Zinc in PDB 8edj: Crystal Structure of RA3G-Ssrna-Ga

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

Resolution Low / High (Å)	42.03 / 1.83
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	55.305, 68.058, 129.312, 90, 90, 90
R / Rfree (%)	16.8 / 19.2

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

Zinc binding site 1 out of 2 in the Crystal Structure of RA3G-Ssrna-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-Ssrna-Ga within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:25.6 occ:0.87 ND1 A:HIS65 2.0 32.8 1.0 O A:HOH515 2.0 27.6 1.0 SG A:CYS100 2.3 30.4 1.0 SG A:CYS97 2.4 29.6 1.0 CE1 A:HIS65 3.0 34.8 1.0 CG A:HIS65 3.1 29.2 1.0 CB A:CYS100 3.1 25.3 1.0 CB A:HIS65 3.5 22.7 1.0 CB A:CYS97 3.5 28.8 1.0 N A:CYS97 3.8 28.2 1.0 OE2 A:GLU67 3.9 32.9 1.0 N A:CYS100 4.0 25.4 1.0 NE2 A:HIS65 4.1 32.3 1.0 OE1 A:GLU67 4.1 25.0 1.0 CA A:CYS97 4.2 27.8 1.0 CA A:CYS100 4.2 29.9 1.0 CD2 A:HIS65 4.2 32.6 1.0 CD A:GLU67 4.3 31.0 1.0 CB A:ALA62 4.5 48.7 1.0 O A:HOH564 4.6 35.7 1.0 C A:CYS97 4.7 29.8 1.0 O A:ALA62 4.7 37.2 1.0 O A:CYS97 4.8 27.7 1.0 C A:PRO96 4.9 27.9 1.0 CA A:ALA62 5.0 41.0 1.0 CA A:HIS65 5.0 24.8 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of RA3G-Ssrna-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-Ssrna-Ga within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:26.9 occ:0.85 O4 A:SO4403 1.9 25.4 0.9 ND1 A:HIS257 2.0 33.3 1.0 SG A:CYS290 2.3 30.9 1.0 SG A:CYS287 2.4 31.9 1.0 CE1 A:HIS257 3.0 34.1 1.0 CG A:HIS257 3.1 32.3 1.0 S A:SO4403 3.2 31.1 0.9 CB A:CYS287 3.4 32.8 1.0 CB A:CYS290 3.4 22.9 1.0 CB A:HIS257 3.4 28.6 1.0 O1 A:SO4403 3.6 27.9 0.9 N A:CYS287 3.7 25.4 1.0 O A:HOH537 3.8 23.9 1.0 O2 A:SO4403 3.9 27.2 0.9 O A:HOH769 4.0 32.0 1.0 CA A:CYS287 4.1 30.1 1.0 NE2 A:HIS257 4.1 33.4 1.0 N A:CYS290 4.2 31.3 1.0 CD2 A:HIS257 4.2 31.3 1.0 O3 A:SO4403 4.3 28.9 0.9 CA A:CYS290 4.4 31.5 1.0 O A:HOH710 4.5 42.3 1.0 C A:CYS287 4.6 31.4 1.0 O A:CYS287 4.7 28.4 1.0 C A:PRO286 4.8 26.2 1.0 O A:HOH592 4.8 26.5 1.0 O A:HOH588 4.9 40.5 1.0 CA A:PRO286 4.9 25.1 1.0 CA A:HIS257 5.0 27.7 1.0

H.Yang, K.Kim, S.Li, J.Pacheco, X.S.Chen. Structural Basis of Sequence-Specific Rna Recognition By the Antiviral Factor APOBEC3G. Nat Commun V. 13 7498 2022.
ISSN: ESSN 2041-1723
PubMed: 36470880
DOI: 10.1038/S41467-022-35201-9