 A:21P1 2.9 41.5 1.0
SI1 A:21P1 3.0 40.8 1.0
C9 A:21P1 4.1 42.0 1.0
C11 A:21P1 4.1 42.5 1.0
C1 A:21P1 4.2 40.8 1.0
C2 A:21P1 4.3 40.5 1.0
CG2 A:ILE268 4.4 47.4 1.0
CE2 A:PHE439 4.6 45.8 1.0
C10 A:21P1 4.6 42.9 1.0
CG1 A:VAL342 4.6 44.1 1.0
CB A:VAL342 4.8 44.3 1.0
CG2 A:ILE345 4.8 40.8 1.0
CG2 A:VAL342 4.9 43.9 1.0
SG A:CYS432 4.9 46.9 1.0
CD1 A:ILE268 5.0 47.0 1.0

Silicon binding site 3 out of 4 in 2zy0

Go back to Silicon Binding Sites List in 2zy0
Silicon binding site 3 out of 4 in the Crystal Structure of the Human Rxr Alpha Ligand Binding Domain Bound to A Synthetic Agonist Compound and A Coactivator Peptide


Mono view


Stereo pair view

A full contact list of Silicon with other atoms in the Si binding site number 3 of Crystal Structure of the Human Rxr Alpha Ligand Binding Domain Bound to A Synthetic Agonist Compound and A Coactivator Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Si2

b:36.1
occ:1.00
SI1 C:21P2 0.0 36.1 1.0
C1 C:21P2 1.9 36.7 1.0
C8 C:21P2 1.9 37.0 1.0
C2 C:21P2 1.9 36.0 1.0
C3 C:21P2 1.9 36.4 1.0
C7 C:21P2 2.8 37.0 1.0
C9 C:21P2 2.9 37.1 1.0
SI2 C:21P2 3.0 36.6 1.0
C12 C:21P2 4.1 36.9 1.0
C10 C:21P2 4.2 37.8 1.0
C5 C:21P2 4.2 36.6 1.0
C6 C:21P2 4.4 36.4 1.0
CG2 C:ILE268 4.6 50.5 1.0
CZ C:PHE313 4.6 42.4 1.0
SG C:CYS432 4.6 43.4 1.0
C11 C:21P2 4.6 37.5 1.0
CD1 C:PHE346 4.9 33.3 1.0
CG2 C:ILE345 5.0 35.3 1.0
CG2 C:VAL349 5.0 34.2 1.0

Silicon binding site 4 out of 4 in 2zy0

Go back to Silicon Binding Sites List in 2zy0
Silicon binding site 4 out of 4 in the Crystal Structure of the Human Rxr Alpha Ligand Binding Domain Bound to A Synthetic Agonist Compound and A Coactivator Peptide


Mono view


Stereo pair view

A full contact list of Silicon with other atoms in the Si binding site number 4 of Crystal Structure of the Human Rxr Alpha Ligand Binding Domain Bound to A Synthetic Agonist Compound and A Coactivator Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Si2

b:36.6
occ:1.00
SI2 C:21P2 0.0 36.6 1.0
C5 C:21P2 1.9 36.6 1.0
C6 C:21P2 1.9 36.4 1.0
C7 C:21P2 1.9 37.0 1.0
C3 C:21P2 1.9 36.4 1.0
C8 C:21P2 2.8 37.0 1.0
C12 C:21P2 2.9 36.9 1.0
SI1 C:21P2 3.0 36.1 1.0
C9 C:21P2 4.1 37.1 1.0
C11 C:21P2 4.2 37.5 1.0
C1 C:21P2 4.2 36.7 1.0
C2 C:21P2 4.3 36.0 1.0
CG2 C:ILE268 4.4 50.5 1.0
CE2 C:PHE439 4.6 44.0 1.0
C10 C:21P2 4.6 37.8 1.0
CD1 C:ILE268 4.7 49.6 1.0
CG1 C:VAL342 4.9 36.8 1.0
CZ C:PHE439 4.9 43.9 1.0
SG C:CYS432 4.9 43.4 1.0
CB C:VAL342 5.0 36.7 1.0
CG2 C:ILE345 5.0 35.3 1.0

Reference:

W.P.Lippert, C.Burschka, K.Gotz, M.Kaupp, D.Ivanova, C.Gaudon, Y.Sato, P.Antony, N.Rochel, D.Moras, H.Gronemeyer, R.Tacke. Silicon Analogues of the Rxr-Selective Retinoid Agonist SR11237 (BMS649): Chemistry and Biology Chemmedchem V. 4 1143 2009.
ISSN: ISSN 1860-7179
PubMed: 19496083
DOI: 10.1002/CMDC.200900090
Page generated: Wed Dec 16 02:09:28 2020

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