Iodine in PDB 5for: Cryptic Tir

The structure of Cryptic Tir, PDB code: 5for was solved by S.Halabi, N.J.Gay, M.C.Moncrieffe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.20 / 2.50
Space group	P 62 2 2
Cell size a, b, c (Å), α, β, γ (°)	135.042, 135.042, 42.912, 90.00, 90.00, 120.00
R / Rfree (%)	18.8 / 24.4

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

Iodine binding site 1 out of 3 in the Cryptic Tir


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Cryptic Tir within 5.0Å range: probe atom residue distance (Å) B Occ A:I1141 b:0.1 occ:0.55 I3 A:I3C1141 0.0 0.1 0.6 C6 A:I3C1141 2.1 48.5 0.6 OE1 A:GLN33 2.8 0.6 1.0 C5 A:I3C1141 3.1 49.3 0.6 C1 A:I3C1141 3.1 60.6 0.6 O8 A:I3C1141 3.2 85.9 0.6 C7 A:I3C1141 3.4 71.7 0.6 N13 A:I3C1141 3.4 30.0 0.6 CD A:GLN33 3.5 0.7 1.0 NE2 A:GLN33 3.6 0.8 1.0 CB A:ARG32 3.9 0.0 1.0 O9 A:I3C1141 4.4 65.2 0.6 C4 A:I3C1141 4.5 66.3 0.6 N A:ARG32 4.5 80.4 1.0 C2 A:I3C1141 4.5 68.0 0.6 OG A:SER31 4.7 66.0 1.0 CA A:ARG32 4.7 89.2 1.0 CG A:GLN33 4.8 97.3 1.0 N A:GLN33 4.8 83.3 1.0 C3 A:I3C1141 5.0 68.4 0.6

Iodine binding site 2 out of 3 in the Cryptic Tir


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Cryptic Tir within 5.0Å range: probe atom residue distance (Å) B Occ A:I1141 b:0.5 occ:0.55 I2 A:I3C1141 0.0 0.5 0.6 C4 A:I3C1141 2.1 66.3 0.6 C3 A:I3C1141 3.0 68.4 0.6 C5 A:I3C1141 3.1 49.3 0.6 O A:SER30 3.2 71.5 1.0 C10 A:I3C1141 3.2 62.1 0.6 N13 A:I3C1141 3.3 30.0 0.6 O12 A:I3C1141 3.5 61.5 0.6 O11 A:I3C1141 3.7 73.3 0.6 C A:SER30 3.9 59.7 1.0 CA A:SER31 4.4 66.9 1.0 C2 A:I3C1141 4.4 68.0 0.6 CB A:SER30 4.5 53.1 1.0 C6 A:I3C1141 4.5 48.5 0.6 N A:SER31 4.5 54.6 1.0 CA A:SER30 4.8 54.6 1.0

Iodine binding site 3 out of 3 in the Cryptic Tir


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Cryptic Tir within 5.0Å range: probe atom residue distance (Å) B Occ A:I1141 b:0.2 occ:0.55 I1 A:I3C1141 0.0 0.2 0.6 C2 A:I3C1141 2.1 68.0 0.6 C3 A:I3C1141 3.0 68.4 0.6 C10 A:I3C1141 3.0 62.1 0.6 O11 A:I3C1141 3.2 73.3 0.6 C1 A:I3C1141 3.3 60.6 0.6 O9 A:I3C1141 3.4 65.2 0.6 CG2 A:VAL131 3.5 67.4 1.0 O12 A:I3C1141 3.5 61.5 0.6 CG1 A:VAL131 3.5 57.4 1.0 C7 A:I3C1141 3.6 71.7 0.6 O A:PRO127 3.8 52.9 1.0 CD1 A:LEU27 3.9 40.5 1.0 C A:PRO127 4.0 48.7 1.0 CA A:GLU128 4.0 62.1 1.0 N A:GLU128 4.1 50.9 1.0 CB A:VAL131 4.1 62.8 1.0 CB A:PRO127 4.3 45.4 1.0 C4 A:I3C1141 4.4 66.3 0.6 OG A:SER31 4.5 66.0 1.0 CB A:SER31 4.6 67.8 1.0 C6 A:I3C1141 4.6 48.5 0.6 O8 A:I3C1141 4.7 85.9 0.6 CB A:GLU128 4.8 71.0 1.0 CA A:PRO127 4.8 47.9 1.0 CG A:LEU27 4.8 50.4 1.0

S.Halabi, E.Sekine, B.Verstak, N.J.Gay, M.C.Moncrieffe. Structure of the Toll/Interleukin-1 Receptor (Tir) Domain of the B-Cell Adaptor That Links Phosphoinositide Metabolism with the Negative Regulation of the Toll-Like Receptor (Tlr) Signalosome. J. Biol. Chem. V. 292 652 2017.
ISSN: ESSN 1083-351X
PubMed: 27909057
DOI: 10.1074/JBC.M116.761528