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:
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: Sun Jul 11 16:16:02 2021
|