Iodine in PDB 5c5a: Crystal Structure of HDM2 in Complex with Nutlin-3A

The structure of Crystal Structure of HDM2 in Complex with Nutlin-3A, PDB code: 5c5a was solved by J.Orts, M.A.Waelti, M.Marsh, L.Vera, A.D.Gossert, P.Guentert, R.Riek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.62 / 1.15
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	41.620, 43.630, 52.670, 90.00, 90.04, 90.00
R / Rfree (%)	15.3 / 16.8

The structure of Crystal Structure of HDM2 in Complex with Nutlin-3A also contains other interesting chemical elements:

Chlorine

(Cl)

6 atoms

The binding sites of Iodine atom in the Crystal Structure of HDM2 in Complex with Nutlin-3A (pdb code 5c5a). 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 HDM2 in Complex with Nutlin-3A, PDB code: 5c5a:
Jump to Iodine binding site number: 1; 2; 3; 4;

Iodine binding site 1 out of 4 in the Crystal Structure of HDM2 in Complex with Nutlin-3A


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 HDM2 in Complex with Nutlin-3A within 5.0Å range: probe atom residue distance (Å) B Occ A:I204 b:15.4 occ:0.43 H A:THR26 2.8 14.3 1.0 H A:LYS51 2.8 17.9 1.0 HA A:GLU25 3.0 18.2 1.0 HB3 A:LYS51 3.2 27.4 1.0 HG2 A:LYS51 3.2 32.2 1.0 HB A:THR49 3.2 18.2 1.0 HE3 A:LYS51 3.2 36.6 1.0 HB3 A:MET50 3.4 15.2 1.0 N A:LYS51 3.6 14.9 1.0 N A:THR26 3.6 11.9 1.0 HG3 A:GLU25 3.6 27.3 1.0 H A:MET50 3.7 14.5 1.0 CA A:GLU25 3.8 15.1 1.0 CB A:LYS51 3.9 22.8 1.0 CG A:LYS51 3.9 26.9 1.0 CE A:LYS51 4.0 30.5 1.0 N A:MET50 4.1 12.1 1.0 CB A:THR49 4.2 15.2 1.0 HE2 A:LYS51 4.2 36.6 1.0 C A:GLU25 4.2 12.6 1.0 CA A:LYS51 4.3 16.4 1.0 HB A:THR26 4.3 15.3 1.0 CB A:MET50 4.3 12.7 1.0 HB2 A:GLU25 4.4 21.7 1.0 O A:THR26 4.4 14.7 1.0 CG A:GLU25 4.4 22.8 1.0 CB A:GLU25 4.4 18.1 1.0 CD A:LYS51 4.4 28.8 1.0 OG1 A:THR49 4.5 16.1 1.0 C A:MET50 4.5 13.0 1.0 CA A:MET50 4.5 12.8 1.0 HD2 A:LYS51 4.6 34.6 1.0 CA A:THR26 4.7 11.7 1.0 HB2 A:LYS51 4.7 27.4 1.0 HG3 A:LYS51 4.7 32.2 1.0 HA A:LYS51 4.8 19.6 1.0 HG2 A:GLU25 4.8 27.3 1.0 HB2 A:MET50 4.8 15.2 1.0 HG23 A:THR49 4.8 18.2 1.0 O A:HOH315 4.9 23.1 1.0 C A:THR49 4.9 11.7 1.0 CB A:THR26 4.9 12.7 1.0 N A:GLU25 4.9 14.5 1.0 O A:GLN24 4.9 15.8 1.0 C A:THR26 5.0 13.2 1.0 CG2 A:THR49 5.0 15.2 1.0

Iodine binding site 2 out of 4 in the Crystal Structure of HDM2 in Complex with Nutlin-3A


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 HDM2 in Complex with Nutlin-3A within 5.0Å range: probe atom residue distance (Å) B Occ B:I204 b:14.6 occ:0.42 H B:THR26 2.8 15.2 1.0 H B:LYS51 2.9 18.2 1.0 HA B:GLU25 2.9 18.4 1.0 HB3 B:LYS51 3.0 28.2 1.0 HE3 B:LYS51 3.2 35.4 1.0 HB B:THR49 3.3 17.7 1.0 HB3 B:MET50 3.4 18.3 1.0 HG2 B:LYS51 3.4 32.4 1.0 HG3 B:GLU25 3.6 27.2 1.0 N B:LYS51 3.6 15.2 1.0 O B:HOH319 3.6 21.5 1.0 N B:THR26 3.6 12.7 1.0 H B:MET50 3.7 15.1 1.0 O B:HOH348 3.8 43.6 1.0 CA B:GLU25 3.8 15.4 1.0 CB B:LYS51 3.8 23.5 1.0 CE B:LYS51 4.0 29.5 1.0 CG B:LYS51 4.0 27.0 1.0 N B:MET50 4.2 12.6 1.0 CB B:THR49 4.2 14.8 1.0 HE2 B:LYS51 4.2 35.4 1.0 C B:GLU25 4.2 13.5 1.0 CA B:LYS51 4.3 16.8 1.0 CB B:MET50 4.3 15.2 1.0 HB B:THR26 4.3 15.9 1.0 CG B:GLU25 4.4 22.7 1.0 O B:THR26 4.4 13.6 1.0 HB2 B:GLU25 4.4 22.5 1.0 CB B:GLU25 4.4 18.7 1.0 CD B:LYS51 4.4 28.0 1.0 OG1 B:THR49 4.4 14.9 1.0 O B:HOH380 4.4 47.7 1.0 HD2 B:LYS51 4.5 33.6 1.0 C B:MET50 4.5 13.0 1.0 CA B:MET50 4.6 13.5 1.0 HB2 B:LYS51 4.6 28.2 1.0 CA B:THR26 4.7 12.1 1.0 HB2 B:MET50 4.7 18.3 1.0 HG2 B:GLU25 4.7 27.2 1.0 HA B:LYS51 4.8 20.1 1.0 O B:GLN24 4.9 16.1 1.0 N B:GLU25 4.9 13.1 1.0 HG23 B:THR49 4.9 19.1 1.0 HG3 B:LYS51 4.9 32.4 1.0 C B:THR49 4.9 11.5 1.0 CB B:THR26 4.9 13.3 1.0

Iodine binding site 3 out of 4 in the Crystal Structure of HDM2 in Complex with Nutlin-3A


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 HDM2 in Complex with Nutlin-3A within 5.0Å range: probe atom residue distance (Å) B Occ B:I205 b:25.1 occ:0.94 HG3 B:LYS51 3.2 32.4 1.0 HB2 B:GLU52 3.4 22.4 1.0 HA B:GLU52 3.8 16.0 1.0 CG B:LYS51 3.9 27.0 1.0 HD2 B:LYS51 4.0 33.6 1.0 HD3 B:LYS51 4.0 33.6 1.0 HG2 B:LYS51 4.0 32.4 1.0 CD B:LYS51 4.2 28.0 1.0 CB B:GLU52 4.2 18.6 1.0 CA B:GLU52 4.3 13.3 1.0 HG3 B:GLU52 4.3 23.5 1.0 N B:GLU52 4.4 13.9 1.0 HG1 B:THR49 4.4 17.9 1.0 H B:GLU52 4.5 16.7 1.0 OG1 B:THR49 4.6 14.9 1.0 CG B:GLU52 4.7 19.6 1.0 C B:LYS51 4.9 13.7 1.0 HB3 B:GLU52 5.0 22.4 1.0

Iodine binding site 4 out of 4 in the Crystal Structure of HDM2 in Complex with Nutlin-3A


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 HDM2 in Complex with Nutlin-3A within 5.0Å range: probe atom residue distance (Å) B Occ B:I206 b:24.1 occ:0.84 H B:LEU33 2.9 14.5 1.0 HD2 B:PRO32 3.0 15.1 1.0 HB3 B:LYS31 3.1 17.3 1.0 HG3 A:LYS51 3.2 32.2 1.0 HG B:LEU33 3.3 21.4 1.0 HB2 B:LEU33 3.4 17.4 1.0 O A:HOH315 3.5 23.1 1.0 HE2 B:LYS31 3.6 23.3 1.0 HD11 B:LEU33 3.6 23.7 1.0 HB2 A:GLU52 3.7 21.7 1.0 HB2 B:PRO32 3.7 17.3 1.0 N B:LEU33 3.7 12.1 1.0 HA A:GLU52 3.8 15.0 1.0 CD B:PRO32 3.9 12.6 1.0 HD2 A:LYS51 3.9 34.6 1.0 CG B:LEU33 4.0 17.9 1.0 CB B:LYS31 4.0 14.4 1.0 CG A:LYS51 4.0 26.9 1.0 CB B:LEU33 4.0 14.5 1.0 HD3 A:LYS51 4.0 34.6 1.0 N B:PRO32 4.1 11.4 1.0 HB2 B:LYS31 4.1 17.3 1.0 CD1 B:LEU33 4.2 19.7 1.0 CD A:LYS51 4.2 28.8 1.0 HG2 A:LYS51 4.3 32.2 1.0 HG3 A:GLU52 4.3 23.5 1.0 CA A:GLU52 4.3 12.5 1.0 CB A:GLU52 4.4 18.1 1.0 HG2 B:PRO32 4.4 17.4 1.0 CB B:PRO32 4.4 14.4 1.0 HG1 A:THR49 4.4 19.3 1.0 N A:GLU52 4.4 12.2 1.0 H A:GLU52 4.5 14.7 1.0 CA B:LEU33 4.5 12.9 1.0 CG B:PRO32 4.5 14.5 1.0 CE B:LYS31 4.5 19.4 1.0 HD13 B:LEU33 4.6 23.7 1.0 CA B:PRO32 4.6 12.0 1.0 C B:PRO32 4.6 12.6 1.0 C B:LYS31 4.6 10.3 1.0 OG1 A:THR49 4.6 16.1 1.0 HD3 B:PRO32 4.6 15.1 1.0 CG A:GLU52 4.8 19.6 1.0 H B:LEU34 4.8 12.1 1.0 HE3 B:LYS31 4.9 23.3 1.0 HB3 B:LEU33 4.9 17.4 1.0 CA B:LYS31 4.9 10.5 1.0 C A:LYS51 4.9 12.5 1.0 CG B:LYS31 4.9 16.8 1.0 HG2 B:LYS31 4.9 20.1 1.0 O B:HOH309 5.0 24.9 1.0

J.Orts, M.A.Waelti, M.Marsh, L.Vera, A.D.Gossert, P.Guentert, R.Riek. uc(Nmr) Molecular Replacement, NMR2 To Be Published.