Magnesium in PDB 7u7c: Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 1.0 Mm MG2+ For 300S

All present enzymatic activity of Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 1.0 Mm MG2+ For 300S:
2.7.7.7;

The structure of Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 1.0 Mm MG2+ For 300S, PDB code: 7u7c 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)	42.20 / 1.55
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	98.341, 98.341, 82.204, 90, 90, 120
R / Rfree (%)	18 / 21.2

The binding sites of Magnesium atom in the Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 1.0 Mm MG2+ For 300S (pdb code 7u7c). 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 300S, PDB code: 7u7c:
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 300S


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 300S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:15.8 occ:1.00 OD1 A:ASP13 2.0 22.1 0.5 O2B A:DGT504 2.2 16.0 0.3 O A:MET14 2.2 20.3 1.0 O2G A:DGT504 2.2 19.9 0.3 OD2 A:ASP115 2.2 22.2 0.8 O1 A:DPO503 2.2 16.2 0.5 O1A A:DGT504 2.3 23.1 0.3 O5 A:DPO503 2.3 19.8 0.5 OP1 P:DG9 2.4 23.1 0.5 OD2 A:ASP13 2.5 33.5 0.5 OD1 A:ASP13 2.7 28.3 0.5 CG A:ASP13 2.9 25.1 0.5 CG A:ASP13 3.0 25.9 0.5 PB A:DGT504 3.1 16.5 0.3 CG A:ASP115 3.2 20.9 0.8 P1 A:DPO503 3.3 17.2 0.5 O3A A:DGT504 3.4 19.0 0.3 C A:MET14 3.4 17.4 1.0 PA A:DGT504 3.4 18.7 0.3 PG A:DGT504 3.4 18.5 0.3 P2 A:DPO503 3.5 18.5 0.5 OD2 A:ASP13 3.5 32.7 0.5 OD1 A:ASP115 3.6 25.4 0.8 MG A:MG505 3.6 22.9 0.5 O3B A:DGT504 3.6 17.1 0.3 O2 A:DPO503 3.7 17.4 0.5 O4 A:DPO503 3.8 17.4 0.5 P P:DG9 3.8 25.0 0.5 N A:MET14 4.0 15.8 1.0 OD2 A:ASP115 4.0 20.9 0.2 NZ A:LYS231 4.0 24.8 1.0 CG A:ASP115 4.0 20.5 0.2 O A:HOH740 4.1 29.0 0.7 O3G A:DGT504 4.1 16.9 0.3 C5' P:DG9 4.1 20.3 0.5 O7 A:DPO503 4.2 17.1 0.5 C5' A:DGT504 4.2 20.3 0.3 CB A:ASP115 4.2 21.1 0.2 CA A:MET14 4.2 15.2 1.0 O A:HOH614 4.2 25.9 0.3 C A:ASP13 4.2 16.2 1.0 O5' A:DGT504 4.3 19.0 0.3 CB A:ASP13 4.3 18.8 0.5 CB A:ASP13 4.3 18.7 0.5 O5' P:DG9 4.3 19.8 0.5 N A:ASP15 4.4 13.3 1.0 N A:CYS16 4.4 16.3 1.0 CA A:ASP15 4.5 14.5 1.0 CB A:ASP115 4.5 21.6 0.8 OD1 A:ASP115 4.5 18.0 0.2 O2A A:DGT504 4.6 24.2 0.3 O1B A:DGT504 4.6 17.9 0.3 C A:ASP15 4.6 17.6 1.0 O1G A:DGT504 4.6 20.2 0.3 OP2 P:DG9 4.6 24.1 0.5 CB A:MET14 4.7 18.2 1.0 O A:ASP13 4.7 18.5 1.0 O6 A:DPO503 4.7 20.2 0.5 CA A:ASP13 4.7 18.0 0.5 O3 A:DPO503 4.7 17.7 0.5 CA A:ASP13 4.7 18.0 0.5 O A:ASP115 4.7 24.6 1.0 N A:PHE17 4.7 15.6 1.0 O3' P:DT8 4.8 22.8 0.5 CB A:PHE17 4.9 13.0 1.0 CE A:LYS231 4.9 39.1 1.0 MG P:MG101 5.0 30.6 0.6

Magnesium binding site 2 out of 3 in the Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 1.0 Mm MG2+ For 300S


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 300S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg505 b:22.9 occ:0.50 OP1 P:DG9 2.1 23.1 0.5 O A:HOH879 2.2 21.5 0.1 OE1 A:GLU116 2.3 34.7 0.5 OD1 A:ASP115 2.3 25.4 0.8 O1A A:DGT504 2.3 23.1 0.3 OD1 A:ASP13 2.3 28.3 0.5 O3' P:DT8 2.4 22.8 0.5 O A:HOH614 2.4 25.9 0.3 OD2 A:ASP13 2.4 32.7 0.5 OD1 A:ASP115 2.5 18.0 0.2 OE2 A:GLU116 2.5 38.5 0.5 O3' P:DT8 2.5 23.1 0.1 P P:DG9 2.7 25.0 0.5 CD A:GLU116 3.1 35.5 0.5 CG A:ASP115 3.1 20.5 0.2 CG A:ASP115 3.3 20.9 0.8 CG A:ASP13 3.3 25.9 0.5 CD A:GLU116 3.4 34.7 0.5 CG A:ASP13 3.4 25.1 0.5 PA A:DGT504 3.5 18.7 0.3 C3' P:DT8 3.5 24.6 0.1 OD1 A:ASP13 3.6 22.1 0.5 MG A:MG501 3.6 15.8 1.0 C3' P:DT8 3.6 22.9 0.5 OD2 A:ASP115 3.6 22.2 0.8 OD2 A:ASP115 3.6 20.9 0.2 OG A:SER113 3.6 28.9 1.0 CB A:GLU116 3.7 28.7 0.5 CB A:GLU116 3.7 28.7 0.5 OE1 A:GLU116 3.7 30.5 0.5 OP2 P:DG9 3.8 24.1 0.5 CG A:GLU116 3.8 28.9 0.5 O2A A:DGT504 3.9 24.2 0.3 C4' P:DT8 3.9 25.8 0.5 OD2 A:ASP13 4.0 33.5 0.5 O5' P:DG9 4.0 19.8 0.5 CG A:GLU116 4.0 28.3 0.5 CB A:ASP115 4.1 21.1 0.2 O5' A:DGT504 4.1 19.0 0.3 C4' P:DT8 4.1 26.8 0.1 C5' P:DT8 4.2 27.4 0.5 C5' P:DG9 4.2 20.3 0.5 C5' A:DGT504 4.3 20.3 0.3 C A:ASP115 4.3 20.6 1.0 O A:ASP115 4.3 24.6 1.0 OE2 A:GLU116 4.4 29.4 0.5 C5' P:DT8 4.4 28.1 0.1 O A:HOH602 4.5 47.4 1.0 N A:GLU116 4.5 17.5 1.0 O A:HOH740 4.5 29.0 0.7 NZ A:LYS224 4.5 30.0 0.2 CB A:ASP13 4.5 18.8 0.5 CB A:ASP115 4.6 21.6 0.8 CB A:ASP13 4.6 18.7 0.5 C2' P:DT8 4.7 22.6 0.5 CA A:ASP115 4.7 18.5 0.2 CA A:GLU116 4.7 22.2 0.5 CA A:GLU116 4.7 22.2 0.5 O3A A:DGT504 4.8 19.0 0.3 CA A:ASP115 4.8 18.2 0.8 CB A:SER113 4.8 23.1 1.0 O2G A:DGT504 4.9 19.9 0.3 C2' P:DT8 4.9 25.1 0.1 O1 A:DPO503 4.9 16.2 0.5 N A:ASP115 4.9 18.3 1.0 O5 A:DPO503 5.0 19.8 0.5

Magnesium binding site 3 out of 3 in the Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 1.0 Mm MG2+ For 300S


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 300S within 5.0Å range: probe atom residue distance (Å) B Occ P:Mg101 b:30.6 occ:0.60 O2A A:DGT504 2.0 24.2 0.3 O A:HOH845 2.1 26.4 0.8 O2 A:DPO503 2.1 17.4 0.5 O A:HOH740 2.2 29.0 0.7 O P:HOH220 2.2 33.0 0.6 OP2 P:DG9 2.2 24.1 0.5 O A:HOH615 2.3 29.5 0.8 O3A A:DGT504 2.3 19.0 0.3 PA A:DGT504 2.6 18.7 0.3 NH1 A:ARG61 2.7 25.8 0.1 O3' P:DT8 3.2 27.2 0.5 P P:DG9 3.3 25.0 0.5 P1 A:DPO503 3.6 17.2 0.5 O1A A:DGT504 3.7 23.1 0.3 PB A:DGT504 3.7 16.5 0.3 CZ A:ARG61 3.7 23.5 0.1 O1G A:DGT504 3.7 20.2 0.3 O3B A:DGT504 3.8 17.1 0.3 O6 A:DPO503 3.8 20.2 0.5 O A:HOH803 3.8 22.8 0.8 OP1 P:DG9 3.8 23.1 0.5 O A:HOH914 3.8 29.3 1.0 O5' A:DGT504 3.8 19.0 0.3 NH2 A:ARG61 3.9 22.6 0.1 O5' P:DG9 3.9 19.8 0.5 O4 A:DPO503 3.9 17.4 0.5 C3' P:DT8 4.0 31.0 0.5 O2G A:DGT504 4.0 19.9 0.3 O5 A:DPO503 4.1 19.8 0.5 PG A:DGT504 4.1 18.5 0.3 P2 A:DPO503 4.2 18.5 0.5 O1B A:DGT504 4.4 17.9 0.3 O3 A:DPO503 4.4 17.7 0.5 O A:HOH614 4.4 25.9 0.3 C3' P:DT8 4.5 24.6 0.1 O1 A:DPO503 4.6 16.2 0.5 C4' P:DT8 4.6 24.9 0.5 O3' P:DT8 4.7 22.8 0.5 O2B A:DGT504 4.8 16.0 0.3 C2' P:DT8 4.8 25.1 0.1 NE A:ARG61 4.9 22.7 0.1 O3' P:DT8 4.9 23.1 0.1 MG A:MG501 5.0 15.8 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