Zinc in PDB 6p3x: Crystal Structure of Full Length APOBEC3G E/Q (pH 7.0)

The structure of Crystal Structure of Full Length APOBEC3G E/Q (pH 7.0), PDB code: 6p3x was solved by 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)	47.84 / 2.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	67.495, 153.241, 67.494, 90.00, 114.87, 90.00
R / Rfree (%)	18.9 / 23.7

The binding sites of Zinc atom in the Crystal Structure of Full Length APOBEC3G E/Q (pH 7.0) (pdb code 6p3x). 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 Full Length APOBEC3G E/Q (pH 7.0), PDB code: 6p3x:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Full Length APOBEC3G E/Q (pH 7.0)


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 Full Length APOBEC3G E/Q (pH 7.0) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn701 b:41.8 occ:1.00 ND1 A:HIS65 2.1 41.1 1.0 O A:HOH838 2.1 42.1 1.0 SG A:CYS100 2.4 48.9 1.0 SG A:CYS97 2.4 40.7 1.0 CE1 A:HIS65 3.0 44.4 1.0 CG A:HIS65 3.1 43.6 1.0 CB A:CYS97 3.2 26.2 1.0 CB A:CYS100 3.3 32.9 1.0 CB A:HIS65 3.4 46.3 1.0 N A:CYS97 3.8 34.8 1.0 CB A:ALA62 4.0 37.2 1.0 CA A:CYS97 4.0 33.9 1.0 OE2 A:GLU67 4.1 45.2 1.0 OE1 A:GLU67 4.1 39.1 1.0 NE2 A:HIS65 4.2 41.0 1.0 N A:CYS100 4.2 26.4 1.0 CD2 A:HIS65 4.2 41.3 1.0 CD A:GLU67 4.3 35.2 1.0 CA A:CYS100 4.4 37.2 1.0 C A:CYS97 4.7 34.4 1.0 O A:ALA62 4.8 41.4 1.0 CA A:ALA62 4.8 43.5 1.0 O A:CYS97 4.9 39.1 1.0 C A:PRO96 4.9 34.4 1.0 O A:HOH839 5.0 55.8 1.0 CA A:HIS65 5.0 41.7 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Full Length APOBEC3G E/Q (pH 7.0)


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 Full Length APOBEC3G E/Q (pH 7.0) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn701 b:39.0 occ:1.00 O B:HOH836 2.1 42.1 1.0 ND1 B:HIS65 2.1 42.0 1.0 SG B:CYS100 2.3 45.1 1.0 SG B:CYS97 2.4 35.9 1.0 CE1 B:HIS65 3.0 46.2 1.0 CG B:HIS65 3.1 45.8 1.0 CB B:CYS100 3.2 32.0 1.0 CB B:CYS97 3.3 29.3 1.0 CB B:HIS65 3.4 37.6 1.0 N B:CYS97 3.9 34.0 1.0 OE2 B:GLU67 4.1 44.2 1.0 OE1 B:GLU67 4.1 40.1 1.0 CA B:CYS97 4.1 35.6 1.0 N B:CYS100 4.1 26.0 1.0 CB B:ALA62 4.1 36.0 1.0 NE2 B:HIS65 4.1 45.2 1.0 CD2 B:HIS65 4.2 42.2 1.0 CD B:GLU67 4.3 34.7 1.0 CA B:CYS100 4.3 41.5 1.0 C B:CYS97 4.7 40.6 1.0 O B:CYS97 4.8 38.0 1.0 O B:ALA62 4.8 42.5 1.0 CA B:ALA62 4.9 43.1 1.0 O B:HOH862 4.9 52.3 1.0 CA B:HIS65 5.0 44.7 1.0 C B:PRO96 5.0 34.1 1.0

H.Yang, F.Ito, A.D.Wolfe, S.Li, N.Mohammadzadeh, R.P.Love, M.Yan, B.Zirkle, A.Gaba, L.Chelico, X.S.Chen. Understanding the Structural Basis of Hiv-1 Restriction By the Full Length Double-Domain APOBEC3G. Nat Commun V. 11 632 2020.
ISSN: ESSN 2041-1723
PubMed: 32005813
DOI: 10.1038/S41467-020-14377-Y