Manganese in PDB 7coa: Ternary Complex of Dna Polymerase Mu with 1-Nt Gapped Dna (T:Dgmpnpp) and Mn

All present enzymatic activity of Ternary Complex of Dna Polymerase Mu with 1-Nt Gapped Dna (T:Dgmpnpp) and Mn:
2.7.7.7;

The structure of Ternary Complex of Dna Polymerase Mu with 1-Nt Gapped Dna (T:Dgmpnpp) and Mn, PDB code: 7coa was solved by M.Guo, Y.Zhao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.94 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	59.95, 68.57, 110.81, 90, 90, 90
R / Rfree (%)	17.5 / 19.9

The structure of Ternary Complex of Dna Polymerase Mu with 1-Nt Gapped Dna (T:Dgmpnpp) and Mn also contains other interesting chemical elements:

Potassium

(K)

1 atom

The binding sites of Manganese atom in the Ternary Complex of Dna Polymerase Mu with 1-Nt Gapped Dna (T:Dgmpnpp) and Mn (pdb code 7coa). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Ternary Complex of Dna Polymerase Mu with 1-Nt Gapped Dna (T:Dgmpnpp) and Mn, PDB code: 7coa:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Ternary Complex of Dna Polymerase Mu with 1-Nt Gapped Dna (T:Dgmpnpp) and Mn


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Ternary Complex of Dna Polymerase Mu with 1-Nt Gapped Dna (T:Dgmpnpp) and Mn within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn502 b:10.2 occ:1.00 OD2 A:ASP330 2.1 16.5 1.0 OD1 A:ASP332 2.1 18.8 1.0 OD2 A:ASP418 2.1 18.9 1.0 O A:HOH607 2.1 22.0 1.0 O P:HOH101 2.2 20.3 1.0 O1A A:XG4501 2.3 19.9 0.5 O1A A:XG4501 2.3 20.1 0.5 O3' P:DA4 2.5 27.0 0.5 CG A:ASP330 3.1 15.4 1.0 CG A:ASP332 3.2 14.2 1.0 CG A:ASP418 3.2 17.2 1.0 PA A:XG4501 3.4 19.4 0.5 PA A:XG4501 3.4 19.3 0.5 OD1 A:ASP330 3.4 17.5 1.0 C3' P:DA4 3.5 22.8 0.5 OD2 A:ASP332 3.6 16.3 1.0 MN A:MN503 3.6 9.3 1.0 C5' A:XG4501 3.7 29.6 0.5 O2A A:XG4501 3.7 20.0 0.5 O2A A:XG4501 3.7 20.4 0.5 CB A:ASP418 3.8 14.4 1.0 O5' A:XG4501 3.8 24.3 0.5 O5' A:XG4501 3.9 24.2 0.5 C5' P:DA4 3.9 22.0 0.5 C4' P:DA4 3.9 21.5 0.5 CE1 A:HIS329 4.2 25.1 1.0 OD1 A:ASP418 4.2 18.5 1.0 O5' P:DA4 4.4 23.2 0.5 CB A:ASP330 4.4 15.5 1.0 OP1 P:DA4 4.4 21.2 0.5 CB A:ASP332 4.5 12.4 1.0 NH1 A:ARG416 4.6 17.3 1.0 OP1 P:DA4 4.7 21.1 0.5 N3A A:XG4501 4.8 17.4 0.5 N3A A:XG4501 4.8 17.4 0.5 O4' A:XG4501 4.8 33.1 0.5 C2' P:DA4 4.9 20.8 0.5 O1G A:XG4501 4.9 19.1 0.5 O1G A:XG4501 4.9 19.1 0.5 ND1 A:HIS329 4.9 25.2 1.0 NE2 A:HIS329 5.0 26.1 1.0

Manganese binding site 2 out of 2 in the Ternary Complex of Dna Polymerase Mu with 1-Nt Gapped Dna (T:Dgmpnpp) and Mn


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Ternary Complex of Dna Polymerase Mu with 1-Nt Gapped Dna (T:Dgmpnpp) and Mn within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn503 b:9.3 occ:1.00 OD1 A:ASP330 2.1 17.5 1.0 OD2 A:ASP332 2.1 16.3 1.0 O1A A:XG4501 2.1 19.9 0.5 O1A A:XG4501 2.1 20.1 0.5 O1B A:XG4501 2.2 17.4 0.5 O1B A:XG4501 2.2 17.5 0.5 O A:HOH742 2.2 16.8 1.0 O1G A:XG4501 2.3 19.1 0.5 O1G A:XG4501 2.3 19.1 0.5 CG A:ASP332 3.1 14.2 1.0 PA A:XG4501 3.1 19.3 0.5 CG A:ASP330 3.2 15.4 1.0 PB A:XG4501 3.2 18.3 0.5 PB A:XG4501 3.2 18.1 0.5 PA A:XG4501 3.2 19.4 0.5 N3A A:XG4501 3.3 17.4 0.5 N3A A:XG4501 3.3 17.4 0.5 OD1 A:ASP332 3.4 18.8 1.0 PG A:XG4501 3.5 17.6 0.5 PG A:XG4501 3.5 17.6 0.5 OD2 A:ASP330 3.5 16.5 1.0 O5' A:XG4501 3.5 24.2 0.5 O3B A:XG4501 3.6 17.9 0.5 O3B A:XG4501 3.6 17.9 0.5 MN A:MN502 3.6 10.2 1.0 O5' A:XG4501 3.7 24.3 0.5 O A:ASP330 4.1 15.3 1.0 ND1 A:HIS329 4.2 25.2 1.0 N A:GLY320 4.2 11.9 1.0 O A:HOH739 4.2 15.9 1.0 O3G A:XG4501 4.2 20.4 0.5 O3G A:XG4501 4.3 20.4 0.5 O A:HOH639 4.3 15.5 1.0 C A:ASP330 4.4 14.2 1.0 C5' A:XG4501 4.4 29.6 0.5 CE1 A:HIS329 4.4 25.1 1.0 CB A:ASP332 4.5 12.4 1.0 CB A:ASP330 4.5 15.5 1.0 O2A A:XG4501 4.5 20.0 0.5 O2A A:XG4501 4.5 20.4 0.5 N A:ASP330 4.5 15.9 1.0 O2B A:XG4501 4.5 17.1 0.5 O2B A:XG4501 4.6 17.2 0.5 CA A:GLY319 4.6 13.3 1.0 O2G A:XG4501 4.6 19.3 0.5 O2G A:XG4501 4.6 19.3 0.5 O A:HOH607 4.6 22.0 1.0 CA A:ASP330 4.7 15.0 1.0 O P:HOH101 4.8 20.3 1.0 N A:ASP332 4.8 11.7 1.0 N A:VAL331 4.9 13.8 1.0 C A:GLY319 5.0 12.2 1.0

M.Guo, Y.Wang, Y.Tang, Z.Chen, J.Hou, J.Dai, Y.Wang, L.Wang, H.Xu, B.Tian, Y.Hua, Y.Zhao. Mechanism of Genome Instability Mediated By Human Dna Polymerase Mu Misincorporation. Nat Commun V. 12 3759 2021.
ISSN: ESSN 2041-1723
PubMed: 34145298
DOI: 10.1038/S41467-021-24096-7