Magnesium in PDB 7m87: Human Dna Pol Eta S113A with Da-Ended Primer and Datp: in Crystallo Reaction For 230 S
Enzymatic activity of Human Dna Pol Eta S113A with Da-Ended Primer and Datp: in Crystallo Reaction For 230 S
All present enzymatic activity of Human Dna Pol Eta S113A with Da-Ended Primer and Datp: in Crystallo Reaction For 230 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 230 S, PDB code: 7m87
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 /
1.85
|
Space group
|
P 61
|
Cell size a, b, c (Å), α, β, γ (°)
|
98.262,
98.262,
81.935,
90,
90,
120
|
R / Rfree (%)
|
20.1 /
22.8
|
Other elements in 7m87:
The structure of Human Dna Pol Eta S113A with Da-Ended Primer and Datp: in Crystallo Reaction For 230 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 230 S
(pdb code 7m87). 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 230 S, PDB code: 7m87:
Jump to Magnesium binding site number:
1;
2;
3;
Magnesium binding site 1 out
of 3 in 7m87
Go back to
Magnesium Binding Sites List in 7m87
Magnesium binding site 1 out
of 3 in the Human Dna Pol Eta S113A with Da-Ended Primer and Datp: in Crystallo Reaction For 230 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 230 S within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg501
b:13.7
occ:0.65
|
OD1
|
A:ASP13
|
2.0
|
22.9
|
0.7
|
OE2
|
A:GLU116
|
2.2
|
25.4
|
1.0
|
OP1
|
P:DA9
|
2.2
|
13.6
|
0.2
|
O3'
|
P:DA8
|
2.2
|
13.8
|
0.3
|
O3'
|
P:DA8
|
2.3
|
13.9
|
0.2
|
OD1
|
A:ASP115
|
2.3
|
12.4
|
1.0
|
O2A
|
A:DTP504
|
2.5
|
12.3
|
0.8
|
O
|
A:HOH678
|
2.6
|
21.6
|
1.0
|
P
|
P:DA9
|
2.7
|
14.2
|
0.2
|
OD1
|
A:ASP13
|
2.9
|
11.6
|
0.3
|
O3'
|
P:DA8
|
3.0
|
17.7
|
0.5
|
OD2
|
A:ASP13
|
3.2
|
14.8
|
0.3
|
C3'
|
P:DA8
|
3.2
|
15.9
|
0.5
|
CG
|
A:ASP115
|
3.2
|
14.6
|
1.0
|
CG
|
A:ASP13
|
3.2
|
13.2
|
0.7
|
CD
|
A:GLU116
|
3.3
|
26.6
|
1.0
|
CG
|
A:ASP13
|
3.3
|
13.7
|
0.3
|
C3'
|
P:DA8
|
3.4
|
17.3
|
0.3
|
OD2
|
A:ASP115
|
3.4
|
15.9
|
1.0
|
CA
|
A:CA502
|
3.5
|
9.9
|
0.5
|
C3'
|
P:DA8
|
3.5
|
17.3
|
0.2
|
MG
|
A:MG503
|
3.5
|
9.8
|
0.5
|
PA
|
A:DTP504
|
3.7
|
15.9
|
0.8
|
OP2
|
P:DA9
|
3.8
|
15.4
|
0.2
|
OD2
|
A:ASP13
|
3.8
|
14.7
|
0.7
|
C4'
|
P:DA8
|
3.9
|
20.4
|
1.0
|
O5'
|
P:DA9
|
4.0
|
13.9
|
0.2
|
CB
|
A:GLU116
|
4.0
|
18.5
|
1.0
|
CG
|
A:GLU116
|
4.0
|
25.8
|
1.0
|
C5'
|
P:DA8
|
4.0
|
18.7
|
0.5
|
C5'
|
P:DA8
|
4.1
|
18.4
|
0.3
|
OE1
|
A:GLU116
|
4.2
|
29.8
|
1.0
|
O5'
|
A:DTP504
|
4.2
|
13.6
|
0.8
|
O1A
|
A:DTP504
|
4.2
|
14.2
|
0.8
|
C5'
|
A:DTP504
|
4.2
|
13.8
|
0.8
|
C5'
|
P:DA9
|
4.2
|
13.7
|
0.2
|
CB
|
A:ASP13
|
4.4
|
12.3
|
0.7
|
C
|
A:ASP115
|
4.5
|
16.0
|
1.0
|
O
|
A:ASP115
|
4.5
|
12.7
|
1.0
|
CB
|
A:ASP13
|
4.6
|
12.2
|
0.3
|
O
|
A:HOH818
|
4.6
|
30.8
|
1.0
|
CB
|
A:ASP115
|
4.6
|
10.4
|
1.0
|
C2'
|
P:DA8
|
4.6
|
18.7
|
0.3
|
C2'
|
P:DA8
|
4.6
|
18.8
|
0.5
|
C2'
|
P:DA8
|
4.6
|
18.6
|
0.2
|
NZ
|
A:LYS224
|
4.6
|
20.5
|
0.6
|
N
|
A:GLU116
|
4.6
|
14.0
|
1.0
|
O5'
|
P:DA8
|
4.8
|
19.6
|
0.3
|
CB
|
A:ALA113
|
4.9
|
15.0
|
1.0
|
CA
|
A:GLU116
|
4.9
|
12.5
|
1.0
|
O5
|
A:DPO505
|
4.9
|
11.3
|
0.2
|
CA
|
A:ASP115
|
5.0
|
14.6
|
1.0
|
O3A
|
A:DTP504
|
5.0
|
13.0
|
0.8
|
O3G
|
A:DTP504
|
5.0
|
10.4
|
0.8
|
|
Magnesium binding site 2 out
of 3 in 7m87
Go back to
Magnesium Binding Sites List in 7m87
Magnesium binding site 2 out
of 3 in the Human Dna Pol Eta S113A with Da-Ended Primer and Datp: in Crystallo Reaction For 230 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 230 S within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg503
b:9.8
occ:0.50
|
CA
|
A:CA502
|
0.0
|
9.9
|
0.5
|
OD1
|
A:ASP13
|
2.2
|
11.6
|
0.3
|
OP1
|
P:DA9
|
2.2
|
13.6
|
0.2
|
OD2
|
A:ASP115
|
2.2
|
15.9
|
1.0
|
OD2
|
A:ASP13
|
2.2
|
14.7
|
0.7
|
O
|
A:MET14
|
2.3
|
10.8
|
1.0
|
O5
|
A:DPO505
|
2.3
|
11.3
|
0.2
|
O1
|
A:DPO505
|
2.3
|
10.9
|
0.2
|
O1B
|
A:DTP504
|
2.3
|
10.5
|
0.8
|
O3G
|
A:DTP504
|
2.3
|
10.4
|
0.8
|
O2A
|
A:DTP504
|
2.3
|
12.3
|
0.8
|
CG
|
A:ASP13
|
2.9
|
13.2
|
0.7
|
OD1
|
A:ASP13
|
3.0
|
22.9
|
0.7
|
CG
|
A:ASP13
|
3.2
|
13.7
|
0.3
|
PB
|
A:DTP504
|
3.3
|
12.7
|
0.8
|
CG
|
A:ASP115
|
3.3
|
14.6
|
1.0
|
P1
|
A:DPO505
|
3.4
|
12.8
|
0.2
|
PA
|
A:DTP504
|
3.4
|
15.9
|
0.8
|
C
|
A:MET14
|
3.4
|
8.9
|
1.0
|
MG
|
A:MG501
|
3.5
|
13.7
|
0.7
|
O3A
|
A:DTP504
|
3.5
|
13.0
|
0.8
|
P2
|
A:DPO505
|
3.5
|
13.3
|
0.2
|
PG
|
A:DTP504
|
3.5
|
13.9
|
0.8
|
OD2
|
A:ASP13
|
3.6
|
14.8
|
0.3
|
P
|
P:DA9
|
3.7
|
14.2
|
0.2
|
O3B
|
A:DTP504
|
3.7
|
13.4
|
0.8
|
O3
|
A:DPO505
|
3.7
|
12.7
|
0.2
|
O4
|
A:DPO505
|
3.7
|
13.5
|
0.2
|
OD1
|
A:ASP115
|
3.7
|
12.4
|
1.0
|
N
|
A:MET14
|
3.9
|
12.0
|
1.0
|
NZ
|
A:LYS231
|
4.0
|
14.3
|
1.0
|
C5'
|
A:DTP504
|
4.0
|
13.8
|
0.8
|
O7
|
A:DPO505
|
4.1
|
12.6
|
0.2
|
O2G
|
A:DTP504
|
4.2
|
12.4
|
0.8
|
O
|
A:HOH818
|
4.2
|
30.8
|
1.0
|
C5'
|
P:DA9
|
4.2
|
13.7
|
0.2
|
CA
|
A:MET14
|
4.2
|
13.1
|
1.0
|
O5'
|
A:DTP504
|
4.2
|
13.6
|
0.8
|
O
|
A:HOH678
|
4.2
|
21.6
|
1.0
|
C
|
A:ASP13
|
4.3
|
10.8
|
1.0
|
O5'
|
P:DA9
|
4.3
|
13.9
|
0.2
|
CB
|
A:ASP13
|
4.3
|
12.3
|
0.7
|
CB
|
A:ASP13
|
4.4
|
12.2
|
0.3
|
N
|
A:ASP15
|
4.5
|
10.1
|
1.0
|
OP2
|
P:DA9
|
4.6
|
15.4
|
0.2
|
N
|
A:CYS16
|
4.6
|
11.4
|
1.0
|
O2B
|
A:DTP504
|
4.6
|
9.5
|
0.8
|
O1A
|
A:DTP504
|
4.6
|
14.2
|
0.8
|
CB
|
A:ASP115
|
4.6
|
10.4
|
1.0
|
CA
|
A:ASP15
|
4.6
|
11.5
|
1.0
|
O3'
|
P:DA8
|
4.7
|
13.9
|
0.2
|
CE
|
A:LYS231
|
4.7
|
24.4
|
1.0
|
CB
|
A:MET14
|
4.7
|
11.5
|
1.0
|
O3'
|
P:DA8
|
4.7
|
13.8
|
0.3
|
O
|
A:ASP13
|
4.7
|
13.0
|
1.0
|
O2
|
A:DPO505
|
4.7
|
9.8
|
0.2
|
CA
|
A:ASP13
|
4.7
|
13.0
|
0.3
|
O6
|
A:DPO505
|
4.7
|
13.3
|
0.2
|
CA
|
A:ASP13
|
4.7
|
13.1
|
0.7
|
O1G
|
A:DTP504
|
4.7
|
13.1
|
0.8
|
N
|
A:PHE17
|
4.8
|
9.6
|
1.0
|
C
|
A:ASP15
|
4.8
|
13.3
|
1.0
|
MG
|
P:MG101
|
4.8
|
15.9
|
0.2
|
CB
|
A:PHE17
|
4.9
|
8.0
|
1.0
|
O
|
A:ASP115
|
4.9
|
12.7
|
1.0
|
|
Magnesium binding site 3 out
of 3 in 7m87
Go back to
Magnesium Binding Sites List in 7m87
Magnesium binding site 3 out
of 3 in the Human Dna Pol Eta S113A with Da-Ended Primer and Datp: in Crystallo Reaction For 230 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 230 S within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
P:Mg101
b:15.9
occ:0.25
|
O1A
|
A:DTP504
|
1.8
|
14.2
|
0.8
|
O3
|
A:DPO505
|
2.0
|
12.7
|
0.2
|
O
|
A:HOH885
|
2.1
|
15.7
|
0.2
|
O
|
A:HOH774
|
2.1
|
32.3
|
1.0
|
O3A
|
A:DTP504
|
2.1
|
13.0
|
0.8
|
OP2
|
P:DA9
|
2.2
|
15.4
|
0.2
|
PA
|
A:DTP504
|
2.4
|
15.9
|
0.8
|
O
|
A:HOH703
|
2.8
|
17.7
|
1.0
|
O
|
A:HOH818
|
2.9
|
30.8
|
1.0
|
NH1
|
A:ARG61
|
3.0
|
25.6
|
0.8
|
O2A
|
A:DTP504
|
3.2
|
12.3
|
0.8
|
P
|
P:DA9
|
3.2
|
14.2
|
0.2
|
P1
|
A:DPO505
|
3.4
|
12.8
|
0.2
|
PB
|
A:DTP504
|
3.5
|
12.7
|
0.8
|
OP1
|
P:DA9
|
3.7
|
13.6
|
0.2
|
O5'
|
A:DTP504
|
3.7
|
13.6
|
0.8
|
NH1
|
A:ARG61
|
3.8
|
22.6
|
0.2
|
O3B
|
A:DTP504
|
3.8
|
13.4
|
0.8
|
NH2
|
A:ARG61
|
3.8
|
14.0
|
0.8
|
O4
|
A:DPO505
|
3.8
|
13.5
|
0.2
|
O5'
|
P:DA9
|
3.8
|
13.9
|
0.2
|
O1G
|
A:DTP504
|
3.8
|
13.1
|
0.8
|
CZ
|
A:ARG61
|
3.8
|
22.4
|
0.8
|
O6
|
A:DPO505
|
3.8
|
13.3
|
0.2
|
O5
|
A:DPO505
|
3.9
|
11.3
|
0.2
|
O
|
A:HOH1022
|
3.9
|
43.8
|
1.0
|
O3G
|
A:DTP504
|
3.9
|
10.4
|
0.8
|
O
|
A:HOH798
|
4.1
|
20.8
|
0.8
|
PG
|
A:DTP504
|
4.1
|
13.9
|
0.8
|
P2
|
A:DPO505
|
4.1
|
13.3
|
0.2
|
O
|
A:HOH678
|
4.1
|
21.6
|
1.0
|
O
|
A:HOH948
|
4.2
|
21.9
|
1.0
|
O2B
|
A:DTP504
|
4.3
|
9.5
|
0.8
|
O1
|
A:DPO505
|
4.3
|
10.9
|
0.2
|
O2
|
A:DPO505
|
4.4
|
9.8
|
0.2
|
O1B
|
A:DTP504
|
4.5
|
10.5
|
0.8
|
O3'
|
P:DA8
|
4.6
|
13.9
|
0.2
|
O3'
|
P:DA8
|
4.7
|
13.8
|
0.3
|
CA
|
A:CA502
|
4.8
|
9.9
|
0.5
|
MG
|
A:MG503
|
4.8
|
9.8
|
0.5
|
CZ
|
A:ARG61
|
4.8
|
25.2
|
0.2
|
C5'
|
A:DTP504
|
4.9
|
13.8
|
0.8
|
C3'
|
P:DA8
|
4.9
|
17.3
|
0.3
|
C8
|
P:DA9
|
4.9
|
17.5
|
0.2
|
C3'
|
P:DA8
|
4.9
|
17.3
|
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
|