Magnesium in PDB 6p0a: Human Dna Ligase 1 Bound to An Adenylated, Dideoxy Terminated Dna Nick with 2 Mm MG2+

All present enzymatic activity of Human Dna Ligase 1 Bound to An Adenylated, Dideoxy Terminated Dna Nick with 2 Mm MG2+:
6.5.1.1;

The structure of Human Dna Ligase 1 Bound to An Adenylated, Dideoxy Terminated Dna Nick with 2 Mm MG2+, PDB code: 6p0a was solved by M.J.Schellenberg, R.S.Williams, P.S.Tumbale, A.A.Riccio, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.51 / 2.05
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	62.644, 110.847, 115.538, 90.00, 90.00, 90.00
R / Rfree (%)	17 / 20.3

The binding sites of Magnesium atom in the Human Dna Ligase 1 Bound to An Adenylated, Dideoxy Terminated Dna Nick with 2 Mm MG2+ (pdb code 6p0a). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Human Dna Ligase 1 Bound to An Adenylated, Dideoxy Terminated Dna Nick with 2 Mm MG2+, PDB code: 6p0a:

Magnesium binding site 1 out of 1 in the Human Dna Ligase 1 Bound to An Adenylated, Dideoxy Terminated Dna Nick with 2 Mm MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human Dna Ligase 1 Bound to An Adenylated, Dideoxy Terminated Dna Nick with 2 Mm MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1001 b:25.5 occ:1.00 OP1 B:DG11 1.9 39.6 1.0 O A:HOH1327 2.0 25.6 1.0 O A:HOH1340 2.1 29.6 1.0 OE1 A:GLU592 2.1 29.5 1.0 O A:HOH1208 2.1 27.2 1.0 O B:HOH132 2.2 36.0 1.0 CD A:GLU592 3.2 30.3 1.0 P B:DG11 3.4 33.3 1.0 H5'' B:DG11 3.5 34.9 1.0 OE2 A:GLU592 3.6 32.3 1.0 HG2 A:GLU346 3.8 46.3 1.0 O A:HOH1463 3.9 52.5 1.0 HA2 A:GLY344 3.9 45.8 1.0 H5' B:DG11 4.1 34.9 1.0 C5' B:DG11 4.1 29.1 1.0 O5' B:DG11 4.1 29.4 1.0 O3' B:DC10 4.2 34.3 1.0 O A:HOH1350 4.2 28.2 1.0 HG3 A:GLU346 4.3 46.3 1.0 OE2 A:GLU346 4.3 42.2 1.0 OP2 B:DG11 4.4 33.0 1.0 CG A:GLU592 4.4 28.1 1.0 CG A:GLU346 4.5 38.6 1.0 O B:HOH145 4.5 31.0 1.0 O A:LEU345 4.5 27.7 1.0 HA A:PRO341 4.5 47.0 1.0 O A:PRO341 4.5 38.9 1.0 HG2 A:GLU592 4.6 33.7 1.0 HG3 A:GLU592 4.6 33.7 1.0 CA A:GLY344 4.8 38.2 1.0 CD A:GLU346 4.9 42.9 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