Magnesium in PDB 7u7a: Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 1.0 Mm MG2+ For 200S

All present enzymatic activity of Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 1.0 Mm MG2+ For 200S:
2.7.7.7;

The structure of Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 1.0 Mm MG2+ For 200S, PDB code: 7u7a 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)	41.99 / 1.58
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	97.924, 97.924, 81.666, 90, 90, 120
R / Rfree (%)	18.7 / 21.7

The binding sites of Magnesium atom in the Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 1.0 Mm MG2+ For 200S (pdb code 7u7a). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 1.0 Mm MG2+ For 200S, PDB code: 7u7a:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 1.0 Mm MG2+ For 200S


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 Ternary Mismatch Complex:Reaction with 1.0 Mm MG2+ For 200S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:27.0 occ:0.60 OE1 A:GLU116 2.1 37.8 0.5 OE1 A:GLU116 2.1 37.9 0.6 OP1 P:DG9 2.2 27.1 0.3 OD1 A:ASP13 2.2 34.1 0.6 OD1 A:ASP115 2.2 29.1 1.0 O A:HOH958 2.2 26.2 0.3 O1A A:DGT504 2.3 27.1 0.3 O A:HOH924 2.4 31.6 0.6 O3' P:DT8 2.4 27.5 0.1 O3' P:DT8 2.4 28.4 0.3 OD2 A:ASP13 2.5 32.5 0.4 P P:DG9 2.8 26.3 0.3 CG A:ASP115 3.1 27.2 1.0 CD A:GLU116 3.2 35.6 0.6 CD A:GLU116 3.2 35.5 0.5 CG A:ASP13 3.3 27.3 0.4 OD2 A:ASP115 3.3 30.2 1.0 C3' P:DT8 3.3 28.4 0.1 CG A:ASP13 3.4 26.4 0.6 PA A:DGT504 3.5 24.7 0.3 OD1 A:ASP13 3.5 24.6 0.4 MG A:MG502 3.6 17.9 0.9 OG A:SER113 3.6 26.3 0.7 CB A:GLU116 3.7 29.4 0.5 C3' P:DT8 3.7 27.3 0.3 CB A:GLU116 3.7 29.5 0.6 O2A A:DGT504 3.8 27.1 0.3 CG A:GLU116 3.8 30.1 0.6 CG A:GLU116 3.9 30.2 0.5 OP2 P:DG9 3.9 26.9 0.3 OD2 A:ASP13 3.9 32.4 0.6 O5' P:DG9 4.0 24.2 0.3 C4' P:DT8 4.0 28.5 0.3 C4' P:DT8 4.0 29.2 0.1 O5' A:DGT504 4.1 23.8 0.3 OE2 A:GLU116 4.1 38.4 0.6 C5' P:DG9 4.2 22.8 0.3 C5' A:DGT504 4.2 22.8 0.3 OE2 A:GLU116 4.2 37.1 0.5 C5' P:DT8 4.2 30.2 0.3 C A:ASP115 4.3 23.4 1.0 O A:HOH828 4.4 35.9 1.0 O A:ASP115 4.4 25.2 1.0 CB A:ASP115 4.4 23.4 1.0 C5' P:DT8 4.4 30.8 0.1 N A:GLU116 4.5 20.7 0.5 N A:GLU116 4.5 20.7 0.6 CB A:ASP13 4.5 19.2 0.6 NZ A:LYS224 4.6 30.6 0.8 CB A:ASP13 4.6 19.3 0.4 CB A:SER113 4.6 24.0 0.3 CA A:GLU116 4.7 22.7 0.5 C2' P:DT8 4.7 27.4 0.1 CA A:GLU116 4.7 22.7 0.6 C2' P:DT8 4.7 26.4 0.3 O3A A:DGT504 4.8 24.0 0.3 O1G A:DGT504 4.8 21.1 0.3 CA A:ASP115 4.8 20.2 1.0 CB A:SER113 4.9 23.5 0.7 O1 A:DPO505 4.9 19.9 0.3 N A:ASP115 5.0 18.0 1.0 O2B A:DGT504 5.0 18.7 0.3

Magnesium binding site 2 out of 3 in the Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 1.0 Mm MG2+ For 200S


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 Ternary Mismatch Complex:Reaction with 1.0 Mm MG2+ For 200S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:17.9 occ:0.90 OD1 A:ASP13 1.9 24.6 0.4 O1G A:DGT504 2.1 21.1 0.3 OD2 A:ASP115 2.1 30.2 1.0 OD2 A:ASP13 2.1 32.4 0.6 O2B A:DGT504 2.2 18.7 0.3 O1 A:DPO505 2.2 19.9 0.3 O A:MET14 2.2 20.9 1.0 O1A A:DGT504 2.3 27.1 0.3 O5 A:DPO505 2.3 21.1 0.3 OP1 P:DG9 2.5 27.1 0.3 CG A:ASP13 2.8 26.4 0.6 OD1 A:ASP13 2.9 34.1 0.6 CG A:ASP13 3.0 27.3 0.4 PB A:DGT504 3.1 19.8 0.3 CG A:ASP115 3.2 27.2 1.0 P1 A:DPO505 3.3 18.2 0.3 PG A:DGT504 3.4 19.5 0.3 O3A A:DGT504 3.4 24.0 0.3 C A:MET14 3.4 16.3 1.0 PA A:DGT504 3.4 24.7 0.3 P2 A:DPO505 3.6 18.8 0.3 OD2 A:ASP13 3.6 32.5 0.4 O3B A:DGT504 3.6 19.9 0.3 MG A:MG501 3.6 27.0 0.6 O2 A:DPO505 3.7 22.5 0.3 OD1 A:ASP115 3.7 29.1 1.0 O4 A:DPO505 3.8 19.9 0.3 P P:DG9 3.9 26.3 0.3 O A:HOH828 3.9 35.9 1.0 N A:MET14 3.9 17.1 1.0 O3G A:DGT504 4.0 17.5 0.3 NZ A:LYS231 4.0 23.6 1.0 C5' P:DG9 4.2 22.8 0.3 C5' A:DGT504 4.2 22.8 0.3 CB A:ASP13 4.2 19.2 0.6 CA A:MET14 4.2 16.6 1.0 CB A:ASP13 4.2 19.3 0.4 C A:ASP13 4.2 17.5 1.0 O5' A:DGT504 4.3 23.8 0.3 O7 A:DPO505 4.3 20.6 0.3 N A:ASP15 4.4 14.6 1.0 O5' P:DG9 4.4 24.2 0.3 O A:HOH924 4.4 31.6 0.6 N A:CYS16 4.4 18.1 1.0 CB A:ASP115 4.4 23.4 1.0 CA A:ASP15 4.5 14.1 1.0 O1B A:DGT504 4.5 19.3 0.3 O2G A:DGT504 4.6 22.1 0.3 O2A A:DGT504 4.6 27.1 0.3 C A:ASP15 4.6 18.5 1.0 O3 A:DPO505 4.6 19.2 0.3 CA A:ASP13 4.6 19.5 0.4 CA A:ASP13 4.6 19.5 0.6 O A:ASP13 4.7 19.0 1.0 O A:ASP115 4.7 25.2 1.0 O6 A:DPO505 4.7 22.8 0.3 N A:PHE17 4.7 15.1 1.0 CB A:MET14 4.7 19.6 1.0 OP2 P:DG9 4.7 26.9 0.3 O3' P:DT8 4.9 28.4 0.3 CB A:PHE17 4.9 13.9 1.0 CE A:LYS231 4.9 36.5 1.0

Magnesium binding site 3 out of 3 in the Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 1.0 Mm MG2+ For 200S


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 1.0 Mm MG2+ For 200S within 5.0Å range: probe atom residue distance (Å) B Occ P:Mg101 b:27.8 occ:0.45 O A:HOH1022 2.0 43.2 1.0 O A:HOH945 2.0 25.7 0.6 O2A A:DGT504 2.1 27.1 0.3 O2 A:DPO505 2.1 22.5 0.3 OP2 P:DG9 2.2 26.9 0.3 O A:HOH806 2.3 29.1 0.6 O3A A:DGT504 2.4 24.0 0.3 NH1 A:ARG61 2.6 26.2 0.2 O A:HOH828 2.6 35.9 1.0 PA A:DGT504 2.7 24.7 0.3 P P:DG9 3.3 26.3 0.3 O3' P:DT8 3.3 31.8 0.6 O2G A:DGT504 3.6 22.1 0.3 P1 A:DPO505 3.6 18.2 0.3 CZ A:ARG61 3.6 25.5 0.2 OP1 P:DG9 3.8 27.1 0.3 O1A A:DGT504 3.8 27.1 0.3 PB A:DGT504 3.8 19.8 0.3 O6 A:DPO505 3.8 22.8 0.3 O3B A:DGT504 3.8 19.9 0.3 O A:HOH1023 3.8 26.0 0.8 C3' P:DT8 3.9 30.9 0.6 NH2 A:ARG61 3.9 21.9 0.2 O A:HOH957 3.9 22.4 0.6 O5' A:DGT504 4.0 23.8 0.3 O1G A:DGT504 4.0 21.1 0.3 O5' P:DG9 4.0 24.2 0.3 O4 A:DPO505 4.0 19.9 0.3 PG A:DGT504 4.1 19.5 0.3 O5 A:DPO505 4.2 21.1 0.3 O A:HOH924 4.3 31.6 0.6 P2 A:DPO505 4.3 18.8 0.3 O3 A:DPO505 4.4 19.2 0.3 O1B A:DGT504 4.5 19.3 0.3 O A:HOH1052 4.6 30.7 0.5 C3' P:DT8 4.6 28.4 0.1 O1 A:DPO505 4.6 19.9 0.3 O3' P:DT8 4.6 28.4 0.3 O A:HOH804 4.6 45.0 1.0 C2' P:DT8 4.7 27.4 0.1 O5' P:DT8 4.7 33.6 0.6 NE A:ARG61 4.8 23.2 0.2 C4' P:DT8 4.8 26.7 0.6 O2B A:DGT504 4.9 18.7 0.3 C3' P:DT8 5.0 27.3 0.3

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