Zinc in PDB 5zvb: APOBEC3F Chimeric Catalytic Domain in Complex with Dna(DT9)

The structure of APOBEC3F Chimeric Catalytic Domain in Complex with Dna(DT9), PDB code: 5zvb was solved by C.Cheng, T.L.Zhang, C.X.Wang, W.X.Lan, J.P.Ding, C.Y.Cao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.01 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.990, 92.702, 93.674, 90.00, 90.00, 90.00
R / Rfree (%)	17.2 / 22

The structure of APOBEC3F Chimeric Catalytic Domain in Complex with Dna(DT9) also contains other interesting chemical elements:

Arsenic

(As)

2 atoms

The binding sites of Zinc atom in the APOBEC3F Chimeric Catalytic Domain in Complex with Dna(DT9) (pdb code 5zvb). 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 Chimeric Catalytic Domain in Complex with Dna(DT9), PDB code: 5zvb:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the APOBEC3F Chimeric Catalytic Domain in Complex with Dna(DT9)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of APOBEC3F Chimeric Catalytic Domain in Complex with Dna(DT9) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:40.4 occ:1.00 O1 A:CAC402 2.2 47.8 0.8 ND1 A:HIS249 2.2 39.2 1.0 SG A:CYS280 2.2 38.0 1.0 SG A:CYS283 2.2 41.2 1.0 CB A:CYS283 3.0 39.6 1.0 CE1 A:HIS249 3.1 44.7 1.0 CG A:HIS249 3.3 41.0 1.0 CB A:CYS280 3.4 37.0 1.0 O A:HOH595 3.6 66.5 1.0 AS A:CAC402 3.6 0.0 0.8 CB A:HIS249 3.6 35.3 1.0 N A:CYS283 3.8 39.0 1.0 N A:CYS280 3.8 35.3 1.0 CA A:CYS283 3.9 36.9 1.0 CA A:CYS280 4.1 36.9 1.0 C2 A:CAC402 4.2 79.3 0.8 NE2 A:HIS249 4.2 48.1 1.0 O2 A:CAC402 4.3 63.2 0.8 OE1 A:GLU251 4.3 37.9 1.0 CD2 A:HIS249 4.3 45.1 1.0 OE2 A:GLU251 4.4 43.7 1.0 CD A:GLU251 4.6 37.4 1.0 O A:CYS280 4.6 35.5 1.0 C A:CYS280 4.6 37.7 1.0 C A:PRO279 5.0 35.7 1.0 C A:GLU282 5.0 41.3 1.0

Zinc binding site 2 out of 2 in the APOBEC3F Chimeric Catalytic Domain in Complex with Dna(DT9)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of APOBEC3F Chimeric Catalytic Domain in Complex with Dna(DT9) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:50.8 occ:1.00 ND1 B:HIS249 2.1 56.9 1.0 O1 B:CAC402 2.2 54.0 0.8 SG B:CYS283 2.2 50.1 1.0 SG B:CYS280 2.2 47.2 1.0 CB B:CYS283 2.9 44.9 1.0 CE1 B:HIS249 3.1 60.5 1.0 CG B:HIS249 3.1 54.5 1.0 AS B:CAC402 3.3 55.2 0.8 CB B:HIS249 3.4 49.7 1.0 CB B:CYS280 3.5 54.2 1.0 O2 B:CAC402 3.6 48.8 0.8 N B:CYS280 3.8 45.0 1.0 C1 B:CAC402 3.9 48.9 0.8 CA B:CYS283 4.0 48.2 1.0 N B:CYS283 4.0 52.8 1.0 O B:HOH578 4.0 54.4 1.0 OE2 B:GLU251 4.1 54.3 1.0 OE1 B:GLU251 4.1 50.7 1.0 CA B:CYS280 4.2 51.5 1.0 NE2 B:HIS249 4.2 58.4 1.0 CD2 B:HIS249 4.2 55.7 1.0 CD B:GLU251 4.3 48.8 1.0 O B:CYS280 4.6 47.4 1.0 C B:CYS280 4.7 53.6 1.0 C B:PRO279 4.9 45.1 1.0 CA B:HIS249 4.9 52.0 1.0

C.Cheng, T.Zhang, C.Wang, W.Lan, J.Ding, C.Cao. Crystal Structure of Cytidine Deaminase Human APOBEC3F Chimeric Catalytic Domain in Complex with Dna Chin.J.Chem. V. 36 1241 2018.
ISSN: ISSN 1001-604X
DOI: 10.1002/CJOC.201800508