Zinc in PDB 8tvc: Crystal Structure of RA3G-Ssdna-Aa

The structure of Crystal Structure of RA3G-Ssdna-Aa, PDB code: 8tvc was solved by H.Yang, J.I.Pacheco, X.S.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.08 / 1.93
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	55.429, 68.461, 126.735, 90, 90, 90
R / Rfree (%)	17.8 / 20.8

The binding sites of Zinc atom in the Crystal Structure of RA3G-Ssdna-Aa (pdb code 8tvc). 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 RA3G-Ssdna-Aa, PDB code: 8tvc:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of RA3G-Ssdna-Aa


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 RA3G-Ssdna-Aa within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:33.0 occ:1.00 O A:HOH511 2.0 29.2 1.0 ND1 A:HIS65 2.2 37.1 1.0 SG A:CYS100 2.3 33.9 1.0 SG A:CYS97 2.3 34.4 1.0 CE1 A:HIS65 3.2 32.4 1.0 CB A:CYS100 3.2 28.9 1.0 CG A:HIS65 3.2 34.5 1.0 CB A:CYS97 3.4 30.6 1.0 CB A:HIS65 3.5 26.2 1.0 N A:CYS97 3.8 32.4 1.0 OE2 A:GLU67 3.9 39.1 1.0 N A:CYS100 4.0 36.4 1.0 CA A:CYS97 4.1 35.9 1.0 CA A:CYS100 4.2 38.2 1.0 OE1 A:GLU67 4.2 29.2 1.0 CD A:GLU67 4.3 39.8 1.0 NE2 A:HIS65 4.3 33.4 1.0 CB A:ALA62 4.3 38.7 1.0 CD2 A:HIS65 4.4 34.2 1.0 O A:HOH616 4.5 33.6 1.0 C A:CYS97 4.6 39.5 1.0 O A:CYS97 4.7 32.5 1.0 O A:ALA62 4.7 43.9 1.0 CA A:ALA62 4.9 47.5 1.0 O A:HOH707 4.9 42.4 1.0 C A:PRO96 5.0 31.2 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of RA3G-Ssdna-Aa


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 RA3G-Ssdna-Aa within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:30.0 occ:1.00 O3 A:PO4403 2.0 34.1 1.0 ND1 A:HIS257 2.2 29.6 1.0 SG A:CYS287 2.3 32.7 1.0 SG A:CYS290 2.3 28.6 1.0 CE1 A:HIS257 3.2 35.9 1.0 CG A:HIS257 3.2 29.6 1.0 P A:PO4403 3.2 32.6 1.0 CB A:CYS290 3.3 32.2 1.0 CB A:CYS287 3.3 31.4 1.0 CB A:HIS257 3.5 27.8 1.0 O4 A:PO4403 3.5 30.2 1.0 N A:CYS287 3.7 28.7 1.0 O A:HOH559 3.9 25.9 1.0 O A:HOH714 4.0 41.6 1.0 O1 A:PO4403 4.0 28.1 1.0 CA A:CYS287 4.0 30.3 1.0 N A:CYS290 4.1 33.3 1.0 CA A:CYS290 4.3 32.8 1.0 NE2 A:HIS257 4.3 33.5 1.0 CD2 A:HIS257 4.3 31.9 1.0 O2 A:PO4403 4.4 31.6 1.0 O A:HOH566 4.4 38.6 1.0 C A:CYS287 4.6 33.3 1.0 O A:CYS287 4.6 34.4 1.0 C A:PRO286 4.7 32.9 1.0 O A:HOH549 4.8 32.5 1.0 O A:HOH560 4.8 27.7 1.0 CA A:PRO286 4.9 28.7 1.0 CA A:HIS257 5.0 26.2 1.0

H.Yang, J.Pacheco, K.Kim, A.Bokani, F.Ito, D.Ebrahimi, X.S.Chen. Molecular Mechanism For Regulating APOBEC3G Dna Editing Function By the Non-Catalytic Domain. Nat Commun V. 15 8773 2024.
ISSN: ESSN 2041-1723
PubMed: 39389938
DOI: 10.1038/S41467-024-52671-1