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

Enzymatic activity of 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;

Protein crystallography data

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

Other elements in 7co8:

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

Magnesium Binding Sites:

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 7co8

Go back to Magnesium Binding Sites List in 7co8
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 7co8

Go back to Magnesium Binding Sites List in 7co8
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 7co8

Go back to Magnesium Binding Sites List in 7co8
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

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: Sun Jul 11 16:16:01 2021

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