Zinc in PDB 4j4j: Crystal Structure of the APOBEC3F Vif Binding Domain

All present enzymatic activity of Crystal Structure of the APOBEC3F Vif Binding Domain:
3.5.4.5;

The structure of Crystal Structure of the APOBEC3F Vif Binding Domain, PDB code: 4j4j was solved by K.K.Siu, A.Sultana, J.E.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.49 / 3.10
Space group	I 4 2 2
Cell size a, b, c (Å), α, β, γ (°)	164.046, 164.046, 135.315, 90.00, 90.00, 90.00
R / Rfree (%)	23.6 / 27.7

The binding sites of Zinc atom in the Crystal Structure of the APOBEC3F Vif Binding Domain (pdb code 4j4j). 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 the APOBEC3F Vif Binding Domain, PDB code: 4j4j:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of the APOBEC3F Vif Binding Domain


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 the APOBEC3F Vif Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:78.5 occ:1.00 ND1 A:HIS249 1.9 85.1 1.0 SG A:CYS283 2.4 90.6 1.0 SG A:CYS280 2.5 85.7 1.0 HB3 A:CYS280 2.6 76.8 1.0 CE1 A:HIS249 2.6 1.0 1.0 CG A:HIS249 2.7 36.4 1.0 H A:CYS280 2.9 76.7 1.0 HE1 A:HIS249 2.9 0.4 1.0 HB3 A:HIS249 3.0 62.2 1.0 CB A:CYS280 3.0 84.7 1.0 HB2 A:CYS283 3.0 78.2 1.0 CB A:HIS249 3.3 65.8 1.0 CB A:CYS283 3.4 87.2 1.0 NE2 A:HIS249 3.4 93.7 1.0 CD2 A:HIS249 3.5 59.6 1.0 HB2 A:HIS249 3.5 62.2 1.0 H A:CYS283 3.6 79.0 1.0 N A:CYS280 3.6 84.8 1.0 HB2 A:CYS280 3.8 76.8 1.0 CA A:CYS280 3.9 85.0 1.0 OE1 A:GLU251 3.9 0.0 1.0 HB3 A:CYS283 4.0 78.2 1.0 HE2 A:HIS249 4.1 90.1 1.0 HD2 A:HIS249 4.3 56.0 1.0 N A:CYS283 4.3 88.0 1.0 CA A:CYS283 4.4 88.2 1.0 HB3 A:GLU282 4.6 0.3 1.0 C A:CYS280 4.6 86.2 1.0 HB2 A:GLU251 4.6 86.2 1.0 HA A:PRO279 4.7 76.8 1.0 CA A:HIS249 4.7 90.1 1.0 HA A:CYS280 4.7 77.0 1.0 O A:CYS280 4.8 86.7 1.0 C A:PRO279 4.8 85.0 1.0 HA A:HIS249 4.8 70.3 1.0 HB3 A:PRO279 4.9 77.5 1.0 HA A:CYS283 5.0 79.0 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the APOBEC3F Vif Binding Domain


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 the APOBEC3F Vif Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:73.3 occ:1.00 ND1 B:HIS249 2.1 81.0 1.0 SG B:CYS283 2.3 0.3 1.0 SG B:CYS280 2.4 79.4 1.0 HB3 B:CYS280 2.6 70.0 1.0 HB3 B:HIS249 2.7 55.8 1.0 CG B:HIS249 2.7 36.5 1.0 HB2 B:CYS283 2.9 73.0 1.0 CE1 B:HIS249 3.0 0.8 1.0 CB B:CYS280 3.0 78.1 1.0 H B:CYS280 3.1 71.1 1.0 CB B:HIS249 3.1 58.0 1.0 CB B:CYS283 3.2 83.2 1.0 HB2 B:HIS249 3.3 55.8 1.0 HE1 B:HIS249 3.3 0.6 1.0 H B:CYS283 3.5 75.1 1.0 OE1 B:GLU251 3.7 0.3 1.0 HB2 B:CYS280 3.7 70.0 1.0 CD2 B:HIS249 3.8 65.5 1.0 N B:CYS280 3.8 77.4 1.0 HB3 B:CYS283 3.8 73.0 1.0 NE2 B:HIS249 3.8 96.5 1.0 CA B:CYS280 3.9 78.2 1.0 N B:CYS283 4.2 81.9 1.0 CA B:CYS283 4.3 81.4 1.0 HB3 B:GLU282 4.4 0.3 1.0 HD2 B:HIS249 4.5 63.4 1.0 C B:CYS280 4.6 80.0 1.0 CA B:HIS249 4.6 82.5 1.0 HE2 B:HIS249 4.6 94.3 1.0 HB2 B:GLU251 4.6 76.6 1.0 O B:CYS280 4.7 80.3 1.0 CD B:GLU251 4.7 0.2 1.0 HA B:CYS280 4.7 70.7 1.0 HA B:HIS249 4.8 73.5 1.0 HA B:CYS283 4.8 73.7 1.0 HA B:PRO279 4.9 72.4 1.0 C B:PRO279 5.0 79.9 1.0

K.K.Siu, A.Sultana, F.C.Azimi, J.E.Lee. Structural Determinants of Hiv-1 Vif Susceptibility and Dna Binding in APOBEC3F. Nat Commun V. 4 2593 2013.
ISSN: ESSN 2041-1723
PubMed: 24185281
DOI: 10.1038/NCOMMS3593