Sodium in PDB 7qdq: Crystal Structure of HDM2 in Complex with Caylin-1

The structure of Crystal Structure of HDM2 in Complex with Caylin-1, PDB code: 7qdq was solved by A.D.Finke, M.A.Walti, M.E.Marsh, J.Orts, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.80 / 1.26
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	41.641, 43.675, 53.351, 90, 90, 90
R / Rfree (%)	18.2 / 21.6

The structure of Crystal Structure of HDM2 in Complex with Caylin-1 also contains other interesting chemical elements:

Chlorine

(Cl)

11 atoms

The binding sites of Sodium atom in the Crystal Structure of HDM2 in Complex with Caylin-1 (pdb code 7qdq). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of HDM2 in Complex with Caylin-1, PDB code: 7qdq:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of HDM2 in Complex with Caylin-1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of HDM2 in Complex with Caylin-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na204 b:16.7 occ:1.00 HE21 A:GLN71 2.2 12.7 1.0 OH A:TYR76 2.3 11.3 0.3 OD2 A:ASP68 2.6 11.2 1.0 NE2 A:GLN71 2.9 10.6 1.0 HB3 A:GLN71 2.9 11.4 1.0 HE22 A:GLN71 3.2 12.7 1.0 HB2 A:ASP68 3.2 13.8 1.0 HE2 A:TYR76 3.4 9.4 0.3 CZ A:TYR76 3.4 7.6 0.3 HB3 A:ASP68 3.5 13.8 1.0 CG A:ASP68 3.5 11.1 1.0 HB A:ILE74 3.6 12.1 1.0 CB A:ASP68 3.6 11.5 1.0 HG13 A:ILE74 3.6 12.7 1.0 CB A:GLN71 3.7 9.5 1.0 HB2 A:GLN71 3.8 11.4 1.0 HG21 A:ILE74 3.8 15.7 1.0 CE2 A:TYR76 3.8 7.8 0.3 CD A:GLN71 4.0 9.7 1.0 CB A:ILE74 4.2 10.1 1.0 CG1 A:ILE74 4.3 10.6 1.0 CG A:GLN71 4.3 9.1 1.0 CG2 A:ILE74 4.4 13.1 1.0 HG12 A:ILE74 4.5 12.7 1.0 HG2 A:GLN71 4.5 10.9 1.0 CE1 A:TYR76 4.6 6.3 0.3 HG22 A:ILE74 4.6 15.7 1.0 OD1 A:ASP68 4.7 11.2 1.0 HE1 A:TYR76 4.8 7.6 0.3 O A:GLN71 4.8 7.6 1.0 CA A:GLN71 5.0 9.2 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of HDM2 in Complex with Caylin-1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of HDM2 in Complex with Caylin-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na205 b:25.2 occ:1.00 HB A:VAL108 2.8 12.0 1.0 O A:VAL109 2.9 15.3 1.0 CB A:VAL108 3.7 10.0 1.0 HG21 A:VAL108 3.8 14.6 1.0 HG23 A:VAL108 3.9 14.6 1.0 H A:VAL109 4.0 10.3 1.0 C A:VAL109 4.0 13.0 1.0 CG2 A:VAL108 4.1 12.2 1.0 HG11 A:VAL108 4.2 14.6 1.0 O A:HOH355 4.2 9.4 1.0 N A:VAL109 4.3 8.6 1.0 HA A:VAL110 4.4 21.4 1.0 CG1 A:VAL108 4.4 12.2 1.0 HG12 A:VAL108 4.6 14.6 1.0 C A:VAL108 4.7 9.4 1.0 CA A:VAL108 4.7 7.9 1.0 HA A:VAL108 4.8 9.5 1.0 CA A:VAL109 4.8 11.1 1.0 HB A:VAL109 4.9 13.2 1.0 N A:VAL110 5.0 13.5 1.0

V.Mertens, M.J.Abi Saad, N.Coudevylle, A.D.Finke, M.E.Marsh, J.Orts. Elucidation of A Nutlin Derivative HDM2 Complex Structure at the Interaction Site By uc(Nmr) Molecular Replacement A Straightforward Derivation To Be Published.