Zinc in PDB 6p40: Crystal Structure of Full Length APOBEC3G Fkl

The structure of Crystal Structure of Full Length APOBEC3G Fkl, PDB code: 6p40 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)	46.70 / 2.45
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	62.067, 86.423, 90.158, 90.00, 101.38, 90.00
R / Rfree (%)	17.3 / 22.8

The binding sites of Zinc atom in the Crystal Structure of Full Length APOBEC3G Fkl (pdb code 6p40). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Full Length APOBEC3G Fkl, PDB code: 6p40:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Full Length APOBEC3G Fkl


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 Fkl within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn701 b:44.6 occ:1.00 ND1 A:HIS65 2.0 40.7 1.0 SG A:CYS100 2.2 35.5 1.0 SG A:CYS97 2.3 36.6 1.0 CE1 A:HIS65 2.9 41.4 1.0 CG A:HIS65 3.0 42.7 1.0 CB A:CYS100 3.1 34.7 1.0 CB A:HIS65 3.4 36.4 1.0 CB A:CYS97 3.4 26.1 1.0 N A:CYS97 3.8 34.2 1.0 OE1 A:GLU67 3.8 56.7 1.0 NE2 A:HIS65 4.0 39.6 1.0 N A:CYS100 4.1 33.4 1.0 CD2 A:HIS65 4.1 42.9 1.0 CA A:CYS97 4.1 29.4 1.0 CA A:CYS100 4.2 36.1 1.0 CD A:GLU67 4.4 56.8 1.0 CB A:ALA62 4.5 36.9 1.0 O A:CYS97 4.6 41.1 1.0 OE2 A:GLU67 4.7 61.7 1.0 C A:CYS97 4.7 36.1 1.0 C A:PRO96 4.9 35.1 1.0 CA A:HIS65 4.9 38.4 1.0 O A:ALA62 5.0 43.3 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Full Length APOBEC3G Fkl


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 Fkl within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn702 b:46.1 occ:1.00 SG A:CYS290 2.1 41.8 1.0 ND1 A:HIS257 2.1 49.2 1.0 SG A:CYS287 2.4 41.5 1.0 O A:HOH859 3.0 40.9 1.0 CE1 A:HIS257 3.0 45.6 1.0 CG A:HIS257 3.1 47.7 1.0 CB A:CYS290 3.3 39.1 1.0 CB A:CYS287 3.4 30.4 1.0 CB A:HIS257 3.5 33.8 1.0 N A:CYS287 3.7 42.1 1.0 CA A:CYS287 4.1 34.7 1.0 NE2 A:HIS257 4.2 45.3 1.0 CD2 A:HIS257 4.2 43.2 1.0 N A:CYS290 4.2 32.1 1.0 CA A:CYS290 4.4 36.0 1.0 C A:CYS287 4.7 37.1 1.0 O A:CYS287 4.8 47.2 1.0 C A:PRO286 4.8 39.3 1.0 CA A:PRO286 4.9 32.4 1.0 O A:HOH857 5.0 43.5 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Full Length APOBEC3G Fkl


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Full Length APOBEC3G Fkl within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn701 b:41.8 occ:1.00 ND1 B:HIS65 2.1 45.1 1.0 SG B:CYS100 2.2 39.2 1.0 O B:HOH828 2.2 59.3 1.0 SG B:CYS97 2.4 51.4 1.0 CB B:CYS97 3.0 19.0 1.0 CE1 B:HIS65 3.0 32.9 1.0 CG B:HIS65 3.1 38.8 1.0 CB B:CYS100 3.2 30.4 1.0 CB B:HIS65 3.5 23.3 1.0 N B:CYS97 3.6 20.7 1.0 CA B:CYS97 3.8 22.6 1.0 OE1 B:GLU67 3.9 50.9 1.0 NE2 B:HIS65 4.1 40.5 1.0 N B:CYS100 4.2 26.6 1.0 CD2 B:HIS65 4.2 40.2 1.0 CA B:CYS100 4.3 33.9 1.0 C B:CYS97 4.4 37.4 1.0 O B:CYS97 4.5 37.9 1.0 CD B:GLU67 4.5 47.8 1.0 CB B:ALA62 4.6 36.3 1.0 OE2 B:GLU67 4.7 57.6 1.0 C B:PRO96 4.8 40.3 1.0 O B:ALA62 4.9 47.5 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Full Length APOBEC3G Fkl


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Full Length APOBEC3G Fkl within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn702 b:55.5 occ:1.00 ND1 B:HIS257 2.0 45.7 1.0 SG B:CYS290 2.2 53.5 1.0 SG B:CYS287 2.2 46.2 1.0 CE1 B:HIS257 2.9 43.6 1.0 CB B:CYS287 3.1 41.0 1.0 CG B:HIS257 3.2 43.2 1.0 CB B:CYS290 3.4 46.4 1.0 N B:CYS287 3.5 39.7 1.0 CB B:HIS257 3.6 40.4 1.0 CA B:CYS287 3.8 45.1 1.0 NE2 B:HIS257 4.1 46.9 1.0 CD2 B:HIS257 4.2 40.9 1.0 N B:CYS290 4.2 39.7 1.0 C B:CYS287 4.4 46.3 1.0 CA B:CYS290 4.5 44.6 1.0 O B:CYS287 4.6 44.4 1.0 C B:PRO286 4.7 46.2 1.0 CA B:PRO286 5.0 40.8 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