Zinc in PDB 3kmd: Crystal Structure of the P53 Core Domain Bound to A Full Consensus Site As A Self-Assembled Tetramer

The structure of Crystal Structure of the P53 Core Domain Bound to A Full Consensus Site As A Self-Assembled Tetramer, PDB code: 3kmd was solved by Y.Chen, R.Dey, L.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.52 / 2.15
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	65.084, 93.713, 145.570, 90.00, 90.00, 90.00
R / Rfree (%)	21.6 / 24

The binding sites of Zinc atom in the Crystal Structure of the P53 Core Domain Bound to A Full Consensus Site As A Self-Assembled Tetramer (pdb code 3kmd). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of the P53 Core Domain Bound to A Full Consensus Site As A Self-Assembled Tetramer, PDB code: 3kmd:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of the P53 Core Domain Bound to A Full Consensus Site As A Self-Assembled Tetramer


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 P53 Core Domain Bound to A Full Consensus Site As A Self-Assembled Tetramer within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1 b:21.5 occ:1.00 ND1 A:HIS179 2.0 14.0 1.0 SG A:CYS242 2.3 18.1 1.0 SG A:CYS176 2.4 19.6 1.0 SG A:CYS238 2.5 18.7 1.0 CE1 A:HIS179 2.9 16.9 1.0 CB A:CYS242 3.0 20.9 1.0 CG A:HIS179 3.1 17.3 1.0 CB A:CYS238 3.3 15.2 1.0 CB A:CYS176 3.5 17.9 1.0 CB A:HIS179 3.5 16.4 1.0 CA A:CYS238 3.8 17.3 1.0 N A:CYS176 4.0 20.1 1.0 NE2 A:HIS179 4.1 16.0 1.0 O A:HOH449 4.2 37.3 1.0 CD2 A:HIS179 4.2 16.8 1.0 CA A:CYS176 4.3 19.6 1.0 CA A:CYS242 4.5 21.5 1.0 N A:HIS179 4.5 19.6 1.0 N A:ASN239 4.5 19.6 1.0 CA A:HIS179 4.6 19.8 1.0 O A:MET237 4.6 16.5 1.0 C A:CYS238 4.7 18.3 1.0 SD B:MET243 4.8 47.1 1.0 O A:HOH46 4.8 20.4 1.0 N A:CYS238 5.0 17.6 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of the P53 Core Domain Bound to A Full Consensus Site As A Self-Assembled Tetramer


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 P53 Core Domain Bound to A Full Consensus Site As A Self-Assembled Tetramer within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1 b:19.0 occ:1.00 ND1 B:HIS179 2.1 20.5 1.0 SG B:CYS242 2.3 15.8 1.0 SG B:CYS238 2.3 18.6 1.0 SG B:CYS176 2.4 17.8 1.0 CB B:CYS242 3.0 16.4 1.0 CE1 B:HIS179 3.1 20.1 1.0 CG B:HIS179 3.1 21.5 1.0 CB B:CYS238 3.3 17.6 1.0 CB B:CYS176 3.4 16.9 1.0 CB B:HIS179 3.5 20.2 1.0 CA B:CYS238 3.8 17.2 1.0 N B:CYS176 4.0 19.0 1.0 NE2 B:HIS179 4.2 21.6 1.0 CD2 B:HIS179 4.3 21.3 1.0 CA B:CYS176 4.3 18.8 1.0 N B:HIS179 4.4 18.7 1.0 CA B:CYS242 4.5 18.4 1.0 CA B:HIS179 4.6 19.9 1.0 N B:ASN239 4.6 16.9 1.0 O B:MET237 4.6 18.4 1.0 O B:HOH39 4.7 18.0 1.0 C B:CYS238 4.7 15.9 1.0 C B:CYS176 4.9 19.5 1.0 N B:CYS238 5.0 19.0 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of the P53 Core Domain Bound to A Full Consensus Site As A Self-Assembled Tetramer


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the P53 Core Domain Bound to A Full Consensus Site As A Self-Assembled Tetramer within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1 b:22.0 occ:1.00 ND1 D:HIS179 2.2 22.6 1.0 SG D:CYS176 2.3 15.9 1.0 SG D:CYS242 2.4 18.4 1.0 SG D:CYS238 2.4 20.9 1.0 CB D:CYS242 3.1 22.3 1.0 CE1 D:HIS179 3.1 22.7 1.0 CG D:HIS179 3.2 24.1 1.0 CB D:CYS238 3.3 17.2 1.0 CB D:CYS176 3.4 14.6 1.0 CB D:HIS179 3.5 21.4 1.0 CA D:CYS238 3.8 16.1 1.0 N D:CYS176 4.0 32.1 1.0 NE2 D:HIS179 4.3 23.3 1.0 CA D:CYS176 4.3 29.2 1.0 CD2 D:HIS179 4.3 22.2 1.0 O D:HOH517 4.4 44.8 1.0 N D:HIS179 4.4 22.5 1.0 CA D:CYS242 4.5 23.1 1.0 N D:ASN239 4.5 19.3 1.0 O D:MET237 4.6 21.0 1.0 CA D:HIS179 4.6 23.2 1.0 C D:CYS238 4.7 15.8 1.0 O D:HOH28 4.9 20.3 1.0 N D:CYS238 4.9 16.0 1.0 C D:CYS176 5.0 30.4 1.0 O D:CYS176 5.0 29.3 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of the P53 Core Domain Bound to A Full Consensus Site As A Self-Assembled Tetramer


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of the P53 Core Domain Bound to A Full Consensus Site As A Self-Assembled Tetramer within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1 b:27.6 occ:1.00 ND1 C:HIS179 2.0 25.9 1.0 SG C:CYS242 2.2 27.2 1.0 SG C:CYS238 2.4 27.9 1.0 SG C:CYS176 2.4 28.3 1.0 CE1 C:HIS179 2.9 27.6 1.0 CB C:CYS242 3.1 24.6 1.0 CG C:HIS179 3.1 28.5 1.0 CB C:CYS238 3.3 24.9 1.0 CB C:CYS176 3.5 25.1 1.0 CB C:HIS179 3.5 31.7 1.0 CA C:CYS238 3.8 24.3 1.0 N C:CYS176 4.1 26.3 1.0 NE2 C:HIS179 4.1 28.1 1.0 CD2 C:HIS179 4.2 28.6 1.0 CA C:CYS176 4.3 26.3 1.0 N C:HIS179 4.4 31.5 1.0 CA C:CYS242 4.5 22.8 1.0 N C:ASN239 4.5 23.9 1.0 O C:MET237 4.6 22.5 1.0 CA C:HIS179 4.6 32.7 1.0 C C:CYS238 4.7 22.9 1.0 O C:HOH322 4.8 24.4 1.0 O C:CYS176 4.9 28.6 1.0 C C:CYS176 4.9 27.1 1.0 SD D:MET243 5.0 44.9 1.0 N C:CYS238 5.0 25.9 1.0

Y.Chen, R.Dey, L.Chen. Crystal Structure of the P53 Core Domain Bound to A Full Consensus Site As A Self-Assembled Tetramer. Structure V. 18 246 2010.
ISSN: ISSN 0969-2126
PubMed: 20159469
DOI: 10.1016/J.STR.2009.11.011