Zinc in PDB 2xwr: Crystal Structure of the Dna-Binding Domain of Human P53 with Extended N Terminus

The structure of Crystal Structure of the Dna-Binding Domain of Human P53 with Extended N Terminus, PDB code: 2xwr was solved by A.C.Joerger, E.Natan, A.R.Fersht, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.82 / 1.68
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	51.500, 68.450, 58.890, 90.00, 99.46, 90.00
R / Rfree (%)	17.3 / 20.9

The binding sites of Zinc atom in the Crystal Structure of the Dna-Binding Domain of Human P53 with Extended N Terminus (pdb code 2xwr). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of the Dna-Binding Domain of Human P53 with Extended N Terminus, PDB code: 2xwr:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of the Dna-Binding Domain of Human P53 with Extended N Terminus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Dna-Binding Domain of Human P53 with Extended N Terminus within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn300 b:19.2 occ:1.00 ND1 A:HIS179 2.2 22.9 1.0 SG A:CYS242 2.2 21.4 1.0 SG A:CYS176 2.3 17.0 1.0 SG A:CYS238 2.4 18.0 1.0 CE1 A:HIS179 3.1 20.6 1.0 CB A:CYS242 3.1 22.0 1.0 CG A:HIS179 3.2 23.0 1.0 CB A:CYS176 3.4 17.2 1.0 CB A:CYS238 3.4 17.1 1.0 CB A:HIS179 3.6 20.7 1.0 CA A:CYS238 3.9 11.3 1.0 N A:CYS176 3.9 15.4 1.0 NE2 A:HIS179 4.2 22.9 1.0 CA A:CYS176 4.3 20.6 1.0 CD2 A:HIS179 4.3 26.9 1.0 N A:ASN239 4.4 16.8 1.0 N A:HIS179 4.5 21.7 1.0 CA A:CYS242 4.5 24.3 1.0 O A:HOH2147 4.6 20.2 1.0 CA A:HIS179 4.7 20.8 1.0 O A:MET237 4.7 15.5 1.0 C A:CYS238 4.7 14.0 1.0 O A:HOH2223 4.7 32.0 1.0 O A:CYS176 4.9 19.1 1.0 C A:CYS176 4.9 20.6 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the Dna-Binding Domain of Human P53 with Extended N Terminus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the Dna-Binding Domain of Human P53 with Extended N Terminus within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn300 b:14.2 occ:1.00 ND1 B:HIS179 1.8 5.5 1.0 SG B:CYS176 2.3 12.4 1.0 SG B:CYS242 2.3 16.6 1.0 SG B:CYS238 2.4 12.2 0.5 SG B:CYS238 2.5 11.1 0.5 CE1 B:HIS179 2.6 19.6 1.0 CG B:HIS179 3.0 13.3 1.0 CB B:CYS242 3.1 13.8 1.0 CB B:CYS176 3.4 15.4 1.0 CB B:CYS238 3.5 14.7 0.5 CB B:HIS179 3.5 12.2 1.0 CB B:CYS238 3.7 14.9 0.5 NE2 B:HIS179 3.8 12.1 1.0 CA B:CYS238 3.9 12.4 0.5 CA B:CYS238 3.9 12.4 0.5 CD2 B:HIS179 4.0 13.0 1.0 N B:CYS176 4.0 10.4 1.0 N B:ASN239 4.2 14.0 1.0 CA B:CYS176 4.3 15.9 1.0 N B:HIS179 4.5 18.4 1.0 O B:HOH2214 4.5 17.5 1.0 CA B:CYS242 4.6 15.8 1.0 C B:CYS238 4.6 17.0 1.0 CA B:HIS179 4.6 13.9 1.0 O B:HOH2210 4.7 28.3 1.0 O B:MET237 4.8 12.2 1.0 O B:HOH2127 4.8 21.5 1.0 C B:CYS176 5.0 16.2 1.0

E.Natan, C.Baloglu, K.Pagel, S.M.Freund, N.Morgner, C.V.Robinson, A.R.Fersht, A.C.Joerger. Interaction of the P53 Dna-Binding Domain with Its N-Terminal Extension Modulates the Stability of the P53 Tetramer. J.Mol.Biol. V. 409 358 2011.
ISSN: ISSN 0022-2836
PubMed: 21457718
DOI: 10.1016/J.JMB.2011.03.047