Sodium in PDB 8v1v: Human Dna Ligase I F872L Bound to Adenylated Nicked Dna

All present enzymatic activity of Human Dna Ligase I F872L Bound to Adenylated Nicked Dna:
6.5.1.1;

The structure of Human Dna Ligase I F872L Bound to Adenylated Nicked Dna, PDB code: 8v1v was solved by P.P.Tumbale, R.S.Williams, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.87 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	72.966, 96.582, 114.767, 90, 90, 90
R / Rfree (%)	17.9 / 22.3

The binding sites of Sodium atom in the Human Dna Ligase I F872L Bound to Adenylated Nicked Dna (pdb code 8v1v). 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 I F872L Bound to Adenylated Nicked Dna, PDB code: 8v1v:

Sodium binding site 1 out of 1 in the Human Dna Ligase I F872L Bound to Adenylated Nicked Dna


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 I F872L Bound to Adenylated Nicked Dna within 5.0Å range: probe atom residue distance (Å) B Occ C:Na102 b:60.3 occ:1.00 OP2 C:DA6 2.1 44.8 1.0 H8 C:DA6 2.7 42.8 1.0 H2' C:DA6 3.0 46.0 1.0 O5' C:DA6 3.1 44.3 1.0 H2'' C:DG5 3.1 46.8 1.0 P C:DA6 3.2 55.2 1.0 C8 C:DA6 3.6 35.6 1.0 O C:HOH209 3.9 45.2 1.0 C2' C:DG5 3.9 39.0 1.0 C2' C:DA6 4.0 38.4 1.0 H2' C:DG5 4.1 46.8 1.0 H3' C:DA6 4.2 43.4 1.0 O3' C:DG5 4.2 49.3 1.0 OP1 C:DA6 4.2 54.6 1.0 H3' C:DG5 4.3 46.6 1.0 C3' C:DG5 4.4 38.9 1.0 N7 C:DA6 4.4 36.7 1.0 H5 C:DC7 4.5 43.0 1.0 H2'' C:DA6 4.5 46.0 1.0 C5' C:DA6 4.5 39.2 1.0 N9 C:DA6 4.6 36.5 1.0 C3' C:DA6 4.6 36.1 1.0 C1' C:DA6 4.8 35.5 1.0 H5' C:DA6 4.9 47.1 1.0 C4' C:DA6 4.9 39.1 1.0

P.P.Tumbale, R.S.Williams. Human Dna Ligase I F872L Bound to Adenylated Nicked Dna To Be Published.