Iodine in PDB 5hk2: Human Sigma-1 Receptor Bound to 4-Ibp

The structure of Human Sigma-1 Receptor Bound to 4-Ibp, PDB code: 5hk2 was solved by H.R.Schmidt, S.Zheng, E.G.Gurpinar, A.Koehl, A.Manglik, A.C.Kruse, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.60 / 3.20
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	85.700, 126.800, 110.800, 90.00, 90.00, 90.00
R / Rfree (%)	21.8 / 26.1

The binding sites of Iodine atom in the Human Sigma-1 Receptor Bound to 4-Ibp (pdb code 5hk2). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 3 binding sites of Iodine where determined in the Human Sigma-1 Receptor Bound to 4-Ibp, PDB code: 5hk2:
Jump to Iodine binding site number: 1; 2; 3;

Iodine binding site 1 out of 3 in the Human Sigma-1 Receptor Bound to 4-Ibp


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Human Sigma-1 Receptor Bound to 4-Ibp within 5.0Å range: probe atom residue distance (Å) B Occ A:I301 b:0.4 occ:1.00 IAP A:61V301 0.0 0.4 1.0 CAM A:61V301 2.1 0.2 1.0 CAL A:61V301 3.0 0.1 1.0 CAN A:61V301 3.0 0.8 1.0 CD1 A:TYR206 3.6 87.5 1.0 CG A:TYR206 3.6 85.6 1.0 CE1 A:TYR206 3.9 84.8 1.0 CG2 A:ILE178 3.9 78.0 1.0 CD2 A:TYR206 4.0 85.8 1.0 CB A:TYR206 4.2 80.9 1.0 CZ A:TYR206 4.2 82.3 1.0 CE2 A:TYR206 4.3 85.2 1.0 CAK A:61V301 4.3 0.0 1.0 CAO A:61V301 4.4 1.0 1.0 CAJ A:61V301 4.9 0.4 1.0 CB A:ALA98 4.9 86.4 1.0 CD2 A:LEU182 4.9 96.5 1.0 CD2 A:LEU95 4.9 82.0 1.0 CA A:TYR206 4.9 79.2 1.0

Iodine binding site 2 out of 3 in the Human Sigma-1 Receptor Bound to 4-Ibp


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Human Sigma-1 Receptor Bound to 4-Ibp within 5.0Å range: probe atom residue distance (Å) B Occ B:I301 b:0.6 occ:1.00 IAP B:61V301 0.0 0.6 1.0 CAM B:61V301 2.1 77.7 1.0 CAN B:61V301 3.0 78.0 1.0 CAL B:61V301 3.0 76.9 1.0 CD1 B:TYR200 3.6 45.5 1.0 CD1 B:LEU176 3.9 53.0 1.0 CE1 B:TYR200 3.9 44.9 1.0 CG B:TYR200 3.9 41.3 1.0 CG2 B:ILE172 4.1 32.1 1.0 CAO B:61V301 4.3 77.0 1.0 CAK B:61V301 4.4 75.3 1.0 CD2 B:LEU89 4.4 42.9 1.0 CB B:TYR200 4.4 39.2 1.0 CZ B:TYR200 4.5 45.7 1.0 CD2 B:TYR200 4.5 40.5 1.0 CD1 B:LEU89 4.6 41.3 1.0 CB B:ALA92 4.6 38.0 1.0 CB B:TYR97 4.7 30.1 1.0 CE2 B:TYR200 4.8 42.2 1.0 CAJ B:61V301 4.9 76.4 1.0 CA B:TYR200 4.9 43.7 1.0 CG B:LEU176 5.0 55.3 1.0 CG B:TYR97 5.0 39.1 1.0

Iodine binding site 3 out of 3 in the Human Sigma-1 Receptor Bound to 4-Ibp


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Human Sigma-1 Receptor Bound to 4-Ibp within 5.0Å range: probe atom residue distance (Å) B Occ C:I301 b:0.6 occ:1.00 IAP C:61V301 0.0 0.6 1.0 CAM C:61V301 2.1 81.6 1.0 CAN C:61V301 3.0 81.2 1.0 CAL C:61V301 3.0 83.8 1.0 CD1 C:TYR206 3.5 57.2 1.0 CE1 C:TYR206 3.7 58.3 1.0 CG2 C:ILE178 3.9 62.4 1.0 CD2 C:LEU182 4.0 68.8 1.0 CG C:TYR206 4.1 54.3 1.0 CAO C:61V301 4.3 81.1 1.0 CD2 C:LEU95 4.3 61.2 1.0 CAK C:61V301 4.3 83.1 1.0 CZ C:TYR206 4.4 59.9 1.0 CD1 C:LEU95 4.4 57.0 1.0 CB C:ALA98 4.4 49.8 1.0 CB C:TYR206 4.6 53.8 1.0 CB C:TYR103 4.7 53.6 1.0 CD2 C:TYR206 4.7 54.5 1.0 CG C:LEU182 4.8 70.2 1.0 CAJ C:61V301 4.8 81.8 1.0 CE2 C:TYR206 4.9 57.9 1.0 CG C:TYR103 4.9 49.5 1.0

H.R.Schmidt, S.Zheng, E.Gurpinar, A.Koehl, A.Manglik, A.C.Kruse. Crystal Structure of the Human Sigma 1 Receptor. Nature V. 532 527 2016.
ISSN: ESSN 1476-4687
PubMed: 27042935
DOI: 10.1038/NATURE17391