Iodine in PDB 4zo1: Crystal Structure of the T3-Bound Tr-Beta Ligand-Binding Domain in Complex with Rxr-Alpha

The structure of Crystal Structure of the T3-Bound Tr-Beta Ligand-Binding Domain in Complex with Rxr-Alpha, PDB code: 4zo1 was solved by J.B.Bruning, D.J.Kojetin, E.Matta-Camacho, T.S.Hughes, S.Srinivasan, J.C.Nwachukwu, V.Cavett, J.Nowak, M.J.Chalmers, D.P.Marciano, T.M.Kamenecka, M.Rance, A.I.Shulman, D.J.Mangelsdorf, P.R.Griffin, K.W.Nettles, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	14.93 / 3.22
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	63.252, 63.252, 225.806, 90.00, 90.00, 120.00
R / Rfree (%)	23.6 / 28.1

The binding sites of Iodine atom in the Crystal Structure of the T3-Bound Tr-Beta Ligand-Binding Domain in Complex with Rxr-Alpha (pdb code 4zo1). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 3 binding sites of Iodine where determined in the Crystal Structure of the T3-Bound Tr-Beta Ligand-Binding Domain in Complex with Rxr-Alpha, PDB code: 4zo1:
Jump to Iodine binding site number: 1; 2; 3;

Iodine binding site 1 out of 3 in the Crystal Structure of the T3-Bound Tr-Beta Ligand-Binding Domain in Complex with Rxr-Alpha


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Crystal Structure of the T3-Bound Tr-Beta Ligand-Binding Domain in Complex with Rxr-Alpha within 5.0Å range: probe atom residue distance (Å) B Occ X:I500 b:0.9 occ:1.00 I1 X:T3500 0.0 0.9 1.0 C5 X:T3500 2.1 94.3 1.0 C3 X:T3500 3.1 94.3 1.0 C7 X:T3500 3.1 93.8 1.0 O X:PHE272 3.2 0.8 1.0 O2 X:T3500 3.3 88.7 1.0 C2 X:T3500 3.5 82.3 1.0 CB X:PHE272 3.7 0.8 1.0 C X:PHE272 3.8 0.7 1.0 CA X:PHE272 3.8 0.8 1.0 CB X:ILE276 3.8 0.3 1.0 C4 X:T3500 3.9 79.1 1.0 CG1 X:ILE276 4.1 0.9 1.0 CA X:ILE276 4.1 0.6 1.0 CG1 X:ILE275 4.2 0.9 1.0 C12 X:T3500 4.2 79.5 1.0 CD2 X:PHE272 4.3 0.5 1.0 C1 X:T3500 4.4 94.9 1.0 CD1 X:LEU330 4.4 89.0 1.0 CG X:PHE272 4.4 0.4 1.0 N X:ILE276 4.4 0.9 1.0 C9 X:T3500 4.5 96.3 1.0 CD1 X:ILE276 4.5 0.8 1.0 C X:ILE275 4.7 0.9 1.0 CD1 X:ILE275 4.7 0.3 1.0 C6 X:T3500 4.7 76.5 1.0 O X:ILE275 4.8 0.9 1.0 N X:THR273 4.9 0.1 1.0 C11 X:T3500 4.9 96.5 1.0 CB X:LEU330 5.0 95.4 1.0

Iodine binding site 2 out of 3 in the Crystal Structure of the T3-Bound Tr-Beta Ligand-Binding Domain in Complex with Rxr-Alpha


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Crystal Structure of the T3-Bound Tr-Beta Ligand-Binding Domain in Complex with Rxr-Alpha within 5.0Å range: probe atom residue distance (Å) B Occ X:I500 b:0.1 occ:1.00 I2 X:T3500 0.0 0.1 1.0 C6 X:T3500 2.1 76.5 1.0 C4 X:T3500 3.0 79.1 1.0 C8 X:T3500 3.1 75.5 1.0 O X:GLY344 3.1 0.0 1.0 O1 X:T3500 3.3 74.1 1.0 C X:GLY344 4.0 0.7 1.0 CD1 X:PHE272 4.2 0.9 1.0 SD X:MET442 4.3 0.6 1.0 CD1 X:PHE269 4.3 0.7 1.0 CA X:GLY345 4.3 0.4 1.0 CB X:PHE272 4.3 0.8 1.0 C2 X:T3500 4.3 82.3 1.0 N X:LEU346 4.4 0.0 1.0 C10 X:T3500 4.4 77.4 1.0 N X:GLY345 4.5 0.3 1.0 CG X:LEU346 4.5 89.1 1.0 CE1 X:PHE269 4.6 0.0 1.0 C X:GLY345 4.6 0.2 1.0 CG X:PHE272 4.6 0.4 1.0 CD2 X:LEU346 4.8 86.4 1.0 C12 X:T3500 4.9 79.5 1.0 CE X:MET442 5.0 90.9 1.0

Iodine binding site 3 out of 3 in the Crystal Structure of the T3-Bound Tr-Beta Ligand-Binding Domain in Complex with Rxr-Alpha


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Crystal Structure of the T3-Bound Tr-Beta Ligand-Binding Domain in Complex with Rxr-Alpha within 5.0Å range: probe atom residue distance (Å) B Occ X:I500 b:0.2 occ:1.00 I3 X:T3500 0.0 0.2 1.0 C9 X:T3500 2.1 96.3 1.0 C11 X:T3500 3.1 96.5 1.0 C7 X:T3500 3.1 93.8 1.0 O2 X:T3500 3.3 88.7 1.0 C2 X:T3500 3.9 82.3 1.0 C12 X:T3500 4.0 79.5 1.0 CB X:ALA317 4.1 65.3 1.0 CD1 X:ILE353 4.1 52.7 1.0 CA X:SER314 4.2 58.0 1.0 CE X:MET310 4.2 54.4 1.0 C1 X:T3500 4.4 94.9 1.0 OG X:SER314 4.4 59.7 1.0 O X:MET313 4.5 59.1 1.0 N X:SER314 4.5 59.1 1.0 C5 X:T3500 4.5 94.3 1.0 CD2 X:LEU330 4.5 80.5 1.0 CD1 X:LEU346 4.6 86.4 1.0 C X:MET313 4.6 60.6 1.0 CB X:SER314 4.8 56.7 1.0 CD2 X:LEU341 4.9 93.6 1.0 SD X:MET310 4.9 0.1 1.0 C3 X:T3500 5.0 94.3 1.0

D.J.Kojetin, E.Matta-Camacho, T.S.Hughes, S.Srinivasan, J.C.Nwachukwu, V.Cavett, J.Nowak, M.J.Chalmers, D.P.Marciano, T.M.Kamenecka, A.I.Shulman, M.Rance, P.R.Griffin, J.B.Bruning, K.W.Nettles. Structural Mechanism For Signal Transduction in Rxr Nuclear Receptor Heterodimers. Nat Commun V. 6 8013 2015.
ISSN: ESSN 2041-1723
PubMed: 26289479
DOI: 10.1038/NCOMMS9013