Magnesium in PDB 7m86: Human Dna Pol Eta S113A with Da-Ended Primer and Datp: in Crystallo Reaction For 140 S
Enzymatic activity of Human Dna Pol Eta S113A with Da-Ended Primer and Datp: in Crystallo Reaction For 140 S
All present enzymatic activity of Human Dna Pol Eta S113A with Da-Ended Primer and Datp: in Crystallo Reaction For 140 S:
2.7.7.7;
Protein crystallography data
The structure of Human Dna Pol Eta S113A with Da-Ended Primer and Datp: in Crystallo Reaction For 140 S, PDB code: 7m86
was solved by
M.T.Gregory,
Y.Gao,
W.Yang,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
29.94 /
1.55
|
Space group
|
P 61
|
Cell size a, b, c (Å), α, β, γ (°)
|
98.156,
98.156,
82.511,
90,
90,
120
|
R / Rfree (%)
|
17.3 /
20.5
|
Other elements in 7m86:
The structure of Human Dna Pol Eta S113A with Da-Ended Primer and Datp: in Crystallo Reaction For 140 S also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Human Dna Pol Eta S113A with Da-Ended Primer and Datp: in Crystallo Reaction For 140 S
(pdb code 7m86). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the
Human Dna Pol Eta S113A with Da-Ended Primer and Datp: in Crystallo Reaction For 140 S, PDB code: 7m86:
Jump to Magnesium binding site number:
1;
2;
3;
Magnesium binding site 1 out
of 3 in 7m86
Go back to
Magnesium Binding Sites List in 7m86
Magnesium binding site 1 out
of 3 in the Human Dna Pol Eta S113A with Da-Ended Primer and Datp: in Crystallo Reaction For 140 S
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Human Dna Pol Eta S113A with Da-Ended Primer and Datp: in Crystallo Reaction For 140 S within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg501
b:13.4
occ:0.65
|
OD1
|
A:ASP13
|
2.0
|
20.2
|
0.6
|
OE2
|
A:GLU116
|
2.2
|
22.1
|
1.0
|
OP1
|
P:DA9
|
2.2
|
11.7
|
0.2
|
O3'
|
P:DA8
|
2.2
|
9.6
|
0.3
|
O3'
|
P:DA8
|
2.3
|
10.5
|
0.2
|
OD1
|
A:ASP115
|
2.3
|
12.8
|
1.0
|
O2A
|
A:DTP504
|
2.5
|
12.6
|
0.8
|
O
|
A:HOH675
|
2.6
|
26.0
|
1.0
|
P
|
P:DA9
|
2.7
|
11.3
|
0.2
|
OD1
|
A:ASP13
|
2.9
|
13.5
|
0.5
|
O3'
|
P:DA8
|
3.0
|
20.2
|
0.5
|
OD2
|
A:ASP13
|
3.2
|
19.3
|
0.5
|
C3'
|
P:DA8
|
3.2
|
13.4
|
0.5
|
CG
|
A:ASP115
|
3.2
|
12.4
|
1.0
|
CG
|
A:ASP13
|
3.2
|
12.1
|
0.6
|
CD
|
A:GLU116
|
3.3
|
31.5
|
1.0
|
CG
|
A:ASP13
|
3.3
|
13.8
|
0.5
|
C3'
|
P:DA8
|
3.4
|
16.7
|
0.3
|
OD2
|
A:ASP115
|
3.4
|
13.7
|
1.0
|
CA
|
A:CA502
|
3.5
|
8.2
|
0.5
|
C3'
|
P:DA8
|
3.5
|
16.8
|
0.2
|
MG
|
A:MG503
|
3.5
|
8.3
|
0.5
|
OP2
|
P:DA9
|
3.8
|
17.0
|
0.2
|
PA
|
A:DTP504
|
3.8
|
11.4
|
0.8
|
OD2
|
A:ASP13
|
3.8
|
12.1
|
0.6
|
C4'
|
P:DA8
|
3.9
|
18.2
|
1.0
|
O5'
|
P:DA9
|
4.0
|
11.6
|
0.2
|
CB
|
A:GLU116
|
4.0
|
20.2
|
1.0
|
CG
|
A:GLU116
|
4.0
|
21.9
|
1.0
|
C5'
|
P:DA8
|
4.0
|
20.6
|
0.5
|
C5'
|
P:DA8
|
4.1
|
19.6
|
0.3
|
OE1
|
A:GLU116
|
4.2
|
31.9
|
1.0
|
O5'
|
A:DTP504
|
4.2
|
10.4
|
0.8
|
C5'
|
P:DA9
|
4.2
|
10.8
|
0.2
|
C5'
|
A:DTP504
|
4.2
|
10.7
|
0.8
|
O1A
|
A:DTP504
|
4.3
|
12.8
|
0.8
|
O
|
A:HOH724
|
4.3
|
35.3
|
1.0
|
CB
|
A:ASP13
|
4.4
|
12.5
|
0.6
|
C
|
A:ASP115
|
4.5
|
10.8
|
1.0
|
O
|
A:ASP115
|
4.5
|
12.0
|
1.0
|
CB
|
A:ASP13
|
4.6
|
12.5
|
0.5
|
CB
|
A:ASP115
|
4.6
|
10.5
|
1.0
|
C2'
|
P:DA8
|
4.6
|
18.8
|
0.3
|
C2'
|
P:DA8
|
4.6
|
18.9
|
0.5
|
C2'
|
P:DA8
|
4.6
|
18.2
|
0.2
|
NZ
|
A:LYS224
|
4.6
|
17.6
|
0.6
|
N
|
A:GLU116
|
4.6
|
10.6
|
1.0
|
O5'
|
P:DA8
|
4.8
|
18.5
|
0.3
|
CB
|
A:ALA113
|
4.9
|
12.1
|
1.0
|
CA
|
A:GLU116
|
4.9
|
13.1
|
1.0
|
O5
|
A:DPO505
|
4.9
|
11.0
|
0.2
|
O3G
|
A:DTP504
|
5.0
|
11.0
|
0.8
|
CA
|
A:ASP115
|
5.0
|
10.6
|
1.0
|
|
Magnesium binding site 2 out
of 3 in 7m86
Go back to
Magnesium Binding Sites List in 7m86
Magnesium binding site 2 out
of 3 in the Human Dna Pol Eta S113A with Da-Ended Primer and Datp: in Crystallo Reaction For 140 S
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Human Dna Pol Eta S113A with Da-Ended Primer and Datp: in Crystallo Reaction For 140 S within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg503
b:8.3
occ:0.50
|
CA
|
A:CA502
|
0.0
|
8.2
|
0.5
|
OD1
|
A:ASP13
|
2.2
|
13.5
|
0.5
|
OP1
|
P:DA9
|
2.2
|
11.7
|
0.2
|
OD2
|
A:ASP115
|
2.2
|
13.7
|
1.0
|
OD2
|
A:ASP13
|
2.2
|
12.1
|
0.6
|
O
|
A:MET14
|
2.3
|
10.7
|
1.0
|
O5
|
A:DPO505
|
2.3
|
11.0
|
0.2
|
O3G
|
A:DTP504
|
2.3
|
11.0
|
0.8
|
O1B
|
A:DTP504
|
2.3
|
9.9
|
0.8
|
O1
|
A:DPO505
|
2.4
|
10.1
|
0.2
|
O2A
|
A:DTP504
|
2.4
|
12.6
|
0.8
|
CG
|
A:ASP13
|
2.9
|
12.1
|
0.6
|
OD1
|
A:ASP13
|
3.0
|
20.2
|
0.6
|
CG
|
A:ASP13
|
3.2
|
13.8
|
0.5
|
CG
|
A:ASP115
|
3.3
|
12.4
|
1.0
|
PB
|
A:DTP504
|
3.3
|
9.6
|
0.8
|
P1
|
A:DPO505
|
3.4
|
10.0
|
0.2
|
C
|
A:MET14
|
3.4
|
8.6
|
1.0
|
PA
|
A:DTP504
|
3.5
|
11.4
|
0.8
|
MG
|
A:MG501
|
3.5
|
13.4
|
0.7
|
P2
|
A:DPO505
|
3.5
|
10.5
|
0.2
|
PG
|
A:DTP504
|
3.5
|
10.8
|
0.8
|
O3A
|
A:DTP504
|
3.6
|
10.2
|
0.8
|
OD2
|
A:ASP13
|
3.6
|
19.3
|
0.5
|
P
|
P:DA9
|
3.7
|
11.3
|
0.2
|
OD1
|
A:ASP115
|
3.7
|
12.8
|
1.0
|
O3B
|
A:DTP504
|
3.8
|
10.5
|
0.8
|
O4
|
A:DPO505
|
3.8
|
10.4
|
0.2
|
O3
|
A:DPO505
|
3.8
|
10.8
|
0.2
|
O
|
A:HOH724
|
3.9
|
35.3
|
1.0
|
N
|
A:MET14
|
3.9
|
8.9
|
1.0
|
NZ
|
A:LYS231
|
4.0
|
13.6
|
1.0
|
C5'
|
A:DTP504
|
4.1
|
10.7
|
0.8
|
O2G
|
A:DTP504
|
4.1
|
9.8
|
0.8
|
O7
|
A:DPO505
|
4.1
|
9.9
|
0.2
|
C5'
|
P:DA9
|
4.2
|
10.8
|
0.2
|
CA
|
A:MET14
|
4.2
|
8.8
|
1.0
|
O
|
A:HOH675
|
4.2
|
26.0
|
1.0
|
O5'
|
A:DTP504
|
4.3
|
10.4
|
0.8
|
C
|
A:ASP13
|
4.3
|
8.7
|
1.0
|
O5'
|
P:DA9
|
4.3
|
11.6
|
0.2
|
CB
|
A:ASP13
|
4.3
|
12.5
|
0.6
|
CB
|
A:ASP13
|
4.4
|
12.5
|
0.5
|
N
|
A:ASP15
|
4.5
|
7.9
|
1.0
|
OP2
|
P:DA9
|
4.6
|
17.0
|
0.2
|
N
|
A:CYS16
|
4.6
|
8.2
|
1.0
|
CB
|
A:ASP115
|
4.6
|
10.5
|
1.0
|
CA
|
A:ASP15
|
4.6
|
8.3
|
1.0
|
O3'
|
P:DA8
|
4.7
|
10.5
|
0.2
|
O6
|
A:DPO505
|
4.7
|
11.5
|
0.2
|
O1A
|
A:DTP504
|
4.7
|
12.8
|
0.8
|
O2B
|
A:DTP504
|
4.7
|
10.6
|
0.8
|
CE
|
A:LYS231
|
4.7
|
20.7
|
1.0
|
CB
|
A:MET14
|
4.7
|
10.0
|
1.0
|
O3'
|
P:DA8
|
4.7
|
9.6
|
0.3
|
O2
|
A:DPO505
|
4.7
|
10.7
|
0.2
|
O
|
A:ASP13
|
4.7
|
11.1
|
1.0
|
CA
|
A:ASP13
|
4.7
|
10.8
|
0.5
|
O1G
|
A:DTP504
|
4.7
|
11.2
|
0.8
|
CA
|
A:ASP13
|
4.7
|
10.8
|
0.6
|
N
|
A:PHE17
|
4.8
|
7.8
|
1.0
|
C
|
A:ASP15
|
4.8
|
9.8
|
1.0
|
MG
|
P:MG101
|
4.8
|
15.6
|
0.2
|
CB
|
A:PHE17
|
4.9
|
7.0
|
1.0
|
O
|
A:ASP115
|
4.9
|
12.0
|
1.0
|
|
Magnesium binding site 3 out
of 3 in 7m86
Go back to
Magnesium Binding Sites List in 7m86
Magnesium binding site 3 out
of 3 in the Human Dna Pol Eta S113A with Da-Ended Primer and Datp: in Crystallo Reaction For 140 S
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Human Dna Pol Eta S113A with Da-Ended Primer and Datp: in Crystallo Reaction For 140 S within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
P:Mg101
b:15.6
occ:0.20
|
O1A
|
A:DTP504
|
1.7
|
12.8
|
0.8
|
O3
|
A:DPO505
|
2.0
|
10.8
|
0.2
|
O
|
A:HOH866
|
2.1
|
9.3
|
0.2
|
O
|
A:HOH772
|
2.1
|
36.9
|
1.0
|
O3A
|
A:DTP504
|
2.1
|
10.2
|
0.8
|
OP2
|
P:DA9
|
2.2
|
17.0
|
0.2
|
PA
|
A:DTP504
|
2.3
|
11.4
|
0.8
|
O
|
A:HOH655
|
2.8
|
17.7
|
1.0
|
NH1
|
A:ARG61
|
3.0
|
26.7
|
0.8
|
O2A
|
A:DTP504
|
3.2
|
12.6
|
0.8
|
P
|
P:DA9
|
3.2
|
11.3
|
0.2
|
O
|
A:HOH724
|
3.3
|
35.3
|
1.0
|
P1
|
A:DPO505
|
3.4
|
10.0
|
0.2
|
PB
|
A:DTP504
|
3.5
|
9.6
|
0.8
|
OP1
|
P:DA9
|
3.7
|
11.7
|
0.2
|
O5'
|
A:DTP504
|
3.7
|
10.4
|
0.8
|
O6
|
A:DPO505
|
3.7
|
11.5
|
0.2
|
O3B
|
A:DTP504
|
3.7
|
10.5
|
0.8
|
O4
|
A:DPO505
|
3.7
|
10.4
|
0.2
|
O1G
|
A:DTP504
|
3.8
|
11.2
|
0.8
|
NH1
|
A:ARG61
|
3.8
|
25.0
|
0.2
|
NH2
|
A:ARG61
|
3.8
|
12.1
|
0.8
|
O
|
A:HOH1017
|
3.8
|
39.5
|
1.0
|
O5'
|
P:DA9
|
3.8
|
11.6
|
0.2
|
CZ
|
A:ARG61
|
3.8
|
24.4
|
0.8
|
O5
|
A:DPO505
|
3.8
|
11.0
|
0.2
|
O3G
|
A:DTP504
|
3.9
|
11.0
|
0.8
|
PG
|
A:DTP504
|
4.0
|
10.8
|
0.8
|
O
|
A:HOH809
|
4.1
|
21.0
|
0.8
|
P2
|
A:DPO505
|
4.1
|
10.5
|
0.2
|
O
|
A:HOH675
|
4.1
|
26.0
|
1.0
|
O
|
A:HOH944
|
4.2
|
22.7
|
1.0
|
O2B
|
A:DTP504
|
4.3
|
10.6
|
0.8
|
O1
|
A:DPO505
|
4.4
|
10.1
|
0.2
|
O2
|
A:DPO505
|
4.4
|
10.7
|
0.2
|
O1B
|
A:DTP504
|
4.5
|
9.9
|
0.8
|
O3'
|
P:DA8
|
4.6
|
10.5
|
0.2
|
O3'
|
P:DA8
|
4.7
|
9.6
|
0.3
|
CA
|
A:CA502
|
4.8
|
8.2
|
0.5
|
MG
|
A:MG503
|
4.8
|
8.3
|
0.5
|
CZ
|
A:ARG61
|
4.8
|
27.2
|
0.2
|
C5'
|
A:DTP504
|
4.9
|
10.7
|
0.8
|
C3'
|
P:DA8
|
4.9
|
16.7
|
0.3
|
C8
|
P:DA9
|
4.9
|
11.2
|
0.2
|
C3'
|
P:DA8
|
4.9
|
16.8
|
0.2
|
|
Reference:
M.T.Gregory,
Y.Gao,
Q.Cui,
W.Yang.
Multiple Deprotonation Paths of the Nucleophile 3'-Oh in the Dna Synthesis Reaction Proc.Natl.Acad.Sci.Usa 2021.
ISSN: ESSN 1091-6490
Page generated: Thu Oct 3 00:23:16 2024
|