Chlorine 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:

Iodine

(I)

4 atoms

The binding sites of Chlorine 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 Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Crystal Structure of HDM2 in Complex with Nutlin-3A, PDB code: 5c5a:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in the Crystal Structure of HDM2 in Complex with Nutlin-3A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl201 b:10.8 occ:1.00 CL1 A:NUT201 0.0 10.8 1.0 C22 A:NUT201 1.7 9.9 1.0 C21 A:NUT201 2.7 9.6 1.0 C23 A:NUT201 2.7 9.9 1.0 H25 A:NUT201 2.8 11.5 1.0 H24 A:NUT201 2.9 11.9 1.0 HB3 A:LEU57 3.2 9.9 1.0 HD13 A:ILE61 3.3 11.3 1.0 HZ A:PHE91 3.3 13.0 1.0 HG21 A:ILE99 3.4 12.6 1.0 HD11 A:ILE61 3.4 11.3 1.0 HE2 A:PHE86 3.5 15.5 1.0 HE1 A:PHE91 3.5 12.2 1.0 HG22 A:ILE99 3.6 12.6 1.0 HZ A:PHE86 3.6 14.3 1.0 CD1 A:ILE61 3.8 9.4 1.0 CZ A:PHE91 3.9 10.8 1.0 HD12 A:ILE99 3.9 14.4 1.0 HB2 A:LEU57 3.9 9.9 1.0 CG2 A:ILE99 3.9 10.5 1.0 HD13 A:LEU57 4.0 13.6 1.0 C20 A:NUT201 4.0 10.5 1.0 C24 A:NUT201 4.0 11.1 1.0 CE1 A:PHE91 4.0 10.2 1.0 CB A:LEU57 4.0 8.3 1.0 HD12 A:ILE61 4.1 11.3 1.0 HG12 A:ILE99 4.1 13.4 1.0 CE2 A:PHE86 4.2 12.9 1.0 HD12 A:ILE103 4.2 11.4 1.0 CZ A:PHE86 4.2 11.9 1.0 HA2 A:GLY58 4.5 10.6 1.0 C19 A:NUT201 4.5 11.5 1.0 HG23 A:ILE99 4.6 12.6 1.0 HD21 A:LEU57 4.6 15.1 1.0 HD23 A:LEU82 4.6 13.7 1.0 CD1 A:ILE99 4.7 12.0 1.0 C A:LEU57 4.7 8.3 1.0 CG1 A:ILE99 4.7 11.2 1.0 CD1 A:LEU57 4.7 11.3 1.0 N A:GLY58 4.7 8.4 1.0 HD22 A:LEU54 4.8 14.0 1.0 H26 A:NUT201 4.8 12.6 1.0 HD12 A:LEU57 4.8 13.6 1.0 HD13 A:LEU82 4.8 15.6 1.0 H23 A:NUT201 4.8 13.3 1.0 H A:GLY58 4.9 10.1 1.0 HD13 A:ILE99 4.9 14.4 1.0 CG A:LEU57 4.9 10.2 1.0 O A:LEU57 5.0 9.2 1.0 CB A:ILE99 5.0 9.0 1.0

Chlorine binding site 2 out of 6 in the Crystal Structure of HDM2 in Complex with Nutlin-3A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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 A:Cl201 b:17.0 occ:1.00 CL A:NUT201 0.0 17.0 1.0 C15 A:NUT201 1.7 14.0 1.0 C14 A:NUT201 2.7 13.0 1.0 C16 A:NUT201 2.7 15.9 1.0 H32 A:NUT201 2.8 15.6 1.0 H31 A:NUT201 2.8 19.1 1.0 HE1 A:TYR100 2.9 18.5 1.0 HD1 A:TYR100 3.0 16.3 1.0 HA A:HIS96 3.1 11.4 1.0 HB A:ILE99 3.2 10.8 1.0 CE1 A:TYR100 3.3 15.4 1.0 CD1 A:TYR100 3.4 13.6 1.0 HG22 A:ILE99 3.4 12.6 1.0 HD21 A:LEU54 3.5 14.0 1.0 HB3 A:HIS96 3.5 13.8 1.0 HG23 A:ILE99 3.5 12.6 1.0 HD23 A:LEU54 3.6 14.0 1.0 CG A:HIS96 3.6 15.0 1.0 CD2 A:HIS96 3.8 14.3 1.0 CB A:HIS96 3.8 11.5 1.0 CA A:HIS96 3.8 9.5 1.0 CG2 A:ILE99 3.8 10.5 1.0 O A:HIS96 3.8 9.2 1.0 ND1 A:HIS96 3.9 20.1 1.0 CB A:ILE99 4.0 9.0 1.0 CD2 A:LEU54 4.0 11.7 1.0 C13 A:NUT201 4.0 13.1 1.0 C17 A:NUT201 4.0 14.8 1.0 HD2 A:HIS96 4.0 17.2 1.0 H A:TYR100 4.1 10.3 1.0 HD1 A:HIS96 4.2 24.1 1.0 NE2 A:HIS96 4.2 18.5 1.0 HD11 A:ILE99 4.2 14.4 1.0 CE1 A:HIS96 4.3 20.6 1.0 C A:HIS96 4.3 8.8 1.0 CZ A:TYR100 4.4 14.1 1.0 HD12 A:ILE99 4.4 14.4 1.0 CG A:TYR100 4.5 10.4 1.0 C12 A:NUT201 4.5 13.4 1.0 HD22 A:LEU54 4.5 14.0 1.0 N A:TYR100 4.6 8.6 1.0 HD11 A:LEU54 4.6 17.0 1.0 HD13 A:LEU54 4.6 17.0 1.0 CD1 A:ILE99 4.7 12.0 1.0 HG21 A:ILE99 4.8 12.6 1.0 HB2 A:HIS96 4.8 13.8 1.0 H33 A:NUT201 4.8 15.7 1.0 H30 A:NUT201 4.8 17.7 1.0 HE1 A:HIS96 4.8 24.7 1.0 O A:HOH357 4.9 30.5 1.0 CG1 A:ILE99 4.9 11.2 1.0 OH A:TYR100 5.0 16.0 1.0 CD1 A:LEU54 5.0 14.2 1.0 N A:HIS96 5.0 9.0 1.0

Chlorine binding site 3 out of 6 in the Crystal Structure of HDM2 in Complex with Nutlin-3A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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 A:Cl203 b:14.5 occ:1.00 H22 A:NUT201 3.0 14.8 1.0 HA A:PHE55 3.2 10.6 1.0 O A:HOH326 3.2 22.3 1.0 H33 A:NUT201 3.4 15.7 1.0 H23 A:NUT201 3.6 13.3 1.0 O A:HOH372 3.7 30.7 1.0 HB2 A:PHE55 3.8 12.6 1.0 HB3 A:LEU54 3.8 11.8 1.0 HD1 A:PHE55 3.9 14.5 1.0 H27 A:NUT201 3.9 15.6 1.0 CA A:PHE55 3.9 8.9 1.0 C18 A:NUT201 4.0 12.4 1.0 N A:PHE55 4.1 9.3 1.0 HG3 B:PRO32 4.2 17.4 1.0 O A:HOH335 4.2 12.6 1.0 H A:PHE55 4.3 11.2 0.0 H A:PHE55 4.3 11.2 1.0 C13 A:NUT201 4.3 13.1 1.0 CB A:PHE55 4.3 10.5 1.0 C11 A:NUT201 4.4 13.0 1.0 C A:LEU54 4.4 9.3 1.0 HB2 A:LEU54 4.5 11.8 1.0 C24 A:NUT201 4.5 11.1 1.0 CB A:LEU54 4.6 9.9 1.0 O A:LEU54 4.6 9.9 1.0 HG2 B:PRO32 4.7 17.4 1.0 CD1 A:PHE55 4.7 12.1 1.0 C12 A:NUT201 4.8 13.4 1.0 C19 A:NUT201 4.8 11.5 1.0 CG B:PRO32 4.9 14.5 1.0 H5 A:NUT201 4.9 27.2 1.0 N1 A:NUT201 5.0 11.4 1.0

Chlorine binding site 4 out of 6 in the Crystal Structure of HDM2 in Complex with Nutlin-3A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl201 b:10.8 occ:1.00 CL1 B:NUT201 0.0 10.8 1.0 C22 B:NUT201 1.7 9.8 1.0 C21 B:NUT201 2.7 9.9 1.0 C23 B:NUT201 2.7 10.3 1.0 H25 B:NUT201 2.8 11.9 1.0 H24 B:NUT201 2.9 12.4 1.0 HB3 B:LEU57 3.3 12.3 1.0 HZ B:PHE91 3.3 12.4 1.0 HD13 B:ILE61 3.3 11.9 1.0 HG21 B:ILE99 3.3 13.2 1.0 HE2 B:PHE86 3.5 14.2 1.0 HD11 B:ILE61 3.5 11.9 1.0 HG22 B:ILE99 3.5 13.2 1.0 HE1 B:PHE91 3.5 12.2 1.0 HZ B:PHE86 3.6 14.5 1.0 CD1 B:ILE61 3.8 9.9 1.0 CZ B:PHE91 3.9 10.3 1.0 CG2 B:ILE99 3.9 11.0 1.0 HD13 B:LEU57 3.9 15.3 1.0 HB2 B:LEU57 3.9 12.3 1.0 HD12 B:ILE99 3.9 13.9 1.0 C20 B:NUT201 4.0 10.4 1.0 C24 B:NUT201 4.0 10.1 1.0 CE1 B:PHE91 4.0 10.2 1.0 CB B:LEU57 4.0 10.2 1.0 HG12 B:ILE99 4.0 14.0 1.0 HD12 B:ILE61 4.1 11.9 1.0 CE2 B:PHE86 4.1 11.8 1.0 HD12 B:ILE103 4.2 11.3 1.0 CZ B:PHE86 4.2 12.1 1.0 HA2 B:GLY58 4.5 10.2 1.0 HG23 B:ILE99 4.5 13.2 1.0 C19 B:NUT201 4.5 10.7 1.0 HD21 B:LEU57 4.6 14.9 1.0 HD23 B:LEU82 4.7 14.8 1.0 CD1 B:LEU57 4.7 12.7 1.0 CD1 B:ILE99 4.7 11.6 1.0 CG1 B:ILE99 4.7 11.6 1.0 C B:LEU57 4.7 8.4 1.0 N B:GLY58 4.7 8.5 1.0 HD12 B:LEU57 4.8 15.3 1.0 HD13 B:LEU82 4.8 15.1 1.0 HD22 B:LEU54 4.8 15.5 1.0 H26 B:NUT201 4.8 12.5 1.0 H23 B:NUT201 4.8 12.1 1.0 H B:GLY58 4.9 10.2 1.0 HD13 B:ILE99 4.9 13.9 1.0 CG B:LEU57 4.9 11.4 1.0 O B:LEU57 4.9 9.4 1.0 CB B:ILE99 5.0 9.9 1.0

Chlorine binding site 5 out of 6 in the Crystal Structure of HDM2 in Complex with Nutlin-3A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of HDM2 in Complex with Nutlin-3A within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl201 b:16.1 occ:1.00 CL B:NUT201 0.0 16.1 1.0 C15 B:NUT201 1.7 13.8 1.0 C14 B:NUT201 2.7 12.8 1.0 C16 B:NUT201 2.7 14.8 1.0 H31 B:NUT201 2.8 17.7 1.0 H32 B:NUT201 2.8 15.3 1.0 HE1 B:TYR100 3.0 17.3 1.0 HA B:HIS96 3.1 11.2 1.0 HD1 B:TYR100 3.1 16.2 1.0 HB B:ILE99 3.2 11.9 1.0 CE1 B:TYR100 3.4 14.4 1.0 CD1 B:TYR100 3.4 13.5 1.0 HD21 B:LEU54 3.5 15.5 1.0 HG22 B:ILE99 3.5 13.2 1.0 HB3 B:HIS96 3.5 13.4 1.0 HG23 B:ILE99 3.5 13.2 1.0 CG B:HIS96 3.6 14.6 1.0 HD23 B:LEU54 3.6 15.5 1.0 CD2 B:HIS96 3.8 15.2 1.0 CA B:HIS96 3.8 9.3 1.0 CB B:HIS96 3.8 11.2 1.0 CG2 B:ILE99 3.8 11.0 1.0 ND1 B:HIS96 3.8 18.7 1.0 O B:HIS96 3.8 9.0 1.0 CB B:ILE99 3.9 9.9 1.0 C13 B:NUT201 4.0 14.0 1.0 C17 B:NUT201 4.0 14.4 1.0 CD2 B:LEU54 4.0 12.9 1.0 HD2 B:HIS96 4.1 18.3 1.0 HD1 B:HIS96 4.1 22.5 1.0 H B:TYR100 4.1 9.9 1.0 NE2 B:HIS96 4.2 18.1 1.0 HD11 B:ILE99 4.2 13.9 1.0 CE1 B:HIS96 4.2 19.1 1.0 C B:HIS96 4.3 8.6 1.0 CZ B:TYR100 4.4 14.3 1.0 HD12 B:ILE99 4.4 13.9 1.0 CG B:TYR100 4.5 10.4 1.0 C12 B:NUT201 4.5 13.9 1.0 HD13 B:LEU54 4.5 16.7 1.0 N B:TYR100 4.6 8.3 1.0 HD22 B:LEU54 4.6 15.5 1.0 HD11 B:LEU54 4.6 16.7 1.0 HH B:TYR100 4.7 19.5 1.0 CD1 B:ILE99 4.7 11.6 1.0 HG21 B:ILE99 4.8 13.2 1.0 O B:HOH355 4.8 33.5 1.0 HB2 B:HIS96 4.8 13.4 1.0 HE1 B:HIS96 4.8 22.9 1.0 H30 B:NUT201 4.8 17.2 1.0 H33 B:NUT201 4.8 16.8 1.0 CD1 B:LEU54 4.9 13.9 1.0 CG1 B:ILE99 4.9 11.6 1.0 N B:HIS96 5.0 9.4 1.0 CA B:ILE99 5.0 9.3 1.0

Chlorine binding site 6 out of 6 in the Crystal Structure of HDM2 in Complex with Nutlin-3A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of HDM2 in Complex with Nutlin-3A within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl203 b:14.4 occ:1.00 H22 B:NUT201 3.0 13.0 1.0 HA B:PHE55 3.2 11.6 1.0 O B:HOH326 3.2 22.5 1.0 H33 B:NUT201 3.4 16.8 1.0 H23 B:NUT201 3.6 12.1 1.0 O B:HOH373 3.7 33.9 1.0 HB2 B:PHE55 3.8 12.3 1.0 HB3 B:LEU54 3.8 12.9 1.0 HD1 B:PHE55 3.9 14.8 1.0 H27 B:NUT201 3.9 15.5 1.0 CA B:PHE55 3.9 9.6 1.0 C18 B:NUT201 4.1 10.9 1.0 N B:PHE55 4.1 9.8 1.0 C13 B:NUT201 4.3 14.0 1.0 O B:HOH332 4.3 12.9 1.0 H B:PHE55 4.3 11.8 1.0 H B:PHE55 4.3 11.8 0.0 CB B:PHE55 4.3 10.3 1.0 C11 B:NUT201 4.4 12.9 1.0 C B:LEU54 4.4 9.8 1.0 HB2 B:LEU54 4.4 12.9 1.0 CB B:LEU54 4.5 10.8 1.0 C24 B:NUT201 4.5 10.1 1.0 O B:LEU54 4.5 10.3 1.0 CD1 B:PHE55 4.7 12.3 1.0 C12 B:NUT201 4.8 13.9 1.0 C19 B:NUT201 4.8 10.7 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.