Iodine in PDB 3d57: Tr Variant D355R

The structure of Tr Variant D355R, PDB code: 3d57 was solved by N.Jouravel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.00 / 2.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	55.557, 92.963, 58.808, 90.00, 110.02, 90.00
R / Rfree (%)	21 / 24

The binding sites of Iodine atom in the Tr Variant D355R (pdb code 3d57). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 6 binding sites of Iodine where determined in the Tr Variant D355R, PDB code: 3d57:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6;

Iodine binding site 1 out of 6 in the Tr Variant D355R


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Tr Variant D355R within 5.0Å range: probe atom residue distance (Å) B Occ A:I500 b:19.5 occ:1.00 I1 A:4HY500 0.0 19.5 1.0 C5 A:4HY500 2.1 19.6 1.0 C7 A:4HY500 3.1 21.5 1.0 C3 A:4HY500 3.1 18.4 1.0 O2 A:4HY500 3.2 20.2 1.0 O A:PHE272 3.4 14.2 1.0 C2 A:4HY500 3.8 27.3 1.0 CG1 A:ILE275 3.9 18.6 1.0 CA A:ILE276 4.0 15.7 1.0 CB A:ILE276 4.1 16.9 1.0 CG1 A:ILE276 4.1 19.6 1.0 C4 A:4HY500 4.2 25.6 1.0 C A:PHE272 4.2 19.3 1.0 N A:ILE276 4.2 17.3 1.0 CD1 A:LEU330 4.3 18.0 1.0 CD1 A:ILE275 4.4 20.7 1.0 CA A:PHE272 4.4 20.0 1.0 CD1 A:ILE276 4.4 21.9 1.0 C9 A:4HY500 4.4 19.2 1.0 CB A:PHE272 4.4 20.9 1.0 C A:ILE275 4.5 20.3 1.0 C1 A:4HY500 4.5 20.7 1.0 C12 A:4HY500 4.5 27.3 1.0 O A:ILE275 4.6 18.8 1.0 CD2 A:PHE272 4.7 23.2 1.0 CB A:LEU330 4.7 17.5 1.0 C11 A:4HY500 5.0 19.8 1.0

Iodine binding site 2 out of 6 in the Tr Variant D355R


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Tr Variant D355R within 5.0Å range: probe atom residue distance (Å) B Occ A:I500 b:35.2 occ:1.00 I2 A:4HY500 0.0 35.2 1.0 C6 A:4HY500 2.1 29.3 1.0 C4 A:4HY500 3.0 25.6 1.0 C8 A:4HY500 3.1 28.1 1.0 O1 A:4HY500 3.2 27.9 1.0 O A:GLY344 3.7 23.9 1.0 CD1 A:PHE269 3.9 18.1 1.0 CB A:PHE272 4.0 20.9 1.0 CE1 A:PHE269 4.1 15.8 1.0 CD1 A:PHE272 4.2 22.0 1.0 C2 A:4HY500 4.3 27.3 1.0 CD2 A:LEU346 4.3 23.4 1.0 CG A:PHE272 4.4 23.9 1.0 C10 A:4HY500 4.4 29.3 1.0 CG A:LEU346 4.4 24.5 1.0 C A:GLY344 4.5 21.8 1.0 SD A:MET442 4.5 26.5 1.0 CE A:MET442 4.6 23.3 1.0 CA A:GLY345 4.6 20.4 1.0 N A:LEU346 4.8 23.3 1.0 C A:GLY345 4.9 21.9 1.0 N A:GLY345 4.9 21.5 1.0 C12 A:4HY500 4.9 27.3 1.0 CG A:PHE269 5.0 19.7 1.0

Iodine binding site 3 out of 6 in the Tr Variant D355R


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Tr Variant D355R within 5.0Å range: probe atom residue distance (Å) B Occ A:I500 b:23.6 occ:1.00 I3 A:4HY500 0.0 23.6 1.0 C9 A:4HY500 2.1 19.2 1.0 C7 A:4HY500 3.1 21.5 1.0 C11 A:4HY500 3.1 19.8 1.0 O2 A:4HY500 3.2 20.2 1.0 CD1 A:ILE353 3.7 12.4 1.0 C2 A:4HY500 3.8 27.3 1.0 C12 A:4HY500 3.9 27.3 1.0 CB A:ALA317 4.1 13.0 1.0 CD1 A:LEU346 4.2 24.0 1.0 CD2 A:LEU330 4.4 20.6 1.0 C1 A:4HY500 4.4 20.7 1.0 C5 A:4HY500 4.4 19.6 1.0 CA A:SER314 4.5 9.4 1.0 OG A:SER314 4.6 14.7 1.0 CE A:MET310 4.6 20.5 1.0 CG2 A:ILE353 4.7 15.7 1.0 CD2 A:LEU341 4.8 18.9 1.0 CD1 A:LEU341 4.8 18.5 1.0 C4 A:4HY500 4.9 25.6 1.0 O A:MET313 4.9 8.1 1.0 SD A:MET310 4.9 27.6 1.0 CG1 A:ILE353 4.9 13.8 1.0 N A:SER314 4.9 11.5 1.0 C3 A:4HY500 5.0 18.4 1.0

Iodine binding site 4 out of 6 in the Tr Variant D355R


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Tr Variant D355R within 5.0Å range: probe atom residue distance (Å) B Occ B:I500 b:22.7 occ:1.00 I1 B:4HY500 0.0 22.7 1.0 C5 B:4HY500 2.1 19.7 1.0 C7 B:4HY500 3.1 20.6 1.0 C3 B:4HY500 3.1 19.3 1.0 O2 B:4HY500 3.2 24.1 1.0 O B:PHE272 3.3 28.9 1.0 C2 B:4HY500 3.7 25.5 1.0 CG1 B:ILE275 4.0 24.6 1.0 CG1 B:ILE276 4.1 19.5 1.0 CB B:ILE276 4.1 21.6 1.0 CA B:ILE276 4.1 21.9 1.0 C4 B:4HY500 4.2 25.9 1.0 C B:PHE272 4.2 27.4 1.0 CD1 B:LEU330 4.3 17.9 1.0 O B:ILE275 4.3 23.2 1.0 N B:ILE276 4.4 22.2 1.0 CA B:PHE272 4.4 28.2 1.0 CD1 B:ILE275 4.4 26.7 1.0 C12 B:4HY500 4.4 25.8 1.0 C B:ILE275 4.4 23.4 1.0 C9 B:4HY500 4.5 20.5 1.0 C1 B:4HY500 4.5 18.3 1.0 CD1 B:ILE276 4.5 21.2 1.0 CB B:PHE272 4.5 29.2 1.0 CB B:LEU330 4.6 16.4 1.0 CD2 B:PHE272 4.8 28.8 1.0 ND2 B:ASN331 5.0 22.2 1.0

Iodine binding site 5 out of 6 in the Tr Variant D355R


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Tr Variant D355R within 5.0Å range: probe atom residue distance (Å) B Occ B:I500 b:32.4 occ:1.00 I2 B:4HY500 0.0 32.4 1.0 C6 B:4HY500 2.1 28.6 1.0 C4 B:4HY500 3.0 25.9 1.0 C8 B:4HY500 3.1 26.7 1.0 O1 B:4HY500 3.2 26.3 1.0 CE B:MET442 3.5 29.4 1.0 O B:GLY344 3.6 22.9 1.0 CB B:PHE272 3.9 29.2 1.0 CD1 B:PHE272 3.9 29.0 1.0 CD1 B:PHE269 4.1 25.3 1.0 C B:GLY344 4.1 22.9 1.0 CG B:PHE272 4.2 30.2 1.0 CA B:GLY345 4.2 20.9 1.0 CE1 B:PHE269 4.3 25.2 1.0 C2 B:4HY500 4.3 25.5 1.0 CD2 B:LEU346 4.4 19.9 1.0 C10 B:4HY500 4.4 27.8 1.0 CG B:LEU346 4.4 19.2 1.0 N B:GLY345 4.4 21.8 1.0 N B:LEU346 4.5 19.6 1.0 C B:GLY345 4.6 21.1 1.0 CE1 B:PHE272 4.8 28.3 1.0 C12 B:4HY500 4.9 25.8 1.0

Iodine binding site 6 out of 6 in the Tr Variant D355R


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Tr Variant D355R within 5.0Å range: probe atom residue distance (Å) B Occ B:I500 b:27.0 occ:1.00 I3 B:4HY500 0.0 27.0 1.0 C9 B:4HY500 2.1 20.5 1.0 C11 B:4HY500 3.1 17.8 1.0 C7 B:4HY500 3.2 20.6 1.0 O2 B:4HY500 3.3 24.1 1.0 CD1 B:ILE353 3.6 13.8 1.0 C2 B:4HY500 3.9 25.5 1.0 C12 B:4HY500 4.1 25.8 1.0 CD1 B:LEU346 4.1 20.6 1.0 CB B:ALA317 4.2 12.0 1.0 OG B:SER314 4.3 16.6 1.0 C1 B:4HY500 4.4 18.3 1.0 CD2 B:LEU330 4.4 17.3 1.0 CA B:SER314 4.5 17.5 1.0 C5 B:4HY500 4.5 19.7 1.0 CD2 B:LEU341 4.6 14.1 1.0 CG2 B:ILE353 4.7 7.8 1.0 NE2 B:HIS435 4.9 33.5 1.0 N B:SER314 4.9 18.7 1.0 O B:MET313 4.9 17.7 1.0 CG1 B:ILE353 4.9 12.1 1.0 CD1 B:LEU341 4.9 12.3 1.0 C4 B:4HY500 4.9 25.9 1.0 CB B:SER314 4.9 17.1 1.0 C3 B:4HY500 5.0 19.3 1.0

N.Jouravel, E.Sablin, M.Togashi, J.D.Baxter, P.Webb, R.J.Fletterick. Molecular Basis For Dimer Formation of Trbeta Variant D355R. Proteins V. 75 111 2008.
ISSN: ISSN 0887-3585
PubMed: 18798561
DOI: 10.1002/PROT.22225