Magnesium in PDB 7u7u: Human Dna Polymerase Eta-Dna-Dgmpnpp Ternary Mismatch Complex in 0.1 Mm MG2+ For 600S

All present enzymatic activity of Human Dna Polymerase Eta-Dna-Dgmpnpp Ternary Mismatch Complex in 0.1 Mm MG2+ For 600S:
2.7.7.7;

The structure of Human Dna Polymerase Eta-Dna-Dgmpnpp Ternary Mismatch Complex in 0.1 Mm MG2+ For 600S, PDB code: 7u7u was solved by C.Chang, Y.Gao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.24 / 1.54
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	98.488, 98.488, 82.046, 90, 90, 120
R / Rfree (%)	19.4 / 22.1

The binding sites of Magnesium atom in the Human Dna Polymerase Eta-Dna-Dgmpnpp Ternary Mismatch Complex in 0.1 Mm MG2+ For 600S (pdb code 7u7u). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Human Dna Polymerase Eta-Dna-Dgmpnpp Ternary Mismatch Complex in 0.1 Mm MG2+ For 600S, PDB code: 7u7u:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Human Dna Polymerase Eta-Dna-Dgmpnpp Ternary Mismatch Complex in 0.1 Mm MG2+ For 600S


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human Dna Polymerase Eta-Dna-Dgmpnpp Ternary Mismatch Complex in 0.1 Mm MG2+ For 600S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:38.3 occ:0.80 OD1 A:ASP115 2.1 32.2 0.5 O A:HOH880 2.1 41.8 0.7 O3' P:DT8 2.2 39.0 0.2 OE1 A:GLU116 2.4 40.9 0.3 OE1 A:GLU116 2.4 42.2 0.7 OD1 A:ASP115 2.4 28.9 0.6 OD2 A:ASP13 2.4 33.5 0.5 O A:HOH813 2.5 46.1 1.0 O1A A:XG4505 2.5 25.3 0.8 OD1 A:ASP13 2.5 28.3 0.3 OD1 A:ASP13 3.0 25.2 0.2 CG A:ASP115 3.0 26.2 0.5 C3' P:DT8 3.3 34.9 0.2 CG A:ASP115 3.4 21.5 0.6 CD A:GLU116 3.4 39.2 0.3 OD2 A:ASP13 3.4 28.2 0.2 OG A:SER113 3.4 35.0 1.0 CG A:ASP13 3.5 28.2 0.2 CG A:ASP13 3.6 26.7 0.3 OD2 A:ASP115 3.6 29.6 0.5 PA A:XG4505 3.6 24.8 0.8 CD A:GLU116 3.6 39.3 0.7 CG A:ASP13 3.6 26.6 0.5 MG A:MG502 3.6 18.2 1.0 OD2 A:ASP115 3.7 23.5 0.6 CB A:GLU116 3.8 33.5 0.3 CB A:GLU116 3.8 33.6 0.7 CG A:GLU116 3.9 34.0 0.3 O5' A:XG4505 4.0 25.4 0.8 O2A A:XG4505 4.0 26.6 0.8 CB A:ASP115 4.1 26.1 0.5 OD2 A:ASP13 4.1 30.7 0.3 OD1 A:ASP13 4.2 31.9 0.5 OE2 A:GLU116 4.3 38.1 0.3 CG A:GLU116 4.3 35.4 0.7 C5' A:XG4505 4.3 23.9 0.8 C4' P:DT8 4.3 33.6 0.2 C2' P:DT8 4.4 35.7 0.2 C A:ASP115 4.5 26.4 1.0 N A:GLU116 4.5 22.8 1.0 OE2 A:GLU116 4.5 40.6 0.7 O A:HOH676 4.5 35.7 1.0 CB A:SER113 4.5 25.7 1.0 CB A:ASP13 4.6 22.5 0.3 O A:ASP115 4.7 30.9 1.0 CB A:ASP13 4.7 22.3 0.5 CB A:ASP115 4.7 22.7 0.6 CA A:GLU116 4.7 26.6 0.3 CA A:GLU116 4.8 26.6 0.7 CA A:ASP115 4.8 22.7 0.5 NZ A:LYS224 4.8 40.9 1.0 O5' P:DT8 4.8 36.6 0.2 CB A:ASP13 4.9 22.4 0.2 C5' P:DT8 4.9 37.8 0.2 O1G A:XG4505 4.9 24.9 0.8 CA A:ASP115 5.0 22.4 0.6

Magnesium binding site 2 out of 2 in the Human Dna Polymerase Eta-Dna-Dgmpnpp Ternary Mismatch Complex in 0.1 Mm MG2+ For 600S


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human Dna Polymerase Eta-Dna-Dgmpnpp Ternary Mismatch Complex in 0.1 Mm MG2+ For 600S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:18.2 occ:1.00 OD1 A:ASP13 2.1 31.9 0.5 OD1 A:ASP13 2.2 25.2 0.2 O A:MET14 2.2 27.2 1.0 OD2 A:ASP115 2.3 23.5 0.6 O1G A:XG4505 2.3 24.9 0.8 OD2 A:ASP13 2.3 30.7 0.3 O1B A:XG4505 2.3 20.6 0.8 O1A A:XG4505 2.4 25.3 0.8 OD1 A:ASP13 2.6 28.3 0.3 CG A:ASP13 2.7 26.6 0.5 CG A:ASP13 2.7 26.7 0.3 OD2 A:ASP13 2.8 33.5 0.5 CG A:ASP13 3.1 28.2 0.2 CG A:ASP115 3.2 21.5 0.6 PB A:XG4505 3.4 21.9 0.8 C A:MET14 3.4 19.5 1.0 PG A:XG4505 3.5 22.0 0.8 PA A:XG4505 3.6 24.8 0.8 OD1 A:ASP115 3.6 28.9 0.6 MG A:MG501 3.6 38.3 0.8 OD2 A:ASP13 3.7 28.2 0.2 O3B A:XG4505 3.8 20.8 0.8 CG A:ASP115 3.8 26.2 0.5 OD2 A:ASP115 3.8 29.6 0.5 N3A A:XG4505 3.8 21.7 0.8 N A:MET14 3.8 19.7 1.0 O A:HOH676 4.0 35.7 1.0 NZ A:LYS231 4.0 26.2 1.0 CB A:ASP115 4.1 26.1 0.5 OD1 A:ASP115 4.1 32.2 0.5 CA A:MET14 4.1 19.1 1.0 CB A:ASP13 4.2 22.3 0.5 O2G A:XG4505 4.2 21.1 0.8 CB A:ASP13 4.2 22.5 0.3 C A:ASP13 4.2 20.9 1.0 CB A:ASP13 4.2 22.4 0.2 C5' A:XG4505 4.2 23.9 0.8 O A:HOH813 4.3 46.1 1.0 N A:ASP15 4.4 17.3 1.0 O5' A:XG4505 4.4 25.4 0.8 CB A:ASP115 4.5 22.7 0.6 CA A:ASP15 4.6 19.4 1.0 N A:CYS16 4.6 20.8 1.0 CA A:ASP13 4.6 21.5 0.2 CA A:ASP13 4.6 21.4 0.5 CA A:ASP13 4.6 21.4 0.3 CB A:MET14 4.7 23.1 1.0 O A:ASP13 4.7 22.6 1.0 C A:ASP15 4.7 24.7 1.0 O2B A:XG4505 4.8 24.5 0.8 N A:PHE17 4.8 19.8 1.0 O3G A:XG4505 4.8 24.4 0.8 O A:ASP115 4.8 30.9 1.0 O2A A:XG4505 4.8 26.6 0.8 CB A:PHE17 4.9 17.9 1.0 CE A:LYS231 5.0 40.3 1.0

C.Chang, C.Lee Luo, Y.Gao. In Crystallo Observation of Three Metal Ion Promoted Dna Polymerase Misincorporation. Nat Commun V. 13 2346 2022.
ISSN: ESSN 2041-1723
PubMed: 35487947
DOI: 10.1038/S41467-022-30005-3