Iodine in PDB 4lnx: Crystal Structure of Tr-Alpha Bound to T4 in A Second Site

The structure of Crystal Structure of Tr-Alpha Bound to T4 in A Second Site, PDB code: 4lnx was solved by A.C.Puhl, R.Aparicio, I.Polikarpov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.60 / 2.05
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	59.744, 80.924, 101.871, 90.00, 90.00, 90.00
R / Rfree (%)	15.5 / 17.7

The structure of Crystal Structure of Tr-Alpha Bound to T4 in A Second Site also contains other interesting chemical elements:

Arsenic

(As)

4 atoms

The binding sites of Iodine atom in the Crystal Structure of Tr-Alpha Bound to T4 in A Second Site (pdb code 4lnx). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 7 binding sites of Iodine where determined in the Crystal Structure of Tr-Alpha Bound to T4 in A Second Site, PDB code: 4lnx:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7;

Iodine binding site 1 out of 7 in the Crystal Structure of Tr-Alpha Bound to T4 in A Second Site


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 Tr-Alpha Bound to T4 in A Second Site within 5.0Å range: probe atom residue distance (Å) B Occ A:I501 b:24.0 occ:0.40 I3 A:T44501 0.0 24.0 0.4 C3 A:T44501 2.1 42.7 0.6 C2 A:T44501 3.1 41.7 0.9 C4 A:T44501 3.1 43.2 0.8 O4 A:T44501 3.4 47.1 0.9 C1' A:T44501 3.8 50.6 0.8 C2' A:T44501 4.0 52.5 0.8 C5 A:T44501 4.4 40.2 0.6 C1 A:T44501 4.4 41.5 0.7 C6' A:T44501 4.7 52.8 0.7 C6 A:T44501 4.9 39.6 1.0 C3' A:T44501 5.0 56.8 0.8

Iodine binding site 2 out of 7 in the Crystal Structure of Tr-Alpha Bound to T4 in A Second Site


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 Tr-Alpha Bound to T4 in A Second Site within 5.0Å range: probe atom residue distance (Å) B Occ A:I501 b:61.9 occ:0.37 I3' A:T44501 0.0 61.9 0.4 C3' A:T44501 2.1 56.8 0.8 C4' A:T44501 2.9 57.9 0.8 O4' A:T44501 3.0 61.5 1.0 C2' A:T44501 3.1 52.5 0.8 O A:HOH614 3.7 48.1 1.0 O A:HOH833 4.2 32.6 1.0 C5' A:T44501 4.2 56.7 0.6 C1' A:T44501 4.4 50.6 0.8 C6' A:T44501 4.8 52.8 0.7

Iodine binding site 3 out of 7 in the Crystal Structure of Tr-Alpha Bound to T4 in A Second Site


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 Tr-Alpha Bound to T4 in A Second Site within 5.0Å range: probe atom residue distance (Å) B Occ A:I501 b:24.2 occ:0.40 I5 A:T44501 0.0 24.2 0.4 C5 A:T44501 2.1 40.2 0.6 C4 A:T44501 3.0 43.2 0.8 O4 A:T44501 3.0 47.1 0.9 C6 A:T44501 3.1 39.6 1.0 O A:LEU368 3.2 23.4 1.0 C1' A:T44501 3.5 50.6 0.8 CG2 A:THR372 3.6 33.1 0.4 OG1 A:THR372 3.6 33.7 0.6 O A:HOH833 3.8 32.6 1.0 CB A:VAL371 3.9 22.5 1.0 C2' A:T44501 4.0 52.5 0.8 CG1 A:VAL371 4.0 22.6 1.0 C A:LEU368 4.0 24.6 1.0 CD2 A:LEU368 4.1 25.2 1.0 CB A:LEU368 4.1 21.4 1.0 C6' A:T44501 4.2 52.8 0.7 CA A:LEU368 4.2 24.6 1.0 C3 A:T44501 4.3 42.7 0.6 N A:THR372 4.3 23.4 1.0 C1 A:T44501 4.4 41.5 0.7 NH1 A:ARG375 4.6 51.1 1.0 CG A:LEU368 4.7 24.5 1.0 CG2 A:VAL371 4.7 25.5 1.0 CB A:THR372 4.8 32.0 0.6 C2 A:T44501 4.8 41.7 0.9 C A:VAL371 4.9 24.7 1.0 CB A:THR372 4.9 31.1 0.4 CA A:VAL371 4.9 20.4 1.0 CA A:THR372 4.9 24.8 0.6 CA A:THR372 5.0 24.2 0.4

Iodine binding site 4 out of 7 in the Crystal Structure of Tr-Alpha Bound to T4 in A Second Site


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Crystal Structure of Tr-Alpha Bound to T4 in A Second Site within 5.0Å range: probe atom residue distance (Å) B Occ A:I501 b:63.2 occ:0.64 I5' A:T44501 0.0 63.2 0.6 C5' A:T44501 2.1 56.7 0.6 C4' A:T44501 3.0 57.9 0.8 O4' A:T44501 3.1 61.5 1.0 C6' A:T44501 3.1 52.8 0.7 SD A:MET369 4.1 42.5 0.5 C3' A:T44501 4.3 56.8 0.8 CE A:MET369 4.4 56.9 0.5 C1' A:T44501 4.4 50.6 0.8 CG2 A:THR372 4.8 33.1 0.4 C2' A:T44501 4.9 52.5 0.8 OG1 A:THR372 4.9 33.7 0.6

Iodine binding site 5 out of 7 in the Crystal Structure of Tr-Alpha Bound to T4 in A Second Site


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Crystal Structure of Tr-Alpha Bound to T4 in A Second Site within 5.0Å range: probe atom residue distance (Å) B Occ A:I502 b:24.5 occ:1.00 I1 A:T3502 0.0 24.5 1.0 C5 A:T3502 2.1 17.8 1.0 C3 A:T3502 3.0 18.3 1.0 O A:PHE218 3.1 21.0 1.0 C7 A:T3502 3.1 19.0 1.0 O2 A:T3502 3.3 20.9 1.0 C2 A:T3502 3.7 19.3 1.0 C A:PHE218 3.8 26.4 1.0 CG1 A:ILE222 3.9 23.4 1.0 CG1 A:ILE221 3.9 26.8 1.0 CB A:ILE222 3.9 23.2 1.0 C4 A:T3502 4.0 16.4 1.0 CB A:PHE218 4.1 21.2 1.0 CA A:PHE218 4.1 26.4 1.0 CD1 A:ILE222 4.2 26.5 1.0 CA A:ILE222 4.2 23.8 1.0 CD1 A:ILE221 4.3 28.8 1.0 CD1 A:LEU276 4.3 18.3 1.0 N A:ILE222 4.4 21.1 1.0 C1 A:T3502 4.4 18.9 1.0 C9 A:T3502 4.4 18.2 1.0 C12 A:T3502 4.5 17.1 1.0 C A:ILE221 4.7 24.4 1.0 CG A:PHE218 4.8 22.5 1.0 N A:THR219 4.9 22.0 1.0 CD2 A:PHE218 4.9 26.3 1.0 C11 A:T3502 4.9 17.3 1.0 CB A:LEU276 4.9 24.1 1.0 C6 A:T3502 5.0 15.5 1.0 O A:ILE221 5.0 27.6 1.0

Iodine binding site 6 out of 7 in the Crystal Structure of Tr-Alpha Bound to T4 in A Second Site


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Crystal Structure of Tr-Alpha Bound to T4 in A Second Site within 5.0Å range: probe atom residue distance (Å) B Occ A:I502 b:27.4 occ:1.00 I2 A:T3502 0.0 27.4 1.0 C6 A:T3502 2.2 15.5 1.0 C8 A:T3502 3.1 18.4 1.0 C4 A:T3502 3.1 16.4 1.0 O1 A:T3502 3.1 16.5 1.0 O A:GLY290 3.4 26.5 1.0 CD1 A:PHE215 4.0 25.5 1.0 CE1 A:PHE215 4.1 26.9 1.0 CA A:GLY291 4.1 20.2 1.0 C A:GLY290 4.3 25.6 1.0 CD2 A:LEU292 4.3 19.8 1.0 C10 A:T3502 4.4 23.5 1.0 C2 A:T3502 4.4 19.3 1.0 C A:GLY291 4.4 24.0 1.0 CG A:LEU292 4.5 19.5 1.0 N A:LEU292 4.5 19.7 1.0 CB A:PHE218 4.5 21.2 1.0 CD1 A:PHE218 4.6 22.3 1.0 N A:GLY291 4.6 23.7 1.0 CE A:MET388 4.8 20.0 1.0 CZ A:PHE401 4.9 30.0 1.0 C12 A:T3502 4.9 17.1 1.0 CG2 A:THR219 5.0 30.2 1.0 CG A:PHE215 5.0 21.2 1.0 CG A:PHE218 5.0 22.5 1.0

Iodine binding site 7 out of 7 in the Crystal Structure of Tr-Alpha Bound to T4 in A Second Site


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Crystal Structure of Tr-Alpha Bound to T4 in A Second Site within 5.0Å range: probe atom residue distance (Å) B Occ A:I502 b:30.2 occ:1.00 I3 A:T3502 0.0 30.2 1.0 C9 A:T3502 2.1 18.2 1.0 C11 A:T3502 3.1 17.3 1.0 C7 A:T3502 3.1 19.0 1.0 O2 A:T3502 3.2 20.9 1.0 CD1 A:ILE299 3.6 19.4 1.0 C2 A:T3502 3.8 19.3 1.0 C12 A:T3502 3.8 17.1 1.0 OG A:SER260 4.1 16.3 0.5 CE A:MET256 4.2 21.3 1.0 CD1 A:LEU292 4.2 16.1 1.0 CA A:SER260 4.2 19.6 1.0 CB A:ALA263 4.2 18.2 1.0 C1 A:T3502 4.4 18.9 1.0 C5 A:T3502 4.4 17.8 1.0 CD2 A:LEU276 4.4 19.9 1.0 O A:MET259 4.6 20.1 1.0 CB A:SER260 4.6 19.8 0.5 N A:SER260 4.6 14.2 1.0 CB A:SER260 4.7 19.5 0.5 C A:MET259 4.8 15.6 1.0 SD A:MET256 4.8 29.9 1.0 CD2 A:LEU287 4.9 23.1 1.0 C3 A:T3502 4.9 18.3 1.0 CG2 A:ILE299 4.9 18.0 1.0 C4 A:T3502 4.9 16.4 1.0 C10 A:T3502 5.0 23.5 1.0 CG1 A:ILE299 5.0 20.6 1.0

P.C.Souza, A.C.Puhl, L.Martinez, R.Aparicio, A.S.Nascimento, A.C.Figueira, P.Nguyen, P.Webb, M.S.Skaf, I.Polikarpov. Identification of A New Hormone-Binding Site on the Surface of Thyroid Hormone Receptor. Mol.Endocrinol. V. 28 534 2014.
ISSN: ISSN 0888-8809
PubMed: 24552590
DOI: 10.1210/ME.2013-1359