Zinc in PDB 8j25: Crystal Structure of Pml B-BOX2 Mutant

The structure of Crystal Structure of Pml B-BOX2 Mutant, PDB code: 8j25 was solved by C.Zhou, N.Zang, J.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.08 / 2.60
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	121.568, 121.568, 161.332, 90, 90, 120
R / Rfree (%)	20.4 / 24.8

The binding sites of Zinc atom in the Crystal Structure of Pml B-BOX2 Mutant (pdb code 8j25). 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 Pml B-BOX2 Mutant, PDB code: 8j25:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Pml B-BOX2 Mutant


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 Pml B-BOX2 Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2501 b:42.5 occ:1.00 NE2 A:HIS194 2.1 46.6 1.0 SG A:CYS212 2.3 42.9 1.0 SG A:CYS215 2.3 36.4 1.0 SG A:CYS189 2.3 45.5 1.0 CE1 A:HIS194 3.1 46.5 1.0 CD2 A:HIS194 3.1 46.6 1.0 CB A:CYS215 3.3 42.6 1.0 CB A:CYS189 3.4 39.0 1.0 CB A:CYS212 3.4 42.7 1.0 N A:CYS212 3.7 41.9 1.0 CB A:ASN191 4.0 47.3 1.0 CA A:CYS212 4.1 43.6 1.0 ND1 A:HIS194 4.2 49.1 1.0 CG A:HIS194 4.2 44.5 1.0 N A:CYS215 4.2 44.9 1.0 CA A:CYS215 4.3 48.1 1.0 ND2 A:ASN191 4.6 50.9 1.0 O A:CYS212 4.7 48.7 1.0 C A:CYS212 4.8 45.9 1.0 CA A:CYS189 4.8 42.7 1.0 C A:LEU211 4.9 44.2 1.0 CG A:ASN191 4.9 48.1 1.0 CG2 A:THR198 4.9 41.3 1.0 N A:ASN191 5.0 51.1 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Pml B-BOX2 Mutant


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 Pml B-BOX2 Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2502 b:67.2 occ:1.00 ND1 A:HIS222 2.1 57.0 1.0 SG A:CYS207 2.3 60.7 1.0 SG A:CYS204 2.3 64.8 1.0 SG A:CYS227 2.3 88.1 1.0 CE1 A:HIS222 3.0 58.9 1.0 CG A:HIS222 3.2 63.2 1.0 CB A:CYS204 3.3 50.6 1.0 CB A:HIS222 3.6 76.0 1.0 CB A:CYS207 3.8 53.2 1.0 N A:CYS207 4.0 53.4 1.0 CB A:CYS227 4.1 98.4 1.0 NE2 A:HIS222 4.1 57.1 1.0 CD2 A:HIS222 4.2 60.3 1.0 CA A:HIS222 4.5 82.2 1.0 CA A:CYS207 4.5 50.7 1.0 CA A:CYS204 4.8 46.8 1.0 N A:GLY206 4.8 57.5 1.0 C A:GLY206 4.8 56.2 1.0 CA A:GLY206 4.9 59.1 1.0 CA A:CYS227 5.0 104.6 1.0

P.Bercier, Q.Q.Wang, N.Zang, J.Zhang, C.Yang, Y.Maimaitiyiming, M.Abou-Ghali, C.Berthier, C.Wu, M.Niwa-Kawakita, T.Dirami, M.C.Geoffroy, O.Ferhi, S.Quentin, S.Benhenda, Y.Ogra, Z.Gueroui, C.Zhou, H.Naranmandura, H.De The, V.Lallemand-Breitenbach. Structural Basis of Pml/Rara Oncoprotein Targeting By Arsenic Unravels A Cysteine Rheostat Controlling Pml Body Assembly and Function. Cancer Discov 2023.
ISSN: ESSN 2159-8290
PubMed: 37655965
DOI: 10.1158/2159-8290.CD-23-0453