Zinc in PDB 6p3y: Crystal Structure of Full Length APOBEC3G E/Q (pH 7.4)

The structure of Crystal Structure of Full Length APOBEC3G E/Q (pH 7.4), PDB code: 6p3y 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)	39.17 / 2.57
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	67.695, 153.849, 67.728, 90.00, 116.37, 90.00
R / Rfree (%)	19.6 / 23.8

The binding sites of Zinc atom in the Crystal Structure of Full Length APOBEC3G E/Q (pH 7.4) (pdb code 6p3y). 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 7.4), PDB code: 6p3y:
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 7.4)


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 7.4) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn701 b:42.5 occ:1.00 ND1 A:HIS65 2.0 56.1 1.0 O A:HOH839 2.1 41.2 1.0 SG A:CYS100 2.3 49.9 1.0 SG A:CYS97 2.5 36.9 1.0 CE1 A:HIS65 2.9 52.5 1.0 CG A:HIS65 3.1 53.0 1.0 CB A:CYS97 3.1 30.7 1.0 CB A:CYS100 3.1 42.1 1.0 CB A:HIS65 3.5 50.8 1.0 N A:CYS97 3.7 32.0 1.0 OE2 A:GLU67 3.9 51.8 1.0 CA A:CYS97 4.0 28.8 1.0 OE1 A:GLU67 4.0 54.5 1.0 NE2 A:HIS65 4.1 54.2 1.0 N A:CYS100 4.1 36.0 1.0 CD2 A:HIS65 4.2 55.9 1.0 CD A:GLU67 4.2 45.9 1.0 CA A:CYS100 4.2 42.1 1.0 CB A:ALA62 4.3 41.0 1.0 C A:CYS97 4.6 31.1 1.0 O A:CYS97 4.8 33.0 1.0 C A:PRO96 4.9 35.7 1.0 O A:ALA62 4.9 46.8 1.0 O A:HOH841 4.9 39.2 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Full Length APOBEC3G E/Q (pH 7.4)


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 7.4) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn701 b:43.1 occ:1.00 ND1 B:HIS65 2.1 57.2 1.0 O B:HOH818 2.2 41.2 1.0 SG B:CYS100 2.2 47.8 1.0 SG B:CYS97 2.5 39.3 1.0 CE1 B:HIS65 3.0 51.6 1.0 CG B:HIS65 3.1 52.2 1.0 CB B:CYS100 3.1 37.4 1.0 CB B:CYS97 3.2 29.9 1.0 CB B:HIS65 3.4 48.6 1.0 OE2 B:GLU67 3.8 46.0 1.0 N B:CYS97 3.8 30.0 1.0 OE1 B:GLU67 4.0 45.7 1.0 CA B:CYS97 4.1 31.5 1.0 NE2 B:HIS65 4.1 52.0 1.0 CD B:GLU67 4.1 40.7 1.0 CD2 B:HIS65 4.2 54.2 1.0 N B:CYS100 4.2 31.9 1.0 CB B:ALA62 4.3 42.7 1.0 CA B:CYS100 4.3 38.8 1.0 C B:CYS97 4.7 36.7 1.0 O B:ALA62 4.8 50.0 1.0 O B:CYS97 4.9 36.5 1.0 C B:PRO96 4.9 33.6 1.0 CA B:HIS65 5.0 46.9 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