Magnesium in PDB 7u7x: Human Dna Polymerase Eta-Dna-Dgmpnpp Ternary Mismatch Complex in 2.0 Mm MG2+ For 600S

All present enzymatic activity of Human Dna Polymerase Eta-Dna-Dgmpnpp Ternary Mismatch Complex in 2.0 Mm MG2+ For 600S:
2.7.7.7;

The structure of Human Dna Polymerase Eta-Dna-Dgmpnpp Ternary Mismatch Complex in 2.0 Mm MG2+ For 600S, PDB code: 7u7x 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)	32.17 / 1.65
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	98.291, 98.291, 81.945, 90, 90, 120
R / Rfree (%)	18.9 / 21

The binding sites of Magnesium atom in the Human Dna Polymerase Eta-Dna-Dgmpnpp Ternary Mismatch Complex in 2.0 Mm MG2+ For 600S (pdb code 7u7x). 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 2.0 Mm MG2+ For 600S, PDB code: 7u7x:
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 2.0 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 2.0 Mm MG2+ For 600S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:23.3 occ:1.00 OD1 A:ASP115 2.0 22.9 0.8 OE1 A:GLU116 2.0 29.7 1.0 OD2 A:ASP13 2.1 34.0 1.0 O A:HOH720 2.2 22.0 0.5 O A:HOH766 2.2 30.8 1.0 O3' P:DT8 2.2 25.1 0.1 O1A A:XG4505 2.2 19.9 0.8 OD1 A:ASP115 2.8 26.1 0.2 CG A:ASP115 3.0 18.7 0.8 CD A:GLU116 3.2 33.1 1.0 CG A:ASP13 3.2 25.5 1.0 CG A:ASP115 3.3 22.3 0.2 OD2 A:ASP115 3.3 24.4 0.8 PA A:XG4505 3.3 20.9 0.8 C3' P:DT8 3.4 28.4 0.1 OD1 A:ASP13 3.6 26.2 1.0 OD2 A:ASP115 3.7 23.5 0.2 MG A:MG502 3.7 18.9 0.9 O2A A:XG4505 3.7 21.4 0.8 O5' A:XG4505 3.8 19.5 0.8 OG A:SER113 3.8 27.9 1.0 OE2 A:GLU116 4.0 31.5 1.0 CB A:GLU116 4.1 24.7 1.0 CG A:GLU116 4.1 25.0 1.0 C5' A:XG4505 4.1 17.9 0.8 O A:HOH699 4.1 29.0 1.0 NZ A:LYS224 4.2 34.8 1.0 CB A:ASP115 4.2 24.8 0.2 CB A:ASP115 4.3 25.0 0.8 C4' P:DT8 4.4 30.0 0.1 O A:HOH923 4.4 29.0 0.5 C2' P:DT8 4.5 28.8 0.1 CB A:ASP13 4.5 21.8 1.0 C A:ASP115 4.5 26.1 1.0 O1G A:XG4505 4.7 19.7 0.8 N A:GLU116 4.7 23.0 1.0 O A:ASP115 4.7 28.1 1.0 O5' P:DT8 4.8 32.4 0.1 CB A:SER113 4.8 23.2 1.0 N3A A:XG4505 4.8 20.2 0.8 CA A:ASP115 4.8 22.6 0.2 CA A:ASP115 4.8 22.6 0.8 C5' P:DT8 4.9 32.3 0.1 O1B A:XG4505 5.0 19.4 0.8

Magnesium binding site 2 out of 2 in the Human Dna Polymerase Eta-Dna-Dgmpnpp Ternary Mismatch Complex in 2.0 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 2.0 Mm MG2+ For 600S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:18.9 occ:0.90 OD1 A:ASP13 1.9 26.2 1.0 OD2 A:ASP115 2.0 24.4 0.8 O A:MET14 2.1 25.3 1.0 O1G A:XG4505 2.1 19.7 0.8 O1B A:XG4505 2.2 19.4 0.8 O1A A:XG4505 2.4 19.9 0.8 CG A:ASP13 2.9 25.5 1.0 CG A:ASP115 3.1 18.7 0.8 PB A:XG4505 3.1 19.9 0.8 C A:MET14 3.2 20.1 1.0 PG A:XG4505 3.3 20.6 0.8 OD2 A:ASP13 3.3 34.0 1.0 PA A:XG4505 3.4 20.9 0.8 O3B A:XG4505 3.6 17.9 0.8 N3A A:XG4505 3.6 20.2 0.8 OD1 A:ASP115 3.6 22.9 0.8 MG A:MG501 3.7 23.3 1.0 NZ A:LYS231 3.7 21.7 1.0 N A:MET14 3.8 18.0 1.0 OD2 A:ASP115 3.8 23.5 0.2 O A:HOH699 3.9 29.0 1.0 O2G A:XG4505 3.9 19.0 0.8 CA A:MET14 4.0 18.5 1.0 CG A:ASP115 4.1 22.3 0.2 CB A:ASP13 4.1 21.8 1.0 C A:ASP13 4.2 16.5 1.0 C5' A:XG4505 4.2 17.9 0.8 CB A:ASP115 4.2 24.8 0.2 N A:ASP15 4.2 20.1 1.0 CB A:ASP115 4.3 25.0 0.8 O5' A:XG4505 4.3 19.5 0.8 CA A:ASP15 4.4 17.1 1.0 N A:CYS16 4.4 22.0 1.0 O A:HOH766 4.5 30.8 1.0 O2B A:XG4505 4.5 20.6 0.8 C A:ASP15 4.5 22.4 1.0 O3G A:XG4505 4.6 21.2 0.8 CB A:MET14 4.6 23.5 1.0 O A:ASP13 4.6 21.1 1.0 CE A:LYS231 4.6 25.9 1.0 CA A:ASP13 4.6 22.3 1.0 N A:PHE17 4.7 20.9 1.0 OD1 A:ASP115 4.7 26.1 0.2 O2A A:XG4505 4.7 21.4 0.8 CB A:PHE17 4.9 15.4 1.0 O A:ASP115 4.9 28.1 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