Zinc in PDB 8vud: Crystal Structure of APOBEC3F-CD1

The structure of Crystal Structure of APOBEC3F-CD1, PDB code: 8vud was solved by H.J.Yang, S.-X.Li, J.Pacheco, X.S.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.21 / 2.60
Space group	P 6
Cell size a, b, c (Å), α, β, γ (°)	124.388, 124.388, 64.011, 90, 90, 120
R / Rfree (%)	17.8 / 23.9

The binding sites of Zinc atom in the Crystal Structure of APOBEC3F-CD1 (pdb code 8vud). 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 APOBEC3F-CD1, PDB code: 8vud:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of APOBEC3F-CD1


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 APOBEC3F-CD1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:50.5 occ:1.00 ND1 A:HIS65 2.1 49.5 1.0 O A:HOH305 2.3 49.2 1.0 SG A:CYS96 2.3 50.9 1.0 SG A:CYS99 2.4 52.7 1.0 CB A:CYS96 2.7 59.3 1.0 CE1 A:HIS65 3.1 43.2 1.0 CG A:HIS65 3.2 51.1 1.0 CB A:CYS99 3.2 52.5 1.0 OD1 A:ASN31 3.5 51.1 1.0 CB A:HIS65 3.5 33.2 1.0 CA A:CYS96 3.8 57.8 1.0 N A:CYS96 3.9 51.0 1.0 N A:CYS99 4.1 46.0 1.0 NE2 A:HIS65 4.2 55.6 1.0 CA A:CYS99 4.2 46.4 1.0 CD2 A:HIS65 4.3 53.8 1.0 OE1 A:GLU67 4.3 41.9 1.0 OE2 A:GLU67 4.3 46.4 1.0 CG A:ASN31 4.4 52.0 1.0 CD A:GLU67 4.4 46.3 1.0 C A:CYS96 4.9 48.4 1.0 C A:PRO95 5.0 43.3 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of APOBEC3F-CD1


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 APOBEC3F-CD1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:112.2 occ:1.00 CD2 A:HIS64 3.3 66.8 1.0 NZ A:LYS102 3.4 60.2 1.0 NE2 A:HIS64 3.6 71.4 1.0 CG A:MET68 4.2 48.1 1.0 CB A:MET68 4.3 37.0 1.0 CE A:LYS102 4.6 80.3 1.0 CD A:LYS102 4.6 75.4 1.0 CG A:HIS64 4.6 69.1 1.0 SD A:MET68 4.8 59.4 1.0 CE1 A:HIS64 4.9 71.5 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of APOBEC3F-CD1


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 APOBEC3F-CD1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:63.0 occ:1.00 ND1 B:HIS65 2.3 55.2 1.0 SG B:CYS99 2.5 64.0 1.0 SG B:CYS96 2.5 68.8 1.0 CB B:CYS96 2.8 67.2 1.0 ND2 B:ASN31 2.9 65.9 1.0 CB B:CYS99 3.1 66.1 1.0 CG B:HIS65 3.2 55.0 1.0 CE1 B:HIS65 3.3 46.8 1.0 CB B:HIS65 3.5 54.5 1.0 N B:CYS96 3.8 61.6 1.0 CA B:CYS96 3.9 64.7 1.0 CG B:ASN31 4.0 63.1 1.0 N B:CYS99 4.0 54.2 1.0 CA B:CYS99 4.2 65.4 1.0 OE2 B:GLU67 4.2 72.1 1.0 NE2 B:HIS65 4.4 59.6 1.0 CD2 B:HIS65 4.4 49.5 1.0 CD B:GLU67 4.4 57.4 1.0 OE1 B:GLU67 4.4 68.7 1.0 OD1 B:ASN31 4.6 61.8 1.0 C B:PRO95 4.9 58.1 1.0 CB B:PRO95 4.9 76.1 1.0 CA B:PRO95 5.0 66.3 1.0 CA B:HIS65 5.0 58.5 1.0 CB B:ASN31 5.0 53.6 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of APOBEC3F-CD1


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 APOBEC3F-CD1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn202 b:103.9 occ:1.00 CD2 B:HIS64 3.2 68.1 1.0 NE2 B:HIS64 3.6 71.9 1.0 CG B:MET68 4.1 54.4 1.0 CB B:MET68 4.2 49.4 1.0 CG B:HIS64 4.4 69.0 1.0 SD B:MET68 4.6 68.9 1.0 CE B:LYS102 4.8 88.8 1.0 NZ B:LYS102 4.8 93.7 1.0 CD B:LYS102 4.8 79.0 1.0 CE1 B:HIS64 4.9 62.1 1.0

J.Pacheco, H.J.Yang, S.-X.Li, X.S.Chen. Crystal Structure of APOBEC3F-CD1 To Be Published.