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Magnesium in PDB 7co9: Ternary Complex of Dna Polymerase Mu with 1-Nt Gapped Dna (T:Dgmpnpp) and Mg

Enzymatic activity of Ternary Complex of Dna Polymerase Mu with 1-Nt Gapped Dna (T:Dgmpnpp) and Mg

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

Protein crystallography data

The structure of Ternary Complex of Dna Polymerase Mu with 1-Nt Gapped Dna (T:Dgmpnpp) and Mg, PDB code: 7co9 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) 27.51 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 60.08, 68.54, 110.82, 90, 90, 90
R / Rfree (%) 17.1 / 19.6

Other elements in 7co9:

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

Potassium (K) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Ternary Complex of Dna Polymerase Mu with 1-Nt Gapped Dna (T:Dgmpnpp) and Mg (pdb code 7co9). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Ternary Complex of Dna Polymerase Mu with 1-Nt Gapped Dna (T:Dgmpnpp) and Mg, PDB code: 7co9:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 7co9

Go back to Magnesium Binding Sites List in 7co9
Magnesium binding site 1 out of 2 in the Ternary Complex of Dna Polymerase Mu with 1-Nt Gapped Dna (T:Dgmpnpp) and Mg


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 1-Nt Gapped Dna (T:Dgmpnpp) and Mg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:16.4
occ:1.00
OD1 A:ASP330 2.0 15.3 1.0
OD2 A:ASP332 2.0 14.6 1.0
O A:HOH717 2.1 16.2 1.0
O1A A:XG4501 2.2 13.7 0.5
O1B A:XG4501 2.2 13.0 0.5
O1A A:XG4501 2.2 25.6 0.5
O1G A:XG4501 2.2 16.6 0.5
O1B A:XG4501 2.2 22.6 0.5
O1G A:XG4501 2.2 23.9 0.5
CG A:ASP332 3.0 14.9 1.0
CG A:ASP330 3.0 16.4 1.0
PB A:XG4501 3.2 13.8 0.5
PB A:XG4501 3.2 23.1 0.5
PA A:XG4501 3.2 28.4 0.5
PA A:XG4501 3.3 16.0 0.5
OD1 A:ASP332 3.3 17.3 1.0
N3A A:XG4501 3.4 23.9 0.5
N3A A:XG4501 3.4 11.9 0.5
PG A:XG4501 3.4 13.5 0.5
PG A:XG4501 3.5 25.0 0.5
OD2 A:ASP330 3.5 18.6 1.0
MG A:MG503 3.6 14.5 1.0
O3B A:XG4501 3.6 16.1 0.5
O3B A:XG4501 3.6 24.8 0.5
O5' A:XG4501 3.7 33.3 0.5
O5' A:XG4501 3.8 22.1 0.5
O A:ASP330 4.0 16.3 1.0
N A:GLY320 4.2 13.7 1.0
O3G A:XG4501 4.2 19.9 0.5
O A:HOH637 4.2 16.5 1.0
ND1 A:HIS329 4.2 16.8 0.5
O3G A:XG4501 4.2 24.8 0.5
O A:HOH704 4.3 18.4 1.0
C A:ASP330 4.3 16.1 1.0
CB A:ASP330 4.4 15.7 1.0
CB A:ASP332 4.4 15.2 1.0
N A:ASP330 4.5 16.0 1.0
C5' A:XG4501 4.5 38.1 0.5
CE1 A:HIS329 4.5 13.7 0.5
O2G A:XG4501 4.6 17.1 0.5
O2A A:XG4501 4.6 19.5 0.5
O2G A:XG4501 4.6 26.0 0.5
O2B A:XG4501 4.6 14.3 0.5
CA A:ASP330 4.6 15.8 1.0
O2A A:XG4501 4.6 31.0 0.5
O2B A:XG4501 4.6 24.2 0.5
CA A:GLY319 4.6 14.1 1.0
O P:HOH103 4.7 21.3 1.0
O A:HOH727 4.8 19.6 1.0
N A:ASP332 4.8 12.8 1.0
N A:VAL331 4.8 15.6 1.0
C A:GLY319 5.0 13.6 1.0

Magnesium binding site 2 out of 2 in 7co9

Go back to Magnesium Binding Sites List in 7co9
Magnesium binding site 2 out of 2 in the Ternary Complex of Dna Polymerase Mu with 1-Nt Gapped Dna (T:Dgmpnpp) and Mg


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 1-Nt Gapped Dna (T:Dgmpnpp) and Mg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg503

b:14.5
occ:1.00
OD2 A:ASP330 2.0 18.6 1.0
OD1 A:ASP332 2.0 17.3 1.0
OD2 A:ASP418 2.0 19.4 1.0
O P:HOH103 2.1 21.3 1.0
O A:HOH727 2.1 19.6 1.0
O1A A:XG4501 2.2 13.7 0.5
O1A A:XG4501 2.2 25.6 0.5
CG A:ASP330 3.0 16.4 1.0
CG A:ASP332 3.1 14.9 1.0
CG A:ASP418 3.2 18.1 1.0
PA A:XG4501 3.4 16.0 0.5
OD1 A:ASP330 3.4 15.3 1.0
PA A:XG4501 3.4 28.4 0.5
O3' P:DA4 3.4 37.5 0.5
OD2 A:ASP332 3.5 14.6 1.0
MG A:MG502 3.6 16.4 1.0
C5' A:XG4501 3.8 38.1 0.5
O2A A:XG4501 3.8 19.5 0.5
O2A A:XG4501 3.8 31.0 0.5
CB A:ASP418 3.8 15.9 1.0
O5' A:XG4501 3.9 22.1 0.5
O5' A:XG4501 3.9 33.3 0.5
C5' P:DA4 4.0 21.9 0.5
OD1 A:ASP418 4.2 19.0 1.0
CE1 A:HIS329 4.2 13.7 0.5
CB A:ASP330 4.3 15.7 1.0
CB A:ASP332 4.4 15.2 1.0
C3' P:DA4 4.4 30.3 0.5
C4' P:DA4 4.4 21.9 0.5
OP1 P:DA4 4.5 21.0 0.5
OP1 P:DA4 4.5 20.8 0.5
NH1 A:ARG416 4.6 18.4 1.0
O5' P:DA4 4.7 23.8 0.5
N3A A:XG4501 4.8 11.9 0.5
N3A A:XG4501 4.8 23.9 0.5
O1G A:XG4501 4.8 16.6 0.5
O1G A:XG4501 4.8 23.9 0.5
O4' A:XG4501 4.9 36.6 0.5
ND1 A:HIS329 5.0 16.8 0.5

Reference:

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
Page generated: Wed Oct 2 14:13:37 2024

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