Manganese in PDB 7u83: Human Dna Polymerase Eta-Dna-Dgmpnpp Ternary Mismatch Complex in 3.0 Mm MN2+ For 600S

All present enzymatic activity of Human Dna Polymerase Eta-Dna-Dgmpnpp Ternary Mismatch Complex in 3.0 Mm MN2+ For 600S:
2.7.7.7;

The structure of Human Dna Polymerase Eta-Dna-Dgmpnpp Ternary Mismatch Complex in 3.0 Mm MN2+ For 600S, PDB code: 7u83 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)	42.14 / 1.55
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	98.27, 98.27, 81.948, 90, 90, 120
R / Rfree (%)	19 / 23.2

The binding sites of Manganese atom in the Human Dna Polymerase Eta-Dna-Dgmpnpp Ternary Mismatch Complex in 3.0 Mm MN2+ For 600S (pdb code 7u83). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Human Dna Polymerase Eta-Dna-Dgmpnpp Ternary Mismatch Complex in 3.0 Mm MN2+ For 600S, PDB code: 7u83:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Human Dna Polymerase Eta-Dna-Dgmpnpp Ternary Mismatch Complex in 3.0 Mm MN2+ For 600S


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Human Dna Polymerase Eta-Dna-Dgmpnpp Ternary Mismatch Complex in 3.0 Mm MN2+ For 600S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn501 b:24.7 occ:0.95 OD1 A:ASP115 2.2 24.2 0.9 OE1 A:GLU116 2.2 25.2 1.0 OD2 A:ASP13 2.2 25.8 1.0 O1A A:XG4505 2.3 24.5 0.9 O A:HOH750 2.3 28.8 1.0 O A:HOH743 2.3 24.7 0.5 OD1 A:ASP115 2.3 20.2 0.1 O3' P:DT8 2.4 26.1 0.3 CG A:ASP115 3.0 23.5 0.1 CG A:ASP115 3.1 21.6 0.9 CD A:GLU116 3.2 29.9 1.0 CG A:ASP13 3.2 26.5 1.0 PA A:XG4505 3.4 23.3 0.9 C3' P:DT8 3.4 21.6 0.3 OD2 A:ASP115 3.5 22.3 0.9 OD2 A:ASP115 3.5 23.3 0.1 MN A:MN502 3.6 22.7 1.0 OD1 A:ASP13 3.7 23.2 1.0 OG A:SER113 3.8 26.8 1.0 O5' A:XG4505 3.8 21.5 0.9 CB A:ASP115 3.8 22.7 0.1 O2A A:XG4505 3.9 24.4 0.9 OE2 A:GLU116 3.9 30.7 1.0 CB A:GLU116 4.1 22.9 1.0 C5' A:XG4505 4.1 20.4 0.9 CG A:GLU116 4.1 23.2 1.0 O A:HOH735 4.1 25.7 1.0 O P:HOH101 4.1 27.7 0.4 NZ A:LYS224 4.2 28.9 1.0 C4' P:DT8 4.4 20.3 0.3 CB A:ASP115 4.5 24.2 0.9 C A:ASP115 4.5 25.3 1.0 CB A:ASP13 4.5 22.7 1.0 C2' P:DT8 4.5 23.1 0.3 O A:ASP115 4.7 25.7 1.0 N A:GLU116 4.7 20.4 1.0 O2G A:XG4505 4.7 24.1 0.9 CA A:ASP115 4.7 22.5 0.1 O5' P:DT8 4.8 28.7 0.3 N3A A:XG4505 4.8 24.3 0.9 CB A:SER113 4.8 22.4 1.0 C5' P:DT8 4.8 31.9 0.3 CA A:ASP115 4.9 22.5 0.9 O1B A:XG4505 4.9 22.0 0.9

Manganese binding site 2 out of 2 in the Human Dna Polymerase Eta-Dna-Dgmpnpp Ternary Mismatch Complex in 3.0 Mm MN2+ For 600S


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Human Dna Polymerase Eta-Dna-Dgmpnpp Ternary Mismatch Complex in 3.0 Mm MN2+ For 600S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn502 b:22.7 occ:1.00 OD1 A:ASP13 2.1 23.2 1.0 O1B A:XG4505 2.1 22.0 0.9 O A:MET14 2.2 23.4 1.0 O2G A:XG4505 2.2 24.1 0.9 OD2 A:ASP115 2.2 22.3 0.9 O1A A:XG4505 2.4 24.5 0.9 CG A:ASP13 3.0 26.5 1.0 PB A:XG4505 3.2 22.6 0.9 CG A:ASP115 3.2 21.6 0.9 C A:MET14 3.3 18.9 1.0 PG A:XG4505 3.4 23.6 0.9 OD2 A:ASP13 3.4 25.8 1.0 PA A:XG4505 3.4 23.3 0.9 O3B A:XG4505 3.6 20.9 0.9 N3A A:XG4505 3.6 24.3 0.9 MN A:MN501 3.6 24.7 0.9 OD1 A:ASP115 3.6 24.2 0.9 O A:HOH697 3.8 28.5 0.9 N A:MET14 3.8 18.3 1.0 OD2 A:ASP115 3.9 23.3 0.1 O A:HOH735 3.9 25.7 1.0 O3G A:XG4505 3.9 23.0 0.9 NZ A:LYS231 4.0 27.8 0.5 CG A:ASP115 4.0 23.5 0.1 CA A:MET14 4.1 17.8 1.0 CB A:ASP115 4.1 22.7 0.1 C5' A:XG4505 4.1 20.4 0.9 C A:ASP13 4.2 18.8 1.0 CB A:ASP13 4.3 22.7 1.0 O5' A:XG4505 4.3 21.5 0.9 N A:ASP15 4.3 19.8 1.0 N A:CYS16 4.4 21.0 1.0 O A:HOH750 4.5 28.8 1.0 CB A:ASP115 4.5 24.2 0.9 CA A:ASP15 4.5 19.9 1.0 OD1 A:ASP115 4.5 20.2 0.1 O2B A:XG4505 4.6 23.7 0.9 C A:ASP15 4.6 22.4 1.0 CB A:MET14 4.6 19.0 1.0 O A:ASP13 4.6 20.5 1.0 O1G A:XG4505 4.7 24.8 0.9 N A:PHE17 4.7 20.1 1.0 O2A A:XG4505 4.7 24.4 0.9 CA A:ASP13 4.7 22.1 1.0 CB A:PHE17 4.8 18.1 1.0 CE A:LYS231 4.9 22.6 0.5 O A:ASP115 5.0 25.7 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