Sodium in PDB 6p0c: Human Dna Ligase 1 Bound to An Adenylated, Hydroxyl Terminated Dna Nick in Edta

All present enzymatic activity of Human Dna Ligase 1 Bound to An Adenylated, Hydroxyl Terminated Dna Nick in Edta:
6.5.1.1;

The structure of Human Dna Ligase 1 Bound to An Adenylated, Hydroxyl Terminated Dna Nick in Edta, PDB code: 6p0c was solved by M.J.Schellenberg, P.S.Tumbale, A.A.Riccio, R.S.Williams, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.60 / 1.55
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	71.235, 101.322, 115.319, 90.00, 90.00, 90.00
R / Rfree (%)	13 / 16.5

The binding sites of Sodium atom in the Human Dna Ligase 1 Bound to An Adenylated, Hydroxyl Terminated Dna Nick in Edta (pdb code 6p0c). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Human Dna Ligase 1 Bound to An Adenylated, Hydroxyl Terminated Dna Nick in Edta, PDB code: 6p0c:

Sodium binding site 1 out of 1 in the Human Dna Ligase 1 Bound to An Adenylated, Hydroxyl Terminated Dna Nick in Edta


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Human Dna Ligase 1 Bound to An Adenylated, Hydroxyl Terminated Dna Nick in Edta within 5.0Å range: probe atom residue distance (Å) B Occ C:Na102 b:32.9 occ:1.00 O D:HOH167 2.2 28.3 1.0 O C:HOH221 2.3 33.1 1.0 O C:HOH239 2.3 35.3 1.0 O C:HOH248 2.4 45.1 1.0 O6 C:DG1 2.4 14.3 1.0 O C:HOH218 2.5 35.7 1.0 H42 D:DC15 3.4 19.8 1.0 C6 C:DG1 3.5 14.0 1.0 H62 D:DA14 3.5 18.2 1.0 N7 C:DG1 3.8 13.7 1.0 H61 D:DA14 3.9 18.2 1.0 C5 C:DG1 4.0 13.5 1.0 N6 D:DA14 4.0 15.2 1.0 N4 D:DC15 4.1 16.5 1.0 H41 D:DC15 4.2 19.8 1.0 O4 C:DT2 4.2 16.0 1.0 O D:HOH114 4.4 25.4 1.0 O D:HOH140 4.5 33.1 1.0 O D:HOH112 4.5 33.0 1.0 O A:HOH1796 4.6 46.7 1.0 O D:HOH198 4.6 66.0 1.0 O B:HOH145 4.7 65.5 1.0 O B:HOH136 4.7 38.6 1.0 N1 C:DG1 4.7 13.7 1.0 H1 C:DG1 4.8 16.4 1.0 H71 C:DT2 4.9 19.1 1.0

P.P.Tumbale, T.J.Jurkiw, M.J.Schellenberg, A.A.Riccio, P.J.O'brien, R.S.Williams. Two-Tiered Enforcement of High-Fidelity Dna Ligation. Nat Commun V. 10 5431 2019.
ISSN: ESSN 2041-1723
PubMed: 31780661
DOI: 10.1038/S41467-019-13478-7