Chlorine in PDB 4yd2: Nicked Complex of Human Dna Polymerase Mu with 2-Nt Gapped Dna Substrate

All present enzymatic activity of Nicked Complex of Human Dna Polymerase Mu with 2-Nt Gapped Dna Substrate:
2.7.7.7;

The structure of Nicked Complex of Human Dna Polymerase Mu with 2-Nt Gapped Dna Substrate, PDB code: 4yd2 was solved by A.F.Moon, R.A.Gosavi, T.A.Kunkel, L.C.Pedersen, K.Bebenek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	22.61 / 2.47
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.083, 68.700, 114.977, 90.00, 90.00, 90.00
R / Rfree (%)	21.2 / 24.2

The structure of Nicked Complex of Human Dna Polymerase Mu with 2-Nt Gapped Dna Substrate also contains other interesting chemical elements:

Sodium

(Na)

3 atoms

The binding sites of Chlorine atom in the Nicked Complex of Human Dna Polymerase Mu with 2-Nt Gapped Dna Substrate (pdb code 4yd2). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Nicked Complex of Human Dna Polymerase Mu with 2-Nt Gapped Dna Substrate, PDB code: 4yd2:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Nicked Complex of Human Dna Polymerase Mu with 2-Nt Gapped Dna Substrate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Nicked Complex of Human Dna Polymerase Mu with 2-Nt Gapped Dna Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl502 b:35.2 occ:0.83 N A:LEU326 3.3 29.0 1.0 N A:GLN327 3.8 30.2 1.0 CA A:LYS325 3.9 23.6 1.0 CB A:LYS325 3.9 23.7 1.0 CD2 A:LEU149 3.9 19.6 1.0 C A:LYS325 4.1 26.4 1.0 O A:GLN327 4.1 31.9 1.0 CA A:LEU326 4.2 30.2 1.0 CG A:GLN327 4.3 37.0 1.0 CG A:LYS325 4.3 27.9 1.0 CE A:LYS325 4.3 36.5 1.0 CB A:LEU326 4.3 31.2 1.0 C A:LEU326 4.5 31.3 1.0 CG A:LEU149 4.6 20.9 1.0 CD1 A:LEU149 4.6 20.7 1.0 CA A:GLN327 4.7 30.9 1.0 C A:GLN327 4.8 30.8 1.0 CB A:GLN327 4.9 33.0 1.0 CG A:LEU326 5.0 31.9 1.0 CD A:LYS325 5.0 32.2 1.0

Chlorine binding site 2 out of 3 in the Nicked Complex of Human Dna Polymerase Mu with 2-Nt Gapped Dna Substrate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Nicked Complex of Human Dna Polymerase Mu with 2-Nt Gapped Dna Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl503 b:40.9 occ:1.00 O A:HOH610 2.9 26.1 1.0 N A:GLU475 3.2 18.9 1.0 O A:HOH624 3.4 11.6 1.0 CA A:SER474 3.5 20.4 1.0 CD2 A:LEU431 3.7 14.5 1.0 CG A:GLU475 3.8 14.7 1.0 C A:SER474 3.8 19.7 1.0 CB A:SER474 3.9 16.9 1.0 O A:HOH716 4.0 26.0 1.0 CB A:GLU475 4.1 15.8 1.0 CA A:GLU475 4.3 17.7 1.0 CB A:PRO428 4.5 18.1 1.0 CD A:GLU475 4.6 16.5 1.0 OE1 A:GLU475 4.7 16.2 1.0 CE2 A:PHE427 4.7 18.7 1.0 O A:ALA473 4.7 23.2 1.0 CA A:PRO428 4.7 17.3 1.0 N A:SER474 4.8 20.3 1.0 CG A:LEU431 5.0 14.4 1.0 O A:SER474 5.0 16.3 1.0

Chlorine binding site 3 out of 3 in the Nicked Complex of Human Dna Polymerase Mu with 2-Nt Gapped Dna Substrate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Nicked Complex of Human Dna Polymerase Mu with 2-Nt Gapped Dna Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl506 b:52.7 occ:1.00 N A:GLY174 3.1 40.0 1.0 O A:HOH714 3.4 15.9 0.6 N A:ARG175 3.4 35.1 1.0 CA A:GLY174 3.4 39.9 1.0 CA A:SER172 3.5 38.9 1.0 C A:SER172 3.5 36.2 1.0 CB A:SER172 3.6 42.4 1.0 N A:GLU173 3.7 40.0 1.0 NH1 A:ARG175 3.8 52.7 1.0 C A:GLY174 3.9 37.3 1.0 O A:SER172 3.9 32.2 1.0 CG A:ARG175 4.2 39.9 1.0 C A:GLU173 4.2 38.9 1.0 OG A:SER172 4.3 47.4 1.0 O A:HOH714 4.3 15.4 0.5 O6 D:DG1 4.4 49.5 1.0 CB A:ARG175 4.4 35.6 1.0 CA A:ARG175 4.5 33.7 1.0 CA A:GLU173 4.6 40.2 1.0 CD A:ARG175 4.6 44.0 1.0 C6 D:DG1 4.7 48.3 1.0 N A:SER172 4.9 37.3 1.0 CZ A:ARG175 4.9 51.7 1.0 C5 D:DG1 5.0 47.5 1.0 N7 D:DG1 5.0 49.1 1.0

A.F.Moon, R.A.Gosavi, T.A.Kunkel, L.C.Pedersen, K.Bebenek. Creative Template-Dependent Synthesis By Human Polymerase Mu. Proc.Natl.Acad.Sci.Usa V. 112 E4530 2015.
ISSN: ESSN 1091-6490
PubMed: 26240373
DOI: 10.1073/PNAS.1505798112