Zinc in PDB 2hdp: Solution Structure of HDM2 Ring Finger Domain

The binding sites of Zinc atom in the Solution Structure of HDM2 Ring Finger Domain (pdb code 2hdp). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Solution Structure of HDM2 Ring Finger Domain, PDB code: 2hdp:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Solution Structure of HDM2 Ring Finger Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Solution Structure of HDM2 Ring Finger Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn492 b:0.0 occ:1.00 SG B:CYS464 2.3 0.0 1.0 SG B:CYS438 2.3 0.0 1.0 SG B:CYS461 2.3 0.0 1.0 SG B:CYS441 2.3 0.0 1.0 H B:CYS441 2.6 0.0 1.0 HB2 B:CYS464 2.6 0.0 1.0 HB2 B:CYS438 3.0 0.0 1.0 CB B:CYS464 3.0 0.0 1.0 H B:CYS464 3.0 0.0 1.0 CB B:CYS438 3.0 0.0 1.0 HB3 B:CYS438 3.1 0.0 1.0 HB3 B:CYS441 3.2 0.0 1.0 H B:CYS461 3.2 0.0 1.0 H B:GLN442 3.2 0.0 1.0 CB B:CYS441 3.3 0.0 1.0 N B:CYS441 3.5 0.0 1.0 CB B:CYS461 3.7 0.0 1.0 HB3 B:CYS464 3.7 0.0 1.0 HB3 B:CYS461 3.8 0.0 1.0 HB B:THR463 3.8 0.0 1.0 N B:CYS464 3.8 0.0 1.0 HB B:ILE440 3.9 0.0 1.0 H B:ILE440 3.9 0.0 1.0 CA B:CYS441 3.9 0.0 1.0 HG2 B:ARG444 4.0 0.0 1.0 CA B:CYS464 4.0 0.0 1.0 N B:CYS461 4.1 0.0 1.0 N B:GLN442 4.2 0.0 1.0 HB2 B:CYS441 4.2 0.0 1.0 H B:VAL439 4.4 0.0 1.0 HA B:CYS464 4.5 0.0 1.0 CA B:CYS461 4.5 0.0 1.0 HD3 B:ARG444 4.5 0.0 1.0 HB2 B:CYS461 4.5 0.0 1.0 CA B:CYS438 4.5 0.0 1.0 HG3 B:ARG444 4.6 0.0 1.0 C B:CYS441 4.6 0.0 1.0 C B:ILE440 4.6 0.0 1.0 H B:GLY443 4.7 0.0 1.0 CG B:ARG444 4.7 0.0 1.0 N B:ILE440 4.8 0.0 1.0 HA B:ALA460 4.8 0.0 1.0 CB B:ILE440 4.8 0.0 1.0 HA B:CYS438 4.9 0.0 1.0 CB B:THR463 4.9 0.0 1.0 HA B:CYS441 4.9 0.0 1.0 HA B:GLN442 4.9 0.0 1.0 H B:ARG444 5.0 0.0 1.0 CA B:ILE440 5.0 0.0 1.0 H B:CYS438 5.0 0.0 1.0 C B:THR463 5.0 0.0 1.0

Zinc binding site 2 out of 4 in the Solution Structure of HDM2 Ring Finger Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Solution Structure of HDM2 Ring Finger Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn493 b:0.0 occ:1.00 NE2 A:HIS452 2.1 0.0 1.0 ND1 A:HIS457 2.1 0.0 1.0 HE1 A:HIS457 2.2 0.0 1.0 SG A:CYS475 2.3 0.0 1.0 SG A:CYS478 2.3 0.0 1.0 HB2 A:CYS478 2.3 0.0 1.0 CE1 A:HIS457 2.4 0.0 1.0 HE1 A:HIS452 2.7 0.0 1.0 CE1 A:HIS452 2.7 0.0 1.0 CB A:CYS478 2.8 0.0 1.0 H A:CYS478 2.9 0.0 1.0 CD2 A:HIS452 3.3 0.0 1.0 HB2 A:CYS475 3.4 0.0 1.0 CB A:CYS475 3.4 0.0 1.0 CG A:HIS457 3.5 0.0 1.0 HB3 A:CYS478 3.5 0.0 1.0 HB3 A:CYS475 3.7 0.0 1.0 NE2 A:HIS457 3.7 0.0 1.0 N A:CYS478 3.8 0.0 1.0 HD2 A:HIS452 3.8 0.0 1.0 HE21 A:GLN480 3.8 0.0 1.0 HB A:VAL477 3.8 0.0 1.0 CA A:CYS478 4.0 0.0 1.0 ND1 A:HIS452 4.0 0.0 1.0 HB2 A:HIS457 4.2 0.0 1.0 CD2 A:HIS457 4.2 0.0 1.0 CG A:HIS452 4.3 0.0 1.0 H A:VAL477 4.4 0.0 1.0 CB A:HIS457 4.4 0.0 1.0 HE2 A:HIS457 4.5 0.0 1.0 HB2 A:GLN480 4.5 0.0 1.0 H A:GLN480 4.7 0.0 1.0 HA A:CYS478 4.7 0.0 1.0 H A:ARG479 4.7 0.0 1.0 CA A:CYS475 4.8 0.0 1.0 NE2 A:GLN480 4.8 0.0 1.0 HD1 A:HIS452 4.8 0.0 1.0 CB A:VAL477 4.9 0.0 1.0 C A:CYS478 4.9 0.0 1.0 HD2 A:PRO476 4.9 0.0 1.0 C A:VAL477 4.9 0.0 1.0 HA A:CYS475 5.0 0.0 1.0

Zinc binding site 3 out of 4 in the Solution Structure of HDM2 Ring Finger Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Solution Structure of HDM2 Ring Finger Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn492 b:0.0 occ:1.00 SG A:CYS464 2.2 0.0 1.0 SG A:CYS438 2.3 0.0 1.0 SG A:CYS461 2.3 0.0 1.0 SG A:CYS441 2.3 0.0 1.0 H A:CYS441 2.4 0.0 1.0 H A:CYS464 2.8 0.0 1.0 HB2 A:CYS441 2.9 0.0 1.0 HB2 A:CYS438 3.0 0.0 1.0 H A:ILE440 3.1 0.0 1.0 CB A:CYS438 3.1 0.0 1.0 CB A:CYS441 3.1 0.0 1.0 H A:VAL439 3.2 0.0 1.0 HA A:CYS438 3.3 0.0 1.0 N A:CYS441 3.3 0.0 1.0 CB A:CYS464 3.4 0.0 1.0 N A:CYS464 3.4 0.0 1.0 HB A:THR463 3.5 0.0 1.0 H A:CYS461 3.5 0.0 1.0 HB2 A:CYS464 3.7 0.0 1.0 CA A:CYS438 3.7 0.0 1.0 HA A:CYS464 3.8 0.0 1.0 H A:GLN442 3.8 0.0 1.0 CB A:CYS461 3.8 0.0 1.0 CA A:CYS464 3.8 0.0 1.0 CA A:CYS441 3.9 0.0 1.0 HB A:ILE440 3.9 0.0 1.0 HB3 A:CYS461 3.9 0.0 1.0 N A:VAL439 4.0 0.0 1.0 N A:ILE440 4.1 0.0 1.0 HB3 A:CYS438 4.1 0.0 1.0 HB3 A:CYS441 4.1 0.0 1.0 C A:CYS438 4.3 0.0 1.0 HB3 A:CYS464 4.4 0.0 1.0 N A:CYS461 4.4 0.0 1.0 H A:GLY443 4.4 0.0 1.0 C A:ILE440 4.4 0.0 1.0 C A:THR463 4.4 0.0 1.0 HG2 A:ARG444 4.5 0.0 1.0 CB A:THR463 4.5 0.0 1.0 HB2 A:CYS461 4.6 0.0 1.0 CA A:CYS461 4.6 0.0 1.0 CA A:ILE440 4.6 0.0 1.0 HA A:CYS441 4.6 0.0 1.0 N A:GLN442 4.7 0.0 1.0 H A:THR463 4.7 0.0 1.0 CB A:ILE440 4.7 0.0 1.0 HG13 A:ILE440 4.8 0.0 1.0 C A:CYS441 4.8 0.0 1.0 CA A:THR463 4.9 0.0 1.0 HG22 A:THR463 4.9 0.0 1.0 HD11 A:ILE440 4.9 0.0 1.0 N A:CYS438 5.0 0.0 1.0

Zinc binding site 4 out of 4 in the Solution Structure of HDM2 Ring Finger Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Solution Structure of HDM2 Ring Finger Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn493 b:0.0 occ:1.00 ND1 B:HIS457 2.1 0.0 1.0 NE2 B:HIS452 2.1 0.0 1.0 HE1 B:HIS457 2.2 0.0 1.0 SG B:CYS475 2.3 0.0 1.0 SG B:CYS478 2.3 0.0 1.0 HB2 B:CYS478 2.3 0.0 1.0 CE1 B:HIS457 2.4 0.0 1.0 CB B:CYS478 2.8 0.0 1.0 CE1 B:HIS452 2.9 0.0 1.0 H B:CYS478 2.9 0.0 1.0 HE1 B:HIS452 3.0 0.0 1.0 CD2 B:HIS452 3.3 0.0 1.0 HB2 B:CYS475 3.4 0.0 1.0 CB B:CYS475 3.4 0.0 1.0 CG B:HIS457 3.5 0.0 1.0 HB3 B:CYS478 3.5 0.0 1.0 HD2 B:HIS452 3.7 0.0 1.0 HB3 B:CYS475 3.7 0.0 1.0 NE2 B:HIS457 3.7 0.0 1.0 N B:CYS478 3.8 0.0 1.0 HB B:VAL477 3.9 0.0 1.0 CA B:CYS478 4.0 0.0 1.0 ND1 B:HIS452 4.1 0.0 1.0 HB2 B:HIS457 4.1 0.0 1.0 CD2 B:HIS457 4.2 0.0 1.0 CG B:HIS452 4.3 0.0 1.0 CB B:HIS457 4.4 0.0 1.0 H B:VAL477 4.4 0.0 1.0 HE2 B:HIS457 4.4 0.0 1.0 HA B:CYS478 4.7 0.0 1.0 H B:GLN480 4.7 0.0 1.0 H B:ARG479 4.7 0.0 1.0 CA B:CYS475 4.8 0.0 1.0 HB2 B:GLN480 4.8 0.0 1.0 O B:GLY456 4.9 0.0 1.0 C B:CYS478 4.9 0.0 1.0 HD2 B:PRO476 4.9 0.0 1.0 HA B:CYS475 4.9 0.0 1.0 CB B:VAL477 4.9 0.0 1.0 C B:VAL477 5.0 0.0 1.0 HD1 B:HIS452 5.0 0.0 1.0

M.Kostic, T.Matt, M.A.Martinez-Yamout, H.J.Dyson, P.E.Wright. Solution Structure of the HDM2 C2H2C4 Ring, A Domain Critical For Ubiquitination of P53. J.Mol.Biol. V. 363 433 2006.
ISSN: ISSN 0022-2836
PubMed: 16965791
DOI: 10.1016/J.JMB.2006.08.027