Zinc in PDB 8j2p: Crystal Structure of Pml B-BOX2

The structure of Crystal Structure of Pml B-BOX2, PDB code: 8j2p 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)	35.38 / 2.09
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	122.55, 122.55, 163.224, 90, 90, 120
R / Rfree (%)	19.1 / 23.5

The binding sites of Zinc atom in the Crystal Structure of Pml B-BOX2 (pdb code 8j2p). 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 Pml B-BOX2, PDB code: 8j2p:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Pml B-BOX2


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 within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn501 b:43.1 occ:1.00 NE2 E:HIS194 2.1 45.5 1.0 SG E:CYS212 2.3 46.7 1.0 SG E:CYS215 2.3 48.4 1.0 SG E:CYS189 2.3 46.0 1.0 CE1 E:HIS194 3.0 48.2 1.0 CD2 E:HIS194 3.0 44.0 1.0 CB E:CYS189 3.4 43.5 1.0 CB E:CYS215 3.4 40.9 1.0 CB E:CYS212 3.5 40.5 1.0 N E:CYS212 3.8 41.3 1.0 CB E:ASN191 4.0 48.9 1.0 ND1 E:HIS194 4.1 47.4 1.0 CG E:HIS194 4.2 49.3 1.0 CA E:CYS212 4.2 38.5 1.0 N E:CYS215 4.2 38.8 1.0 CA E:CYS215 4.4 45.4 1.0 ND2 E:ASN191 4.6 49.5 1.0 CA E:CYS189 4.8 47.9 1.0 O E:CYS212 4.8 42.6 1.0 CG E:ASN191 4.8 49.4 1.0 CG2 E:THR198 4.9 42.1 1.0 C E:CYS212 4.9 36.8 1.0 C E:LEU211 4.9 44.5 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Pml B-BOX2


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 within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn502 b:56.1 occ:1.00 ND1 E:HIS222 2.1 59.0 1.0 SG E:CYS204 2.3 51.7 1.0 SG E:CYS227 2.3 87.9 1.0 SG E:CYS207 2.3 59.4 1.0 CE1 E:HIS222 3.0 68.3 1.0 CG E:HIS222 3.1 60.8 1.0 CB E:CYS204 3.2 48.7 1.0 CB E:HIS222 3.5 72.0 1.0 CB E:CYS207 3.7 50.7 1.0 CB E:CYS227 3.7 83.4 1.0 N E:CYS207 3.9 45.1 1.0 CA E:HIS222 3.9 79.9 1.0 NE2 E:HIS222 4.2 71.1 1.0 CD2 E:HIS222 4.2 63.3 1.0 CA E:CYS207 4.4 48.6 1.0 CA E:CYS204 4.6 48.1 1.0 C E:GLY206 4.8 46.5 1.0 N E:GLY206 4.8 50.2 1.0 CA E:GLY206 4.9 47.3 1.0 N E:HIS222 4.9 84.7 1.0 CA E:CYS227 4.9 94.8 1.0 C E:HIS222 4.9 90.0 1.0 C E:CYS204 5.0 46.9 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Pml B-BOX2


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 Pml B-BOX2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:44.0 occ:1.00 NE2 A:HIS194 2.1 48.0 1.0 SG A:CYS215 2.3 47.5 1.0 SG A:CYS212 2.3 44.8 1.0 SG A:CYS189 2.3 44.3 1.0 CE1 A:HIS194 3.0 46.3 1.0 CD2 A:HIS194 3.0 44.5 1.0 CB A:CYS189 3.4 41.2 1.0 CB A:CYS215 3.4 45.4 1.0 CB A:CYS212 3.6 40.4 1.0 N A:CYS212 3.8 43.1 1.0 CB A:ASN191 4.1 52.2 1.0 ND1 A:HIS194 4.1 47.7 1.0 CG A:HIS194 4.2 52.3 1.0 N A:CYS215 4.2 37.6 1.0 CA A:CYS212 4.2 38.9 1.0 CA A:CYS215 4.4 47.7 1.0 ND2 A:ASN191 4.7 50.6 1.0 CA A:CYS189 4.8 45.4 1.0 O A:CYS212 4.8 45.2 1.0 C A:CYS212 4.9 36.2 1.0 CG2 A:THR198 4.9 39.7 1.0 CG A:ASN191 4.9 52.3 1.0 C A:LEU211 5.0 40.9 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Pml B-BOX2


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 Pml B-BOX2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:55.1 occ:1.00 ND1 A:HIS222 2.1 58.1 1.0 SG A:CYS204 2.3 51.7 1.0 SG A:CYS227 2.3 88.8 1.0 SG A:CYS207 2.3 59.9 1.0 CE1 A:HIS222 3.0 63.6 1.0 CG A:HIS222 3.1 65.2 1.0 CB A:CYS204 3.1 48.5 1.0 CB A:HIS222 3.5 72.2 1.0 CB A:CYS207 3.6 50.3 1.0 N A:CYS207 3.9 50.7 1.0 CA A:HIS222 4.0 80.5 1.0 CB A:CYS227 4.0 93.9 1.0 NE2 A:HIS222 4.1 67.5 1.0 CD2 A:HIS222 4.2 59.5 1.0 CA A:CYS207 4.3 50.4 1.0 CA A:CYS204 4.6 42.7 1.0 C A:GLY206 4.9 52.8 1.0 N A:GLY206 4.9 51.3 1.0 N A:HIS222 5.0 80.6 1.0 C A:CYS204 5.0 45.6 1.0 C A:HIS222 5.0 89.6 1.0 CA A:GLY206 5.0 53.5 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