Zinc in PDB 8cx0: Cryo-Em Structure of Human APOBEC3G/Hiv-1 Vif/Cbfbeta/Elob/Eloc Monomeric Complex

All present enzymatic activity of Cryo-Em Structure of Human APOBEC3G/Hiv-1 Vif/Cbfbeta/Elob/Eloc Monomeric Complex:
3.5.4.38;

The binding sites of Zinc atom in the Cryo-Em Structure of Human APOBEC3G/Hiv-1 Vif/Cbfbeta/Elob/Eloc Monomeric Complex (pdb code 8cx0). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Cryo-Em Structure of Human APOBEC3G/Hiv-1 Vif/Cbfbeta/Elob/Eloc Monomeric Complex, PDB code: 8cx0:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Cryo-Em Structure of Human APOBEC3G/Hiv-1 Vif/Cbfbeta/Elob/Eloc Monomeric Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cryo-Em Structure of Human APOBEC3G/Hiv-1 Vif/Cbfbeta/Elob/Eloc Monomeric Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:89.8 occ:1.00 ND1 A:HIS257 2.3 50.2 1.0 SG A:CYS288 2.3 61.8 1.0 SG A:CYS291 2.3 56.6 1.0 CE1 A:HIS257 2.9 50.2 1.0 CB A:CYS288 3.0 61.8 1.0 CG A:HIS257 3.2 50.2 1.0 CB A:CYS291 3.3 56.6 1.0 N A:CYS288 3.4 61.8 1.0 CA A:CYS288 3.8 61.8 1.0 CB A:HIS257 3.8 50.2 1.0 NE2 A:HIS257 3.9 50.2 1.0 CD2 A:HIS257 4.1 50.2 1.0 OE1 A:GLU259 4.2 49.9 1.0 OE2 A:GLU259 4.2 49.9 1.0 CD A:GLU259 4.3 49.9 1.0 N A:CYS291 4.4 56.6 1.0 CA A:CYS291 4.5 56.6 1.0 C A:CYS288 4.6 61.8 1.0 C A:PRO287 4.6 56.6 1.0 O A:CYS288 4.9 61.8 1.0 CA A:PRO287 4.9 56.6 1.0

Zinc binding site 2 out of 3 in the Cryo-Em Structure of Human APOBEC3G/Hiv-1 Vif/Cbfbeta/Elob/Eloc Monomeric Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cryo-Em Structure of Human APOBEC3G/Hiv-1 Vif/Cbfbeta/Elob/Eloc Monomeric Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:61.3 occ:1.00 SG A:CYS97 2.3 39.0 1.0 ND1 A:HIS65 2.3 38.8 1.0 SG A:CYS100 2.3 42.3 1.0 CB A:CYS100 3.1 42.3 1.0 CE1 A:HIS65 3.2 38.8 1.0 CG A:HIS65 3.4 38.8 1.0 CB A:CYS97 3.5 39.0 1.0 CB A:HIS65 3.7 38.8 1.0 N A:CYS97 3.8 39.0 1.0 OE2 A:GLU67 3.8 35.7 1.0 OE1 A:GLU67 4.1 35.7 1.0 CD1 A:LEU62 4.1 44.4 1.0 CD A:GLU67 4.1 35.7 1.0 N A:CYS100 4.2 42.3 1.0 CA A:CYS97 4.2 39.0 1.0 CA A:CYS100 4.2 42.3 1.0 NE2 A:HIS65 4.3 38.8 1.0 CD2 A:HIS65 4.4 38.8 1.0 C A:CYS97 4.8 39.0 1.0 O A:CYS97 4.9 39.0 1.0 C A:PRO96 4.9 32.8 1.0

Zinc binding site 3 out of 3 in the Cryo-Em Structure of Human APOBEC3G/Hiv-1 Vif/Cbfbeta/Elob/Eloc Monomeric Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Cryo-Em Structure of Human APOBEC3G/Hiv-1 Vif/Cbfbeta/Elob/Eloc Monomeric Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:75.6 occ:1.00 NE2 B:HIS139 2.0 59.1 1.0 NE2 B:HIS108 2.1 51.2 1.0 SG B:CYS133 2.3 67.1 1.0 SG B:CYS114 2.3 63.2 1.0 CE1 B:HIS139 3.0 59.1 1.0 CD2 B:HIS139 3.0 59.1 1.0 CD2 B:HIS108 3.0 51.2 1.0 CE1 B:HIS108 3.0 51.2 1.0 CB B:CYS114 3.1 63.2 1.0 CB B:CYS133 3.5 67.1 1.0 CA B:CYS114 3.7 63.2 1.0 O B:TYR135 3.8 52.5 1.0 O B:ASP113 4.1 59.8 1.0 ND1 B:HIS139 4.1 59.1 1.0 CG C:ARG151 4.1 62.1 1.0 ND1 B:HIS108 4.2 51.2 1.0 CG B:HIS139 4.2 59.1 1.0 CG B:HIS108 4.2 51.2 1.0 CA B:CYS133 4.3 67.1 1.0 N B:CYS114 4.6 63.2 1.0 C B:ASP113 4.7 59.8 1.0 CB C:ARG151 4.7 62.1 1.0 C B:TYR135 4.8 52.5 1.0 C B:CYS114 4.9 63.2 1.0 N B:PHE115 4.9 73.3 1.0 N B:TYR135 4.9 52.5 1.0

Y.Li, C.Langley, C.M.Azumaya, I.Echeverria, N.M.Chesarino, M.Emerman, Y.Cheng, J.D.Gross. The Structural Basis of Hiv-1 Vif Antagonism of Human APOBEC3G Nature 2023.
ISSN: ESSN 1476-4687