Zinc in PDB 7pc6: Dna-Binding Domain of A P53 Homolog From the Hydrothermal Vent Annelid Alvinella Pompejana

The structure of Dna-Binding Domain of A P53 Homolog From the Hydrothermal Vent Annelid Alvinella Pompejana, PDB code: 7pc6 was solved by D.-I.Balourdas, S.Knapp, T.Soussi, A.C.Joerger, Structural Genomicsconsortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.70 / 1.92
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	55.9, 69.985, 114.849, 88.07, 89.92, 81.51
R / Rfree (%)	18.3 / 22.5

The binding sites of Zinc atom in the Dna-Binding Domain of A P53 Homolog From the Hydrothermal Vent Annelid Alvinella Pompejana (pdb code 7pc6). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Dna-Binding Domain of A P53 Homolog From the Hydrothermal Vent Annelid Alvinella Pompejana, PDB code: 7pc6:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Dna-Binding Domain of A P53 Homolog From the Hydrothermal Vent Annelid Alvinella Pompejana


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Dna-Binding Domain of A P53 Homolog From the Hydrothermal Vent Annelid Alvinella Pompejana within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:44.8 occ:1.00 ND1 A:HIS87 2.0 38.1 1.0 SG A:CYS150 2.4 47.8 1.0 SG A:CYS146 2.4 40.2 1.0 SG A:CYS84 2.5 41.1 1.0 CE1 A:HIS87 2.9 47.2 1.0 CG A:HIS87 3.0 40.8 1.0 CB A:CYS146 3.3 40.1 1.0 CB A:CYS150 3.4 50.1 1.0 CB A:HIS87 3.4 38.1 1.0 CB A:CYS84 3.5 43.3 1.0 CA A:CYS146 4.0 43.6 1.0 N A:CYS84 4.0 37.6 1.0 NE2 A:HIS87 4.0 43.1 1.0 CD2 A:HIS87 4.1 43.8 1.0 CA A:CYS84 4.3 39.9 1.0 N A:HIS87 4.4 44.0 1.0 CA A:HIS87 4.6 41.8 1.0 N A:PHE147 4.6 42.4 1.0 O A:MET145 4.7 40.4 1.0 CA A:CYS150 4.7 57.4 1.0 O A:CYS84 4.8 41.5 1.0 C A:CYS146 4.9 46.3 1.0 C A:CYS84 4.9 43.5 1.0

Zinc binding site 2 out of 8 in the Dna-Binding Domain of A P53 Homolog From the Hydrothermal Vent Annelid Alvinella Pompejana


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Dna-Binding Domain of A P53 Homolog From the Hydrothermal Vent Annelid Alvinella Pompejana within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:42.8 occ:1.00 ND1 B:HIS87 2.0 42.1 1.0 SG B:CYS150 2.3 41.3 1.0 SG B:CYS84 2.4 42.0 1.0 SG B:CYS146 2.5 39.1 1.0 CE1 B:HIS87 2.9 40.9 1.0 CG B:HIS87 3.1 41.4 1.0 CB B:CYS150 3.2 45.1 1.0 CB B:CYS146 3.4 33.7 1.0 CB B:HIS87 3.5 42.7 1.0 CB B:CYS84 3.5 38.1 1.0 CA B:CYS146 4.0 35.5 1.0 N B:CYS84 4.0 39.7 1.0 NE2 B:HIS87 4.1 46.3 1.0 CD2 B:HIS87 4.2 45.6 1.0 CA B:CYS84 4.4 41.9 1.0 N B:PHE147 4.6 39.2 1.0 CA B:CYS150 4.6 49.9 1.0 O B:HOH469 4.6 39.8 1.0 N B:HIS87 4.7 47.2 1.0 O B:MET145 4.7 42.9 1.0 CA B:HIS87 4.7 46.9 1.0 O B:HOH477 4.7 44.9 1.0 C B:CYS146 4.8 38.9 1.0 O B:CYS84 5.0 43.5 1.0

Zinc binding site 3 out of 8 in the Dna-Binding Domain of A P53 Homolog From the Hydrothermal Vent Annelid Alvinella Pompejana


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Dna-Binding Domain of A P53 Homolog From the Hydrothermal Vent Annelid Alvinella Pompejana within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn301 b:40.6 occ:1.00 ND1 C:HIS87 2.1 36.9 1.0 SG C:CYS84 2.3 43.2 1.0 SG C:CYS150 2.4 43.4 1.0 SG C:CYS146 2.4 34.1 1.0 CG C:HIS87 3.1 36.9 1.0 CE1 C:HIS87 3.1 43.3 1.0 CB C:CYS150 3.2 43.4 1.0 CB C:CYS146 3.3 33.7 1.0 CB C:HIS87 3.4 37.3 1.0 CB C:CYS84 3.5 39.0 1.0 CA C:CYS146 3.9 35.1 1.0 N C:CYS84 4.0 37.7 1.0 NE2 C:HIS87 4.2 40.4 1.0 CD2 C:HIS87 4.2 41.1 1.0 CA C:CYS84 4.3 42.5 1.0 N C:PHE147 4.4 39.9 1.0 N C:HIS87 4.5 41.0 1.0 O C:HOH443 4.6 33.9 1.0 CA C:HIS87 4.6 43.5 1.0 CA C:CYS150 4.6 40.9 1.0 O C:MET145 4.7 37.4 1.0 C C:CYS146 4.7 38.2 1.0 O C:HOH402 4.8 52.9 1.0 O C:CYS84 4.9 39.0 1.0

Zinc binding site 4 out of 8 in the Dna-Binding Domain of A P53 Homolog From the Hydrothermal Vent Annelid Alvinella Pompejana


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Dna-Binding Domain of A P53 Homolog From the Hydrothermal Vent Annelid Alvinella Pompejana within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn301 b:34.6 occ:1.00 ND1 D:HIS87 2.1 33.1 1.0 SG D:CYS150 2.3 34.8 1.0 SG D:CYS84 2.3 33.9 1.0 SG D:CYS146 2.3 34.9 1.0 CE1 D:HIS87 3.0 39.3 1.0 CG D:HIS87 3.1 34.0 1.0 CB D:CYS150 3.2 33.5 1.0 CB D:CYS146 3.2 29.0 1.0 CB D:HIS87 3.5 33.8 1.0 CB D:CYS84 3.5 37.5 1.0 CA D:CYS146 3.9 28.5 1.0 N D:CYS84 3.9 33.3 1.0 O D:HOH519 4.0 49.3 1.0 NE2 D:HIS87 4.2 39.1 1.0 CD2 D:HIS87 4.2 36.9 1.0 CA D:CYS84 4.3 33.0 1.0 N D:HIS87 4.5 42.6 1.0 N D:PHE147 4.5 32.0 1.0 O D:HOH465 4.5 31.0 1.0 CA D:CYS150 4.6 37.4 1.0 CA D:HIS87 4.6 38.2 1.0 O D:MET145 4.7 32.2 1.0 C D:CYS146 4.8 32.6 1.0 O D:CYS84 4.8 37.3 1.0 O D:HOH403 4.8 39.7 1.0 C D:CYS84 4.9 39.4 1.0

Zinc binding site 5 out of 8 in the Dna-Binding Domain of A P53 Homolog From the Hydrothermal Vent Annelid Alvinella Pompejana


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Dna-Binding Domain of A P53 Homolog From the Hydrothermal Vent Annelid Alvinella Pompejana within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn301 b:44.0 occ:1.00 ND1 E:HIS87 2.1 45.4 1.0 SG E:CYS150 2.3 45.2 1.0 SG E:CYS84 2.4 45.0 1.0 SG E:CYS146 2.4 40.8 1.0 CE1 E:HIS87 2.9 46.8 1.0 CG E:HIS87 3.2 43.9 1.0 CB E:CYS150 3.2 47.6 1.0 CB E:CYS146 3.3 35.6 1.0 CB E:CYS84 3.5 45.4 1.0 CB E:HIS87 3.6 34.0 1.0 N E:CYS84 3.9 37.6 1.0 CA E:CYS146 3.9 38.0 1.0 NE2 E:HIS87 4.1 43.6 1.0 CD2 E:HIS87 4.2 39.8 1.0 CA E:CYS84 4.3 43.0 1.0 N E:HIS87 4.5 46.4 1.0 N E:PHE147 4.5 42.8 1.0 O E:HOH459 4.5 39.2 1.0 CA E:CYS150 4.6 47.5 1.0 CA E:HIS87 4.7 43.0 1.0 O E:MET145 4.7 38.9 1.0 C E:CYS146 4.8 38.9 1.0 O E:CYS84 4.8 42.9 1.0 C E:CYS84 4.9 44.4 1.0

Zinc binding site 6 out of 8 in the Dna-Binding Domain of A P53 Homolog From the Hydrothermal Vent Annelid Alvinella Pompejana


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Dna-Binding Domain of A P53 Homolog From the Hydrothermal Vent Annelid Alvinella Pompejana within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn301 b:44.6 occ:1.00 ND1 F:HIS87 2.1 42.1 1.0 SG F:CYS84 2.3 44.4 1.0 SG F:CYS150 2.3 45.6 1.0 SG F:CYS146 2.5 37.3 1.0 CE1 F:HIS87 3.1 46.6 1.0 CB F:CYS150 3.1 45.0 1.0 CG F:HIS87 3.1 43.0 1.0 CB F:CYS146 3.3 33.2 1.0 CB F:HIS87 3.5 42.4 1.0 CB F:CYS84 3.5 43.2 1.0 CA F:CYS146 3.9 36.0 1.0 N F:CYS84 4.0 37.3 1.0 NE2 F:HIS87 4.2 46.2 1.0 CD2 F:HIS87 4.2 44.9 1.0 CA F:CYS84 4.3 42.0 1.0 N F:PHE147 4.5 41.6 1.0 CA F:CYS150 4.5 46.2 1.0 N F:HIS87 4.5 45.9 1.0 O F:HOH448 4.6 35.6 1.0 CA F:HIS87 4.6 47.5 1.0 O F:MET145 4.7 40.0 1.0 C F:CYS146 4.8 39.8 1.0 O F:CYS84 4.9 43.1 1.0 C F:CYS84 5.0 43.4 1.0

Zinc binding site 7 out of 8 in the Dna-Binding Domain of A P53 Homolog From the Hydrothermal Vent Annelid Alvinella Pompejana


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Dna-Binding Domain of A P53 Homolog From the Hydrothermal Vent Annelid Alvinella Pompejana within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn301 b:42.5 occ:1.00 ND1 G:HIS87 2.1 41.8 1.0 SG G:CYS150 2.3 41.6 1.0 SG G:CYS84 2.3 43.1 1.0 SG G:CYS146 2.4 39.9 1.0 CE1 G:HIS87 3.1 45.3 1.0 CG G:HIS87 3.1 43.6 1.0 CB G:CYS150 3.2 45.5 1.0 CB G:CYS146 3.3 36.8 1.0 CB G:HIS87 3.5 41.4 1.0 CB G:CYS84 3.5 42.0 1.0 CA G:CYS146 3.9 39.7 1.0 N G:CYS84 4.0 41.1 1.0 NE2 G:HIS87 4.2 40.5 1.0 CD2 G:HIS87 4.2 43.5 1.0 CA G:CYS84 4.3 39.8 1.0 O G:HOH463 4.5 39.4 1.0 N G:PHE147 4.5 42.3 1.0 N G:HIS87 4.5 44.5 1.0 CA G:CYS150 4.6 50.2 1.0 CA G:HIS87 4.6 41.5 1.0 O G:MET145 4.7 37.2 1.0 O G:CYS84 4.8 38.8 1.0 C G:CYS146 4.8 38.5 1.0 C G:CYS84 4.9 43.3 1.0

Zinc binding site 8 out of 8 in the Dna-Binding Domain of A P53 Homolog From the Hydrothermal Vent Annelid Alvinella Pompejana


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Dna-Binding Domain of A P53 Homolog From the Hydrothermal Vent Annelid Alvinella Pompejana within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn301 b:43.7 occ:1.00 ND1 H:HIS87 2.2 40.2 1.0 SG H:CYS150 2.4 40.6 1.0 SG H:CYS84 2.4 43.4 1.0 SG H:CYS146 2.5 39.4 1.0 CE1 H:HIS87 3.1 41.8 1.0 CG H:HIS87 3.1 38.9 1.0 CB H:CYS150 3.2 40.5 1.0 CB H:CYS146 3.3 36.1 1.0 CB H:HIS87 3.4 36.0 1.0 CB H:CYS84 3.6 38.4 1.0 CA H:CYS146 3.9 31.4 1.0 N H:CYS84 4.1 41.3 1.0 NE2 H:HIS87 4.2 45.7 1.0 CD2 H:HIS87 4.3 41.5 1.0 N H:PHE147 4.4 39.1 1.0 CA H:CYS84 4.4 36.2 1.0 N H:HIS87 4.5 41.3 1.0 CA H:CYS150 4.6 41.2 1.0 CA H:HIS87 4.6 39.5 1.0 O H:HOH458 4.6 36.0 1.0 O H:HOH401 4.7 41.5 1.0 C H:CYS146 4.7 36.2 1.0 O H:MET145 4.8 40.0 1.0 O H:CYS84 4.9 41.0 1.0

Q.Zhang, D.I.Balourdas, B.Baron, A.Senitzki, T.E.Haran, K.G.Wiman, T.Soussi, A.C.Joerger. Evolutionary History of the P53 Family Dna-Binding Domain: Insights From An Alvinella Pompejana Homolog. Cell Death Dis V. 13 214 2022.
ISSN: ISSN 2041-4889
PubMed: 35256607
DOI: 10.1038/S41419-022-04653-8