Magnesium in PDB 7co8: Ternary Complex of Dna Polymerase Mu with 2-Nt Gapped Dna (T:Dgmpnpp)

All present enzymatic activity of Ternary Complex of Dna Polymerase Mu with 2-Nt Gapped Dna (T:Dgmpnpp):
2.7.7.7;

The structure of Ternary Complex of Dna Polymerase Mu with 2-Nt Gapped Dna (T:Dgmpnpp), PDB code: 7co8 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)	29.08 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.31, 69.2, 117.86, 90, 90, 90
R / Rfree (%)	17.9 / 19.5

The structure of Ternary Complex of Dna Polymerase Mu with 2-Nt Gapped Dna (T:Dgmpnpp) also contains other interesting chemical elements:

Potassium

(K)

1 atom

The binding sites of Magnesium atom in the Ternary Complex of Dna Polymerase Mu with 2-Nt Gapped Dna (T:Dgmpnpp) (pdb code 7co8). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Ternary Complex of Dna Polymerase Mu with 2-Nt Gapped Dna (T:Dgmpnpp), PDB code: 7co8:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Ternary Complex of Dna Polymerase Mu with 2-Nt Gapped Dna (T:Dgmpnpp)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Ternary Complex of Dna Polymerase Mu with 2-Nt Gapped Dna (T:Dgmpnpp) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:16.1 occ:1.00 OD2 A:ASP330 2.0 19.4 1.0 O A:HOH648 2.1 18.3 1.0 OD2 A:ASP418 2.1 18.4 1.0 OD1 A:ASP332 2.1 16.4 1.0 O2A A:XG4501 2.3 19.0 1.0 O3' P:DA4 2.3 20.2 1.0 CG A:ASP330 3.0 19.4 1.0 CG A:ASP332 3.2 15.5 1.0 CG A:ASP418 3.2 18.5 1.0 C3' P:DA4 3.4 23.9 1.0 OD1 A:ASP330 3.4 16.4 1.0 PA A:XG4501 3.4 18.6 1.0 OD2 A:ASP332 3.6 14.9 1.0 MG A:MG504 3.6 16.4 1.0 O1A A:XG4501 3.8 20.9 1.0 O5' A:XG4501 3.8 22.2 1.0 CB A:ASP418 3.9 14.8 1.0 C4' P:DA4 4.0 25.1 1.0 C5' P:DA4 4.2 19.5 1.0 OD1 A:ASP418 4.2 18.1 1.0 C5' A:XG4501 4.3 21.2 1.0 CE1 A:HIS329 4.3 16.8 0.5 CB A:ASP330 4.4 15.1 1.0 OP1 P:DA4 4.5 21.5 1.0 CB A:ASP332 4.5 11.6 1.0 NH1 A:ARG416 4.6 18.9 1.0 CZ3 A:TRP434 4.7 22.0 1.0 C2' P:DA4 4.7 23.8 1.0 O5' P:DA4 4.7 22.9 1.0 O3G A:XG4501 4.8 18.9 1.0 N3A A:XG4501 4.8 15.1 1.0

Magnesium binding site 2 out of 3 in the Ternary Complex of Dna Polymerase Mu with 2-Nt Gapped Dna (T:Dgmpnpp)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Ternary Complex of Dna Polymerase Mu with 2-Nt Gapped Dna (T:Dgmpnpp) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg504 b:16.4 occ:1.00 OD1 A:ASP330 2.0 16.4 1.0 OD2 A:ASP332 2.1 14.9 1.0 O A:HOH725 2.2 15.6 1.0 O1B A:XG4501 2.2 16.4 1.0 O2A A:XG4501 2.2 19.0 1.0 O3G A:XG4501 2.2 18.9 1.0 CG A:ASP330 3.1 19.4 1.0 CG A:ASP332 3.1 15.5 1.0 PB A:XG4501 3.1 17.7 1.0 PA A:XG4501 3.3 18.6 1.0 N3A A:XG4501 3.4 15.1 1.0 PG A:XG4501 3.4 18.4 1.0 OD1 A:ASP332 3.4 16.4 1.0 OD2 A:ASP330 3.5 19.4 1.0 O3B A:XG4501 3.5 17.8 1.0 MG A:MG503 3.6 16.1 1.0 O A:ASP330 4.1 14.6 1.0 O2G A:XG4501 4.2 20.2 1.0 ND1 A:HIS329 4.2 19.5 0.5 O A:HOH680 4.2 13.6 1.0 C A:ASP330 4.3 14.7 1.0 O5' A:XG4501 4.3 22.2 1.0 N A:GLY320 4.3 14.3 1.0 O A:HOH634 4.3 22.0 1.0 C5' A:XG4501 4.3 21.2 1.0 O1A A:XG4501 4.4 20.9 1.0 CB A:ASP330 4.4 15.1 1.0 CB A:ASP332 4.4 11.6 1.0 O1G A:XG4501 4.5 24.8 1.0 CE1 A:HIS329 4.5 16.8 0.5 N A:ASP330 4.5 17.3 1.0 O2B A:XG4501 4.5 19.8 1.0 CA A:GLY319 4.6 13.1 1.0 CA A:ASP330 4.6 13.4 1.0 O A:HOH648 4.6 18.3 1.0 N A:ASP332 4.7 11.8 1.0 N A:VAL331 4.8 13.2 1.0

Magnesium binding site 3 out of 3 in the Ternary Complex of Dna Polymerase Mu with 2-Nt Gapped Dna (T:Dgmpnpp)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Ternary Complex of Dna Polymerase Mu with 2-Nt Gapped Dna (T:Dgmpnpp) within 5.0Å range: probe atom residue distance (Å) B Occ T:Mg101 b:39.7 occ:1.00 O T:HOH211 1.8 37.8 1.0 O T:HOH230 1.9 33.4 1.0 O D:HOH103 2.0 34.6 1.0 O T:HOH228 2.1 35.7 1.0 O D:HOH116 2.2 34.9 1.0 O A:HOH865 2.6 39.2 1.0 O6 D:DG1 3.9 20.2 1.0 O T:HOH219 4.0 36.1 1.0 O T:HOH213 4.1 28.6 1.0 O T:HOH209 4.2 34.1 1.0 O T:HOH207 4.4 39.5 1.0 O6 T:DG3 4.5 22.4 1.0 N4 T:DC4 4.5 19.5 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