Zinc in PDB 5keg: Crystal Structure of APOBEC3A in Complex with A Single-Stranded Dna

The structure of Crystal Structure of APOBEC3A in Complex with A Single-Stranded Dna, PDB code: 5keg was solved by T.Kouno, B.J.Hilbert, T.Silvas, W.E.Royer, H.Matsuo, C.A.Schiffer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.71 / 2.20
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	56.583, 72.666, 114.971, 90.00, 90.00, 90.00
R / Rfree (%)	17.7 / 22.5

The structure of Crystal Structure of APOBEC3A in Complex with A Single-Stranded Dna also contains other interesting chemical elements:

Calcium	(Ca)	1 atom
Chlorine	(Cl)	1 atom

The binding sites of Zinc atom in the Crystal Structure of APOBEC3A in Complex with A Single-Stranded Dna (pdb code 5keg). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Crystal Structure of APOBEC3A in Complex with A Single-Stranded Dna, PDB code: 5keg:

Zinc binding site 1 out of 1 in the Crystal Structure of APOBEC3A in Complex with A Single-Stranded Dna


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 APOBEC3A in Complex with A Single-Stranded Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:38.4 occ:1.00 ND1 A:HIS70 2.1 36.2 1.0 SG A:CYS106 2.1 36.9 1.0 SG A:CYS101 2.3 38.0 1.0 CL A:CL203 2.4 37.7 1.0 CB A:CYS106 3.0 35.2 1.0 CE1 A:HIS70 3.0 38.1 1.0 CG A:HIS70 3.1 31.4 1.0 CB A:CYS101 3.3 30.8 1.0 CB A:HIS70 3.4 34.5 1.0 N A:CYS101 4.0 32.3 1.0 CA A:CYS101 4.1 36.6 1.0 NE2 A:HIS70 4.2 39.9 1.0 CD2 A:HIS70 4.2 32.4 1.0 CA A:CYS106 4.3 28.6 1.0 CB A:TRP104 4.3 41.0 1.0 N A:CYS106 4.3 32.2 1.0 O A:CYS101 4.4 32.0 1.0 C A:CYS101 4.5 33.8 1.0 C4 B:DC3 4.9 34.9 1.0 N3 B:DC3 4.9 32.9 1.0 CA A:HIS70 4.9 28.6 1.0 O B:HOH101 4.9 34.6 1.0

T.Kouno, T.V.Silvas, B.J.Hilbert, S.M.D.Shandilya, M.F.Bohn, B.A.Kelch, W.E.Royer, M.Somasundaran, N.Kurt Yilmaz, H.Matsuo, C.A.Schiffer. Crystal Structure of APOBEC3A Bound to Single-Stranded Dna Reveals Structural Basis For Cytidine Deamination and Specificity. Nat Commun V. 8 15024 2017.
ISSN: ESSN 2041-1723
PubMed: 28452355
DOI: 10.1038/NCOMMS15024