Zinc in PDB 5hx5: APOBEC3F Catalytic Domain Crystal Structure

The structure of APOBEC3F Catalytic Domain Crystal Structure, PDB code: 5hx5 was solved by N.M.Shaban, K.Shi, H.Aihara, R.S.Harris, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.94 / 2.33
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	35.940, 50.900, 100.860, 90.00, 90.75, 90.00
R / Rfree (%)	22.7 / 26.4

The binding sites of Zinc atom in the APOBEC3F Catalytic Domain Crystal Structure (pdb code 5hx5). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the APOBEC3F Catalytic Domain Crystal Structure, PDB code: 5hx5:
Jump to Zinc binding site number: 1; 2;

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of APOBEC3F Catalytic Domain Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:54.2 occ:1.00 ND1 A:HIS249 2.0 64.0 1.0 SG A:CYS283 2.3 52.5 1.0 SG A:CYS280 2.3 51.8 1.0 O A:HOH517 2.5 41.5 1.0 CE1 A:HIS249 2.9 64.2 1.0 CB A:CYS283 3.1 48.5 1.0 CB A:CYS280 3.2 48.0 1.0 CG A:HIS249 3.2 63.6 1.0 N A:CYS280 3.6 44.4 1.0 CB A:HIS249 3.6 59.4 1.0 CA A:CYS280 3.9 42.1 1.0 OE1 A:GLU251 4.0 58.0 1.0 NE2 A:HIS249 4.0 65.2 1.0 N A:CYS283 4.1 55.8 1.0 CA A:CYS283 4.2 52.4 1.0 CD2 A:HIS249 4.2 66.0 1.0 CD A:GLU251 4.5 59.1 1.0 C A:CYS280 4.6 39.3 1.0 O A:CYS280 4.6 34.6 1.0 C A:PRO279 4.7 43.7 1.0 OE2 A:GLU251 4.7 63.3 1.0 CA A:PRO279 4.9 34.7 1.0

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of APOBEC3F Catalytic Domain Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:67.7 occ:1.00 ND1 B:HIS249 2.0 91.3 1.0 SG B:CYS280 2.3 61.4 1.0 SG B:CYS283 2.4 62.9 1.0 O B:HOH522 2.5 56.4 1.0 CE1 B:HIS249 2.9 91.3 1.0 CB B:CYS280 3.0 59.6 1.0 CG B:HIS249 3.1 90.1 1.0 CB B:CYS283 3.2 58.1 1.0 CB B:HIS249 3.5 81.1 1.0 N B:CYS280 3.6 53.4 1.0 CA B:CYS280 3.9 58.7 1.0 OE2 B:GLU251 4.0 81.2 1.0 NE2 B:HIS249 4.1 91.6 1.0 CD2 B:HIS249 4.2 93.1 1.0 CA B:CYS283 4.5 57.7 1.0 N B:CYS283 4.5 60.6 1.0 CD B:GLU251 4.6 79.5 1.0 C B:CYS280 4.7 53.5 1.0 C B:PRO279 4.8 51.3 1.0 O B:CYS280 4.8 48.3 1.0 OE1 B:GLU251 4.8 83.7 1.0

N.M.Shaban, K.Shi, M.Li, H.Aihara, R.S.Harris. 1.92 Angstrom Zinc-Free APOBEC3F Catalytic Domain Crystal Structure. J.Mol.Biol. V. 428 2307 2016.
ISSN: ESSN 1089-8638
PubMed: 27139641
DOI: 10.1016/J.JMB.2016.04.026