Zinc in PDB 6p3z: Crystal Structure of Full Length APOBEC3G E/Q (pH 5.2)

The structure of Crystal Structure of Full Length APOBEC3G E/Q (pH 5.2), PDB code: 6p3z 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)	48.17 / 2.84
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	67.788, 153.513, 67.800, 90.00, 114.14, 90.00
R / Rfree (%)	20.4 / 24.6

The binding sites of Zinc atom in the Crystal Structure of Full Length APOBEC3G E/Q (pH 5.2) (pdb code 6p3z). 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 5.2), PDB code: 6p3z:
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 5.2)


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 5.2) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn701 b:37.3 occ:1.00 ND1 A:HIS65 2.2 34.4 1.0 SG A:CYS97 2.4 31.1 1.0 SG A:CYS100 2.5 55.2 1.0 CE1 A:HIS65 3.1 34.8 1.0 CG A:HIS65 3.2 31.9 1.0 CB A:CYS100 3.2 29.2 1.0 CB A:CYS97 3.4 21.1 1.0 CB A:HIS65 3.5 25.0 1.0 OE2 A:GLU67 3.5 42.8 1.0 N A:CYS97 3.7 30.8 1.0 CD A:GLU67 4.0 35.3 1.0 OE1 A:GLU67 4.1 42.9 1.0 CA A:CYS97 4.1 20.4 1.0 NE2 A:HIS65 4.3 32.4 1.0 CD2 A:HIS65 4.3 35.6 1.0 N A:CYS100 4.4 26.8 1.0 CA A:CYS100 4.4 33.1 1.0 CB A:ALA62 4.5 21.8 1.0 C A:CYS97 4.8 24.7 1.0 C A:PRO96 4.9 20.3 1.0 CA A:HIS65 5.0 34.5 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Full Length APOBEC3G E/Q (pH 5.2)


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 5.2) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn701 b:34.0 occ:1.00 ND1 B:HIS65 2.2 24.5 1.0 SG B:CYS97 2.4 28.3 1.0 SG B:CYS100 2.4 38.3 1.0 CE1 B:HIS65 3.1 23.0 1.0 CG B:HIS65 3.2 27.4 1.0 CB B:CYS100 3.3 36.0 1.0 CB B:CYS97 3.3 16.1 1.0 OE2 B:GLU67 3.5 46.1 1.0 CB B:HIS65 3.5 22.3 1.0 N B:CYS97 3.8 40.6 1.0 CD B:GLU67 4.1 37.5 1.0 CA B:CYS97 4.1 29.0 1.0 OE1 B:GLU67 4.1 47.8 1.0 NE2 B:HIS65 4.2 25.2 1.0 CD2 B:HIS65 4.3 31.5 1.0 N B:CYS100 4.4 27.3 1.0 CA B:CYS100 4.5 31.5 1.0 CB B:ALA62 4.5 21.1 1.0 C B:CYS97 4.9 25.2 1.0 C B:PRO96 4.9 25.0 1.0 O B:ALA62 5.0 37.5 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