Zinc in PDB 5tkm: Crystal Structure of Human APOBEC3B N-Terminal Domain

The structure of Crystal Structure of Human APOBEC3B N-Terminal Domain, PDB code: 5tkm was solved by X.Xiao, H.Yang, V.Arutiunian, G.Besse, C.Morimoto, B.Zirkle, X.S.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.37 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.739, 60.802, 111.515, 90.00, 90.00, 90.00
R / Rfree (%)	18.8 / 20.3

The binding sites of Zinc atom in the Crystal Structure of Human APOBEC3B N-Terminal Domain (pdb code 5tkm). 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 Human APOBEC3B N-Terminal Domain, PDB code: 5tkm:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Human APOBEC3B N-Terminal 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 Human APOBEC3B N-Terminal Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:24.7 occ:1.00 ND1 A:HIS66 2.0 22.0 1.0 O A:HOH526 2.1 22.1 1.0 SG A:CYS100 2.3 24.5 1.0 SG A:CYS97 2.3 22.9 1.0 CE1 A:HIS66 2.8 30.6 1.0 CG A:HIS66 3.1 27.0 1.0 CB A:CYS100 3.2 23.8 1.0 CB A:CYS97 3.3 23.4 1.0 CB A:HIS66 3.5 24.4 1.0 N A:CYS100 3.9 23.0 1.0 N A:CYS97 4.0 23.2 1.0 NE2 A:HIS66 4.0 28.1 1.0 O A:HOH541 4.0 26.7 1.0 OE1 A:GLU68 4.0 26.5 1.0 CA A:CYS100 4.1 24.7 1.0 CD2 A:HIS66 4.1 23.9 1.0 CA A:CYS97 4.2 22.6 1.0 CB A:PRO63 4.4 32.7 1.0 CA A:PRO63 4.5 35.6 1.0 O A:CYS97 4.6 23.2 1.0 C A:CYS97 4.6 25.5 1.0 CD A:GLU68 4.8 25.8 1.0 O A:HOH587 4.9 45.5 1.0 O A:HOH522 4.9 26.7 1.0 C A:ASP99 5.0 25.7 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Human APOBEC3B N-Terminal 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 Human APOBEC3B N-Terminal Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:24.4 occ:1.00 ND1 B:HIS66 2.0 21.3 1.0 O B:HOH524 2.1 21.8 1.0 SG B:CYS100 2.3 24.8 1.0 SG B:CYS97 2.3 22.8 1.0 CE1 B:HIS66 2.8 29.5 1.0 CG B:HIS66 3.1 26.4 1.0 CB B:CYS100 3.2 22.7 1.0 CB B:CYS97 3.3 22.2 1.0 CB B:HIS66 3.5 24.8 1.0 N B:CYS100 3.9 22.9 1.0 N B:CYS97 4.0 23.2 1.0 NE2 B:HIS66 4.0 28.7 1.0 O B:HOH531 4.0 27.1 1.0 OE1 B:GLU68 4.0 24.8 1.0 CA B:CYS100 4.1 23.4 1.0 CD2 B:HIS66 4.1 25.0 1.0 CA B:CYS97 4.2 23.1 1.0 CB B:PRO63 4.4 33.3 1.0 CA B:PRO63 4.5 34.5 1.0 O B:CYS97 4.6 22.5 1.0 C B:CYS97 4.6 25.3 1.0 CD B:GLU68 4.8 26.3 1.0 O B:HOH587 5.0 47.7 1.0 C B:ASP99 5.0 25.1 1.0 O B:HOH527 5.0 26.2 1.0

X.Xiao, H.Yang, V.Arutiunian, Y.Fang, G.Besse, C.Morimoto, B.Zirkle, X.S.Chen. Structural Determinants of APOBEC3B Non-Catalytic Domain For Molecular Assembly and Catalytic Regulation. Nucleic Acids Res. V. 45 7494 2017.
ISSN: ESSN 1362-4962
PubMed: 28575276
DOI: 10.1093/NAR/GKX362