Zinc in PDB 6nil: Cryoem Structure of the Truncated Hiv-1 Vif/Cbfbeta/A3F Complex

All present enzymatic activity of Cryoem Structure of the Truncated Hiv-1 Vif/Cbfbeta/A3F Complex:
3.5.4.38;

The binding sites of Zinc atom in the Cryoem Structure of the Truncated Hiv-1 Vif/Cbfbeta/A3F Complex (pdb code 6nil). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Cryoem Structure of the Truncated Hiv-1 Vif/Cbfbeta/A3F Complex, PDB code: 6nil:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Cryoem Structure of the Truncated Hiv-1 Vif/Cbfbeta/A3F Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cryoem Structure of the Truncated Hiv-1 Vif/Cbfbeta/A3F Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:0.7 occ:1.00 SG A:CYS280 2.5 0.4 1.0 SG A:CYS283 2.5 0.7 1.0 OE1 A:GLU251 2.7 0.9 1.0 ND1 A:HIS249 2.7 0.1 1.0 CG A:HIS249 3.2 0.7 1.0 CB A:HIS249 3.3 0.1 1.0 CE1 A:HIS249 3.7 1.0 1.0 CD A:GLU251 3.7 0.1 1.0 CB A:CYS280 3.8 0.7 1.0 CB A:CYS283 3.8 0.7 1.0 OE2 A:GLU251 4.0 0.5 1.0 N A:CYS280 4.1 0.5 1.0 CD2 A:HIS249 4.3 0.3 1.0 N A:ALA250 4.5 94.9 1.0 NE2 A:HIS249 4.5 0.7 1.0 CA A:HIS249 4.5 0.3 1.0 CA A:CYS280 4.6 0.1 1.0 C A:HIS249 4.8 0.3 1.0 N A:GLU251 4.9 0.3 1.0

Zinc binding site 2 out of 4 in the Cryoem Structure of the Truncated Hiv-1 Vif/Cbfbeta/A3F Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cryoem Structure of the Truncated Hiv-1 Vif/Cbfbeta/A3F Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn501 b:0.7 occ:1.00 SG D:CYS280 2.5 0.4 1.0 SG D:CYS283 2.5 0.7 1.0 OE1 D:GLU251 2.7 0.9 1.0 ND1 D:HIS249 2.7 0.1 1.0 CG D:HIS249 3.2 0.7 1.0 CB D:HIS249 3.3 0.1 1.0 CE1 D:HIS249 3.7 1.0 1.0 CD D:GLU251 3.7 0.1 1.0 CB D:CYS280 3.8 0.7 1.0 CB D:CYS283 3.8 0.7 1.0 OE2 D:GLU251 4.0 0.5 1.0 N D:CYS280 4.1 0.5 1.0 CD2 D:HIS249 4.3 0.3 1.0 N D:ALA250 4.5 94.9 1.0 NE2 D:HIS249 4.5 0.7 1.0 CA D:HIS249 4.5 0.3 1.0 CA D:CYS280 4.6 0.1 1.0 C D:HIS249 4.8 0.3 1.0 N D:GLU251 4.9 0.3 1.0

Zinc binding site 3 out of 4 in the Cryoem Structure of the Truncated Hiv-1 Vif/Cbfbeta/A3F Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Cryoem Structure of the Truncated Hiv-1 Vif/Cbfbeta/A3F Complex within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn501 b:0.7 occ:1.00 SG G:CYS280 2.5 0.4 1.0 SG G:CYS283 2.5 0.7 1.0 OE1 G:GLU251 2.7 0.9 1.0 ND1 G:HIS249 2.7 0.1 1.0 CG G:HIS249 3.2 0.7 1.0 CB G:HIS249 3.3 0.1 1.0 CE1 G:HIS249 3.7 1.0 1.0 CD G:GLU251 3.7 0.1 1.0 CB G:CYS280 3.8 0.7 1.0 CB G:CYS283 3.8 0.7 1.0 OE2 G:GLU251 4.0 0.5 1.0 N G:CYS280 4.1 0.5 1.0 CD2 G:HIS249 4.3 0.3 1.0 N G:ALA250 4.5 94.9 1.0 NE2 G:HIS249 4.5 0.7 1.0 CA G:HIS249 4.5 0.3 1.0 CA G:CYS280 4.6 0.1 1.0 C G:HIS249 4.8 0.3 1.0 N G:GLU251 4.9 0.3 1.0

Zinc binding site 4 out of 4 in the Cryoem Structure of the Truncated Hiv-1 Vif/Cbfbeta/A3F Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Cryoem Structure of the Truncated Hiv-1 Vif/Cbfbeta/A3F Complex within 5.0Å range: probe atom residue distance (Å) B Occ J:Zn501 b:0.7 occ:1.00 SG J:CYS280 2.5 0.4 1.0 SG J:CYS283 2.5 0.7 1.0 OE1 J:GLU251 2.7 0.9 1.0 ND1 J:HIS249 2.7 0.1 1.0 CG J:HIS249 3.2 0.7 1.0 CB J:HIS249 3.3 0.1 1.0 CE1 J:HIS249 3.7 1.0 1.0 CD J:GLU251 3.7 0.1 1.0 CB J:CYS280 3.8 0.7 1.0 CB J:CYS283 3.8 0.7 1.0 OE2 J:GLU251 4.0 0.5 1.0 N J:CYS280 4.1 0.5 1.0 CD2 J:HIS249 4.3 0.3 1.0 N J:ALA250 4.5 94.9 1.0 NE2 J:HIS249 4.5 0.7 1.0 CA J:HIS249 4.5 0.3 1.0 CA J:CYS280 4.6 0.1 1.0 C J:HIS249 4.8 0.3 1.0 N J:GLU251 4.9 0.3 1.0

Y.Hu, B.A.Desimmie, H.C.Nguyen, S.J.Ziegler, T.C.Cheng, J.Chen, J.Wang, H.Wang, K.Zhang, V.K.Pathak, Y.Xiong. Structural Basis of Antagonism of Human APOBEC3F By Hiv-1 Vif. Nat.Struct.Mol.Biol. V. 26 1176 2019.
ISSN: ESSN 1545-9985
PubMed: 31792451
DOI: 10.1038/S41594-019-0343-6