Zinc in PDB 4iou: Crystal Structure of the Hiv-1 Vif Binding, Catalytically Active Domain of APOBEC3F

The structure of Crystal Structure of the Hiv-1 Vif Binding, Catalytically Active Domain of APOBEC3F, PDB code: 4iou was solved by M.Bohn, S.M.D.Shandilya, C.A.Schiffer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.46 / 2.75
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	50.790, 66.910, 75.640, 110.75, 94.41, 108.83
R / Rfree (%)	19.3 / 23.3

The binding sites of Zinc atom in the Crystal Structure of the Hiv-1 Vif Binding, Catalytically Active Domain of APOBEC3F (pdb code 4iou). 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 the Hiv-1 Vif Binding, Catalytically Active Domain of APOBEC3F, PDB code: 4iou:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of the Hiv-1 Vif Binding, Catalytically Active Domain of APOBEC3F


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 Hiv-1 Vif Binding, Catalytically Active Domain of APOBEC3F within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:61.2 occ:1.00 ND1 A:HIS249 2.1 53.6 1.0 SG A:CYS280 2.5 53.5 1.0 SG A:CYS283 2.5 60.8 1.0 CE1 A:HIS249 2.9 58.2 1.0 CB A:CYS280 3.0 36.6 1.0 CB A:CYS283 3.1 42.1 1.0 CG A:HIS249 3.2 57.7 1.0 N A:CYS280 3.4 44.1 1.0 CB A:HIS249 3.7 55.6 1.0 CA A:CYS280 3.8 38.0 1.0 OE1 A:GLU251 3.8 48.2 1.0 NE2 A:HIS249 4.1 50.4 1.0 CD A:GLU251 4.2 53.7 1.0 N A:CYS283 4.2 45.5 1.0 CD2 A:HIS249 4.2 60.6 1.0 CA A:CYS283 4.3 41.1 1.0 O A:CYS280 4.3 39.1 1.0 C A:CYS280 4.4 41.9 1.0 OE2 A:GLU251 4.4 56.7 1.0 C A:PRO279 4.6 42.9 1.0 CA A:PRO279 4.9 41.0 1.0 CG A:GLU251 4.9 46.4 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of the Hiv-1 Vif Binding, Catalytically Active Domain of APOBEC3F


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 Hiv-1 Vif Binding, Catalytically Active Domain of APOBEC3F within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1001 b:49.3 occ:1.00 ND1 B:HIS249 2.1 45.7 1.0 SG B:CYS283 2.4 47.6 1.0 SG B:CYS280 2.5 47.0 1.0 CE1 B:HIS249 3.0 45.8 1.0 CB B:CYS280 3.0 38.2 1.0 CB B:CYS283 3.0 41.5 1.0 CG B:HIS249 3.1 48.0 1.0 O B:HOH1123 3.2 36.2 1.0 N B:CYS280 3.3 32.6 1.0 CB B:HIS249 3.5 44.0 1.0 CA B:CYS280 3.7 33.0 1.0 OE1 B:GLU251 3.8 42.7 1.0 NE2 B:HIS249 4.1 45.0 1.0 CD B:GLU251 4.1 47.3 1.0 N B:CYS283 4.2 42.6 1.0 CA B:CYS283 4.2 43.6 1.0 CD2 B:HIS249 4.2 44.5 1.0 OE2 B:GLU251 4.3 48.3 1.0 O B:CYS280 4.4 42.4 1.0 C B:CYS280 4.4 40.6 1.0 C B:PRO279 4.5 38.1 1.0 CA B:PRO279 4.7 31.9 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of the Hiv-1 Vif Binding, Catalytically Active Domain of APOBEC3F


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 the Hiv-1 Vif Binding, Catalytically Active Domain of APOBEC3F within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1001 b:50.2 occ:1.00 ND1 C:HIS249 2.1 50.7 1.0 SG C:CYS280 2.4 37.1 1.0 SG C:CYS283 2.5 57.3 1.0 CB C:CYS283 3.0 40.9 1.0 CE1 C:HIS249 3.0 37.3 1.0 CG C:HIS249 3.1 52.1 1.0 CB C:CYS280 3.4 31.2 1.0 CB C:HIS249 3.4 43.6 1.0 N C:CYS280 3.6 36.3 1.0 OE1 C:GLU251 3.8 47.1 1.0 CA C:CYS280 4.0 38.5 1.0 NE2 C:HIS249 4.1 36.5 1.0 OE2 C:GLU251 4.2 49.5 1.0 CD C:GLU251 4.2 49.8 1.0 CD2 C:HIS249 4.2 44.3 1.0 CA C:CYS283 4.2 42.5 1.0 N C:CYS283 4.3 39.6 1.0 O C:CYS280 4.4 36.9 1.0 C C:CYS280 4.6 40.0 1.0 C C:PRO279 4.7 39.0 1.0 CA C:PRO279 4.9 39.5 1.0 CA C:HIS249 4.9 46.2 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of the Hiv-1 Vif Binding, Catalytically Active Domain of APOBEC3F


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 the Hiv-1 Vif Binding, Catalytically Active Domain of APOBEC3F within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1001 b:45.5 occ:1.00 ND1 D:HIS249 2.0 43.0 1.0 O D:HOH1108 2.0 25.3 1.0 SG D:CYS280 2.4 43.6 1.0 SG D:CYS283 2.4 39.5 1.0 CE1 D:HIS249 2.6 49.2 1.0 CB D:CYS280 2.7 27.2 1.0 CB D:CYS283 2.9 28.2 1.0 CG D:HIS249 3.2 42.3 1.0 N D:CYS280 3.5 32.3 1.0 CA D:CYS280 3.6 28.9 1.0 N D:CYS283 3.8 34.1 1.0 CB D:HIS249 3.8 40.1 1.0 NE2 D:HIS249 3.9 46.2 1.0 CA D:CYS283 3.9 32.5 1.0 O D:CYS280 4.1 25.7 1.0 CD2 D:HIS249 4.1 44.5 1.0 C D:CYS280 4.1 32.6 1.0 OE1 D:GLU251 4.3 37.0 1.0 CD D:GLU251 4.7 39.9 1.0 C D:PRO279 4.7 33.6 1.0 OE2 D:GLU251 4.8 42.1 1.0 C D:GLU282 4.9 32.8 1.0

M.F.Bohn, S.M.Shandilya, J.S.Albin, T.Kouno, B.D.Anderson, R.M.Mcdougle, M.A.Carpenter, A.Rathore, L.Evans, A.N.Davis, J.Zhang, Y.Lu, M.Somasundaran, H.Matsuo, R.S.Harris, C.A.Schiffer. Crystal Structure of the Dna Cytosine Deaminase APOBEC3F: the Catalytically Active and Hiv-1 Vif-Binding Domain. Structure V. 21 1042 2013.
ISSN: ISSN 0969-2126
PubMed: 23685212
DOI: 10.1016/J.STR.2013.04.010