Iodine in PDB 5cr1: Crystal Structure of Ttr/Resveratrol/T4 Complex

The structure of Crystal Structure of Ttr/Resveratrol/T4 Complex, PDB code: 5cr1 was solved by G.Zanotti, P.Florio, C.Folli, M.Cianci, D.Del Rio, R.Berni, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.82 / 1.55
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	42.536, 85.633, 63.826, 90.00, 90.00, 90.00
R / Rfree (%)	16.6 / 19.3

The binding sites of Iodine atom in the Crystal Structure of Ttr/Resveratrol/T4 Complex (pdb code 5cr1). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 4 binding sites of Iodine where determined in the Crystal Structure of Ttr/Resveratrol/T4 Complex, PDB code: 5cr1:
Jump to Iodine binding site number: 1; 2; 3; 4;

Iodine binding site 1 out of 4 in the Crystal Structure of Ttr/Resveratrol/T4 Complex


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 Ttr/Resveratrol/T4 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:I201 b:27.4 occ:0.40 I3 A:T44201 0.0 27.4 0.4 C3 A:T44201 2.1 55.7 0.4 O A:HOH331 2.6 37.0 1.0 C2 A:T44201 3.0 59.3 0.4 C4 A:T44201 3.0 48.8 0.4 HB2 A:ALA108 3.2 17.6 1.0 HG21 A:VAL121 3.3 26.4 1.0 O4 A:T44201 3.3 43.9 0.4 HG21 A:THR106 3.5 23.7 1.0 HG23 A:VAL121 3.7 26.4 1.0 C1' A:T44201 3.7 39.4 0.4 HG22 A:THR106 3.9 23.7 1.0 CB A:ALA108 3.9 14.7 1.0 CG2 A:VAL121 4.0 22.0 1.0 C2' A:T44201 4.1 37.5 0.4 HB3 A:ALA108 4.1 17.6 1.0 HB1 A:ALA108 4.1 17.6 1.0 CG2 A:THR106 4.2 19.8 1.0 C1 A:T44201 4.3 63.9 0.4 C5 A:T44201 4.3 50.4 0.4 O A:HOH355 4.4 35.2 1.0 HG2 A:LYS15 4.5 25.6 1.0 C6' A:T44201 4.5 43.8 0.4 HB3 A:LYS15 4.6 17.4 1.0 HG22 A:VAL121 4.6 26.4 1.0 HB A:THR106 4.6 21.8 1.0 HB A:VAL121 4.7 21.0 1.0 N8 A:T44201 4.7 54.1 0.4 HG23 A:THR119 4.8 26.7 1.0 C6 A:T44201 4.8 59.2 0.4 HG23 A:THR106 4.9 23.7 1.0 CB A:VAL121 5.0 17.5 1.0

Iodine binding site 2 out of 4 in the Crystal Structure of Ttr/Resveratrol/T4 Complex


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 Ttr/Resveratrol/T4 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:I201 b:0.7 occ:0.40 I3' A:T44201 0.0 0.7 0.4 C3' A:T44201 2.1 42.8 0.4 C2' A:T44201 3.0 37.5 0.4 C4' A:T44201 3.0 39.0 0.4 O4' A:T44201 3.2 13.3 0.4 C1' A:T44201 4.3 39.4 0.4 C5' A:T44201 4.3 44.8 0.4 C6' A:T44201 4.8 43.8 0.4

Iodine binding site 3 out of 4 in the Crystal Structure of Ttr/Resveratrol/T4 Complex


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 Ttr/Resveratrol/T4 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:I201 b:29.3 occ:0.40 I5 A:T44201 0.0 29.3 0.4 C5 A:T44201 2.1 50.4 0.4 HE2 A:LYS15 2.7 47.9 1.0 HD11 A:LEU17 2.9 28.2 1.0 C6 A:T44201 3.0 59.2 0.4 C4 A:T44201 3.0 48.8 0.4 O4 A:T44201 3.1 43.9 0.4 HD21 A:LEU17 3.4 24.4 1.0 CE A:LYS15 3.5 39.9 1.0 HZ1 A:LYS15 3.5 41.4 1.0 HE3 A:LYS15 3.7 47.9 1.0 O A:HOH341 3.8 40.2 1.0 CD1 A:LEU17 3.8 23.5 1.0 C1' A:T44201 3.8 39.4 0.4 NZ A:LYS15 3.9 34.5 1.0 HZ3 A:LYS15 4.1 41.4 1.0 HG2 A:LYS15 4.2 25.6 1.0 CD2 A:LEU17 4.2 20.4 1.0 HD13 A:LEU17 4.2 28.2 1.0 C2' A:T44201 4.3 37.5 0.4 C1 A:T44201 4.3 63.9 0.4 C3 A:T44201 4.3 55.7 0.4 HD12 A:LEU17 4.3 28.2 1.0 HG A:LEU17 4.4 19.2 1.0 CG A:LEU17 4.4 16.0 1.0 HD22 A:LEU17 4.6 24.4 1.0 C6' A:T44201 4.7 43.8 0.4 HZ2 A:LYS15 4.7 41.4 1.0 CD A:LYS15 4.7 35.4 1.0 CG A:LYS15 4.8 21.3 1.0 C2 A:T44201 4.8 59.3 0.4 HG3 A:LYS15 4.9 25.6 1.0 HD23 A:LEU17 4.9 24.4 1.0

Iodine binding site 4 out of 4 in the Crystal Structure of Ttr/Resveratrol/T4 Complex


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 Ttr/Resveratrol/T4 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:I201 b:0.7 occ:0.40 I5' A:T44201 0.0 0.7 0.4 C5' A:T44201 2.1 44.8 0.4 HB2 A:LEU110 2.2 16.2 1.0 C6' A:T44201 3.0 43.8 0.4 CB A:LEU110 3.0 13.5 1.0 C4' A:T44201 3.0 39.0 0.4 N A:LEU110 3.1 11.9 1.0 HB3 A:LEU110 3.2 16.2 1.0 C A:ALA109 3.2 13.5 1.0 O4' A:T44201 3.3 13.3 0.4 H A:LEU110 3.3 14.3 1.0 CA A:LEU110 3.4 10.8 1.0 HA A:LEU110 3.6 13.0 1.0 HA A:ALA109 3.6 14.2 1.0 O A:ALA109 3.6 14.9 1.0 HB1 A:ALA108 3.6 17.6 1.0 CA A:ALA109 3.8 11.8 1.0 N A:ALA109 3.8 12.4 1.0 HD12 A:LEU17 3.9 28.2 1.0 H A:ALA109 4.0 14.9 1.0 HD22 A:LEU110 4.0 21.7 1.0 HD13 A:LEU110 4.0 16.2 1.0 HB2 A:LEU17 4.1 15.4 1.0 CG A:LEU110 4.2 12.6 1.0 C A:ALA108 4.2 15.7 1.0 C1' A:T44201 4.3 39.4 0.4 HB3 A:ALA108 4.3 17.6 1.0 C3' A:T44201 4.3 42.8 0.4 CB A:ALA108 4.4 14.7 1.0 O A:SER117 4.4 17.4 1.0 HB3 A:SER117 4.4 20.9 0.8 HB2 A:SER117 4.5 22.3 0.2 CD1 A:LEU110 4.5 13.5 1.0 CD2 A:LEU110 4.5 18.1 1.0 HG22 A:THR119 4.6 26.7 1.0 O A:ALA108 4.7 16.6 1.0 HD12 A:LEU110 4.7 16.2 1.0 HA A:THR118 4.7 17.4 1.0 HG A:LEU17 4.7 19.2 1.0 HD23 A:LEU110 4.7 21.7 1.0 H A:LEU17 4.7 15.1 1.0 CD1 A:LEU17 4.8 23.5 1.0 C2' A:T44201 4.8 37.5 0.4 C A:LEU110 4.9 12.3 1.0 CA A:ALA108 4.9 14.2 1.0 HG A:LEU110 5.0 15.1 1.0

P.Florio, C.Folli, M.Cianci, D.Del Rio, G.Zanotti, R.Berni. Transthyretin Binding Heterogeneity and Anti-Amyloidogenic Activity of Natural Polyphenols and Their Metabolites. J.Biol.Chem. V. 290 29769 2015.
ISSN: ESSN 1083-351X
PubMed: 26468275
DOI: 10.1074/JBC.M115.690172