Chlorine in PDB 6bkg: Human Ligiv Catalytic Domain with Bound Dna-Adenylate Intermediate in Closed Conformation

All present enzymatic activity of Human Ligiv Catalytic Domain with Bound Dna-Adenylate Intermediate in Closed Conformation:
6.5.1.1;

The structure of Human Ligiv Catalytic Domain with Bound Dna-Adenylate Intermediate in Closed Conformation, PDB code: 6bkg was solved by A.F.Moon, P.P.Tumbale, M.J.Schellenberg, R.S.Williams, J.G.Williams, T.A.Kunkel, L.C.Pedersen, B.Bebenek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.20 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	72.657, 102.747, 110.131, 90.00, 90.00, 90.00
R / Rfree (%)	20.1 / 24.5

The structure of Human Ligiv Catalytic Domain with Bound Dna-Adenylate Intermediate in Closed Conformation also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Chlorine atom in the Human Ligiv Catalytic Domain with Bound Dna-Adenylate Intermediate in Closed Conformation (pdb code 6bkg). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Human Ligiv Catalytic Domain with Bound Dna-Adenylate Intermediate in Closed Conformation, PDB code: 6bkg:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the Human Ligiv Catalytic Domain with Bound Dna-Adenylate Intermediate in Closed Conformation


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Human Ligiv Catalytic Domain with Bound Dna-Adenylate Intermediate in Closed Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl701 b:80.8 occ:1.00 OD1 A:ASN209 3.6 62.2 1.0 O A:VAL206 3.6 45.2 1.0 O A:SER205 3.7 46.6 1.0 C A:VAL206 4.3 41.6 1.0 CG A:ASN209 4.5 62.2 1.0 NH1 A:ARG40 4.5 55.8 1.0 CA A:HIS208 4.6 46.6 1.0 N A:HIS208 4.7 44.2 1.0 N A:ASN209 4.7 51.8 1.0 CA A:VAL206 4.7 43.7 1.0 O A:PHE207 4.8 46.3 1.0 C A:PHE207 4.8 43.3 1.0 C A:SER205 4.9 43.8 1.0 C A:HIS208 4.9 48.0 1.0 CB A:PRO231 5.0 59.0 1.0 ND2 A:ASN209 5.0 65.1 1.0

Chlorine binding site 2 out of 2 in the Human Ligiv Catalytic Domain with Bound Dna-Adenylate Intermediate in Closed Conformation


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Human Ligiv Catalytic Domain with Bound Dna-Adenylate Intermediate in Closed Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl702 b:85.2 occ:1.00 CB A:ASP300 3.4 47.6 1.0 CA A:TYR298 3.5 36.1 1.0 CD1 A:TYR298 3.6 39.8 1.0 N A:GLN301 3.7 38.0 1.0 N A:ASP300 3.8 43.8 1.0 C A:TYR298 3.8 37.2 1.0 CA A:ASP300 4.0 45.3 1.0 O A:ASN297 4.0 34.9 1.0 O A:TYR298 4.1 39.5 1.0 CG A:ASP300 4.1 49.9 1.0 CB A:TYR298 4.1 34.8 1.0 C A:ASP300 4.2 44.9 1.0 CG A:TYR298 4.2 37.5 1.0 CB A:GLN301 4.4 44.9 1.0 CE1 A:TYR298 4.4 41.6 1.0 N A:THR299 4.4 37.3 1.0 N A:TYR298 4.6 37.0 1.0 CA A:GLN301 4.6 43.7 1.0 C A:ASN297 4.7 38.4 1.0 C A:THR299 4.8 42.0 1.0

A.M.Kaminski, P.P.Tumbale, M.J.Schellenberg, R.S.Williams, J.G.Williams, T.A.Kunkel, L.C.Pedersen, K.Bebenek. Structures of Dna-Bound Human Ligase IV Catalytic Core Reveal Insights Into Substrate Binding and Catalysis. Nat Commun V. 9 2642 2018.
ISSN: ESSN 2041-1723
PubMed: 29980672
DOI: 10.1038/S41467-018-05024-8