Zinc in PDB 8tx4: Crystal Structure of RA3G-Ssdna-Ga

The structure of Crystal Structure of RA3G-Ssdna-Ga, PDB code: 8tx4 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)	63.95 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	55.295, 67.977, 127.906, 90, 90, 90
R / Rfree (%)	17.5 / 21.8

The binding sites of Zinc atom in the Crystal Structure of RA3G-Ssdna-Ga (pdb code 8tx4). 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-Ga, PDB code: 8tx4:
Jump to Zinc binding site number: 1; 2;

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


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-Ga within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:28.7 occ:1.00 O A:HOH517 1.9 27.4 1.0 ND1 A:HIS65 2.2 30.4 1.0 SG A:CYS97 2.3 31.3 1.0 SG A:CYS100 2.3 26.6 1.0 CB A:CYS100 3.1 24.2 1.0 CE1 A:HIS65 3.2 36.1 1.0 CG A:HIS65 3.2 31.6 1.0 CB A:CYS97 3.5 29.6 1.0 CB A:HIS65 3.5 26.3 1.0 OE2 A:GLU67 3.7 28.0 1.0 N A:CYS97 3.8 25.3 1.0 N A:CYS100 4.0 31.3 1.0 OE1 A:GLU67 4.1 24.9 1.0 CB A:ALA62 4.1 44.2 1.0 CD A:GLU67 4.1 31.7 1.0 CA A:CYS100 4.2 31.8 1.0 CA A:CYS97 4.2 29.6 1.0 NE2 A:HIS65 4.3 33.9 1.0 CD2 A:HIS65 4.3 33.7 1.0 O A:HOH590 4.5 28.5 1.0 O A:ALA62 4.5 39.9 1.0 CA A:ALA62 4.6 38.4 1.0 C A:CYS97 4.7 30.2 1.0 O A:HOH725 4.8 44.6 1.0 O A:CYS97 4.8 28.8 1.0 O A:HOH734 4.9 43.2 1.0 C A:PRO96 5.0 32.3 1.0

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


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-Ga within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:25.3 occ:1.00 O3 A:PO4403 2.0 23.1 1.0 ND1 A:HIS257 2.2 24.4 1.0 SG A:CYS290 2.3 23.4 1.0 SG A:CYS287 2.3 26.3 1.0 CE1 A:HIS257 3.2 29.2 1.0 CG A:HIS257 3.2 24.8 1.0 P A:PO4403 3.2 26.5 1.0 CB A:CYS290 3.3 25.7 1.0 CB A:CYS287 3.4 26.1 1.0 O2 A:PO4403 3.5 25.0 1.0 CB A:HIS257 3.5 22.6 1.0 N A:CYS287 3.6 25.9 1.0 O A:HOH559 3.9 20.0 1.0 O A:HOH509 3.9 30.0 1.0 O4 A:PO4403 4.0 22.7 1.0 CA A:CYS287 4.0 28.0 1.0 N A:CYS290 4.1 29.8 1.0 CA A:CYS290 4.2 27.4 1.0 NE2 A:HIS257 4.3 25.2 1.0 O A:HOH555 4.3 29.4 1.0 CD2 A:HIS257 4.4 30.2 1.0 O1 A:PO4403 4.4 23.7 1.0 OG A:SER289 4.4 50.2 1.0 C A:CYS287 4.6 29.0 1.0 O A:CYS287 4.7 26.6 1.0 C A:PRO286 4.7 24.7 1.0 O A:HOH562 4.8 21.0 1.0 CA A:PRO286 4.8 23.2 1.0 O A:HOH800 4.9 45.8 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