Chlorine in PDB 5td5: Crystal Structure of Human APOBEC3B Variant Complexed with Ssdna

The structure of Crystal Structure of Human APOBEC3B Variant Complexed with Ssdna, PDB code: 5td5 was solved by K.Shi, S.Banerjee, K.Kurahashi, H.Aihara, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	83.49 / 1.72
Space group	P 64 2 2
Cell size a, b, c (Å), α, β, γ (°)	96.411, 96.411, 84.875, 90.00, 90.00, 120.00
R / Rfree (%)	18 / 20.9

The structure of Crystal Structure of Human APOBEC3B Variant Complexed with Ssdna also contains other interesting chemical elements:

Zinc	(Zn)	1 atom
Iodine	(I)	9 atoms

The binding sites of Chlorine atom in the Crystal Structure of Human APOBEC3B Variant Complexed with Ssdna (pdb code 5td5). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Crystal Structure of Human APOBEC3B Variant Complexed with Ssdna, PDB code: 5td5:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the Crystal Structure of Human APOBEC3B Variant Complexed with Ssdna


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Human APOBEC3B Variant Complexed with Ssdna within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl416 b:49.9 occ:1.00 HD2 A:ARG372 3.1 53.0 1.0 HG3 A:ARG372 3.5 57.0 1.0 NE A:ARG372 3.7 37.9 1.0 CD A:ARG372 3.7 44.2 1.0 HE A:ARG372 3.8 45.5 1.0 CG A:ARG372 4.0 47.5 1.0 CZ A:ARG372 4.2 37.6 1.0 HG2 A:ARG372 4.2 57.0 1.0 HH11 A:ARG372 4.6 42.4 1.0 I A:IOD406 4.6 0.4 0.3 NH1 A:ARG372 4.6 35.3 1.0 HD3 A:ARG372 4.6 53.0 1.0 NH2 A:ARG372 4.7 48.4 1.0 HH21 A:ARG372 4.8 58.1 1.0

Chlorine binding site 2 out of 2 in the Crystal Structure of Human APOBEC3B Variant Complexed with Ssdna


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Human APOBEC3B Variant Complexed with Ssdna within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl417 b:38.4 occ:1.00 ZN A:ZN401 2.2 23.7 1.0 H A:CYS284 2.3 32.7 1.0 HB2 A:CYS289 2.8 44.7 1.0 HA A:PRO283 2.9 31.0 1.0 N A:CYS284 3.1 27.3 1.0 O C:HOH203 3.1 28.5 1.0 HB3 A:CYS289 3.1 44.7 1.0 CB A:CYS289 3.2 37.2 1.0 HB3 A:HIS253 3.2 35.1 1.0 H42 C:DC0 3.3 34.7 1.0 SG A:CYS289 3.4 45.6 1.0 HB3 A:PRO283 3.4 31.5 1.0 ND1 A:HIS253 3.4 29.9 1.0 N4 C:DC0 3.5 28.9 1.0 HB2 A:HIS253 3.5 35.1 1.0 HB3 A:CYS284 3.6 30.6 1.0 CA A:PRO283 3.6 25.8 1.0 HB3 A:ALA255 3.7 30.5 1.0 CB A:HIS253 3.7 29.2 1.0 C4 C:DC0 3.8 22.9 1.0 SG A:CYS284 3.8 34.1 1.0 H41 C:DC0 3.8 34.7 1.0 N3 C:DC0 3.8 23.1 1.0 C A:PRO283 3.9 28.9 1.0 CB A:CYS284 3.9 25.5 1.0 CG A:HIS253 4.0 32.0 1.0 CB A:PRO283 4.0 26.3 1.0 CA A:CYS284 4.1 27.1 1.0 HB2 A:ALA255 4.1 30.5 1.0 H A:ALA255 4.3 35.0 1.0 CB A:ALA255 4.3 25.4 1.0 O A:CYS284 4.5 27.2 1.0 CE1 A:HIS253 4.6 30.9 1.0 C5 C:DC0 4.6 28.2 1.0 HB2 A:PRO283 4.6 31.5 1.0 CA A:CYS289 4.7 41.9 1.0 C2 C:DC0 4.7 27.7 1.0 C A:CYS284 4.7 28.2 1.0 HG3 A:PRO283 4.8 35.6 1.0 HE1 A:HIS253 4.8 37.1 1.0 HA A:CYS284 4.9 32.5 1.0 H A:CYS289 4.9 43.0 1.0 HB2 A:CYS284 4.9 30.6 1.0 N A:PRO283 4.9 26.1 1.0 H5 C:DC0 4.9 33.8 1.0 HB1 A:ALA255 5.0 30.5 1.0 HG A:LEU256 5.0 47.1 1.0

K.Shi, M.A.Carpenter, S.Banerjee, N.M.Shaban, K.Kurahashi, D.J.Salamango, J.L.Mccann, G.J.Starrett, J.V.Duffy, O.Demir, R.E.Amaro, D.A.Harki, R.S.Harris, H.Aihara. Structural Basis For Targeted Dna Cytosine Deamination and Mutagenesis By APOBEC3A and APOBEC3B. Nat. Struct. Mol. Biol. V. 24 131 2017.
ISSN: ESSN 1545-9985
PubMed: 27991903
DOI: 10.1038/NSMB.3344