Magnesium in PDB 7m8a: Human Dna Pol Eta S113A with Ra-Ended Primer and Datp: in Crystallo Reaction For 40 S
Enzymatic activity of Human Dna Pol Eta S113A with Ra-Ended Primer and Datp: in Crystallo Reaction For 40 S
All present enzymatic activity of Human Dna Pol Eta S113A with Ra-Ended Primer and Datp: in Crystallo Reaction For 40 S:
2.7.7.7;
Protein crystallography data
The structure of Human Dna Pol Eta S113A with Ra-Ended Primer and Datp: in Crystallo Reaction For 40 S, PDB code: 7m8a
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)
|
29.98 /
1.91
|
Space group
|
P 61
|
Cell size a, b, c (Å), α, β, γ (°)
|
98.393,
98.393,
82.025,
90,
90,
120
|
R / Rfree (%)
|
16.6 /
21.5
|
Other elements in 7m8a:
The structure of Human Dna Pol Eta S113A with Ra-Ended Primer and Datp: in Crystallo Reaction For 40 S also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Human Dna Pol Eta S113A with Ra-Ended Primer and Datp: in Crystallo Reaction For 40 S
(pdb code 7m8a). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the
Human Dna Pol Eta S113A with Ra-Ended Primer and Datp: in Crystallo Reaction For 40 S, PDB code: 7m8a:
Jump to Magnesium binding site number:
1;
2;
Magnesium binding site 1 out
of 2 in 7m8a
Go back to
Magnesium Binding Sites List in 7m8a
Magnesium binding site 1 out
of 2 in the Human Dna Pol Eta S113A with Ra-Ended Primer and Datp: in Crystallo Reaction For 40 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 Ra-Ended Primer and Datp: in Crystallo Reaction For 40 S within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg502
b:24.4
occ:0.55
|
CA
|
A:CA501
|
0.1
|
24.3
|
0.3
|
O5
|
A:DPO507
|
2.0
|
21.1
|
0.4
|
O1B
|
A:DTP506
|
2.1
|
18.6
|
0.4
|
O1
|
A:DPO507
|
2.2
|
18.7
|
0.4
|
O3G
|
A:DTP506
|
2.2
|
22.6
|
0.4
|
OD1
|
A:ASP13
|
2.2
|
22.6
|
0.7
|
OD2
|
A:ASP115
|
2.2
|
32.3
|
1.0
|
O
|
A:MET14
|
2.4
|
20.9
|
1.0
|
OD2
|
A:ASP13
|
2.4
|
23.3
|
0.3
|
OP1
|
P:DA9
|
2.5
|
23.0
|
0.5
|
O2A
|
A:DTP506
|
2.5
|
23.0
|
0.4
|
OD1
|
A:ASP13
|
2.8
|
28.2
|
0.3
|
CG
|
A:ASP13
|
2.9
|
23.8
|
0.3
|
MG
|
A:MG508
|
3.0
|
26.5
|
0.3
|
PB
|
A:DTP506
|
3.1
|
25.3
|
0.4
|
P2
|
A:DPO507
|
3.2
|
26.0
|
0.4
|
P1
|
A:DPO507
|
3.3
|
24.8
|
0.4
|
PG
|
A:DTP506
|
3.3
|
27.8
|
0.4
|
CG
|
A:ASP13
|
3.3
|
26.5
|
0.7
|
CG
|
A:ASP115
|
3.4
|
31.3
|
1.0
|
O4
|
A:DPO507
|
3.5
|
22.2
|
0.4
|
O3B
|
A:DTP506
|
3.5
|
21.8
|
0.4
|
O3A
|
A:DTP506
|
3.5
|
24.5
|
0.4
|
PA
|
A:DTP506
|
3.6
|
25.7
|
0.4
|
C
|
A:MET14
|
3.6
|
16.0
|
1.0
|
O2G
|
A:DTP506
|
3.8
|
18.8
|
0.4
|
P
|
P:DA9
|
3.9
|
24.6
|
0.5
|
O
|
A:HOH604
|
3.9
|
23.8
|
1.0
|
O6
|
A:DPO507
|
3.9
|
20.4
|
0.4
|
OD2
|
A:ASP13
|
3.9
|
37.4
|
0.7
|
O2
|
A:DPO507
|
3.9
|
27.0
|
0.4
|
C5'
|
A:DTP506
|
4.0
|
24.8
|
0.4
|
OD1
|
A:ASP115
|
4.1
|
26.1
|
1.0
|
O
|
A:HOH733
|
4.1
|
38.4
|
1.0
|
N
|
A:MET14
|
4.2
|
15.8
|
1.0
|
C5'
|
P:DA9
|
4.2
|
24.5
|
0.5
|
O5'
|
A:DTP506
|
4.3
|
25.0
|
0.4
|
O5'
|
P:DA9
|
4.3
|
25.1
|
0.5
|
CB
|
A:ASP13
|
4.3
|
20.1
|
0.3
|
N
|
A:CYS16
|
4.3
|
15.7
|
1.0
|
C
|
A:ASP13
|
4.4
|
16.8
|
0.7
|
C
|
A:ASP13
|
4.4
|
16.9
|
0.3
|
CA
|
A:MET14
|
4.4
|
13.1
|
1.0
|
O2B
|
A:DTP506
|
4.4
|
19.0
|
0.4
|
O7
|
A:DPO507
|
4.5
|
25.1
|
0.4
|
CB
|
A:ASP115
|
4.5
|
16.2
|
1.0
|
CB
|
A:ASP13
|
4.5
|
19.5
|
0.7
|
N
|
A:ASP15
|
4.5
|
14.1
|
1.0
|
NZ
|
A:LYS231
|
4.5
|
41.8
|
1.0
|
O3
|
A:DPO507
|
4.5
|
20.4
|
0.4
|
CA
|
A:ASP15
|
4.6
|
13.8
|
1.0
|
O1G
|
A:DTP506
|
4.6
|
24.7
|
0.4
|
O3'
|
P:A8
|
4.6
|
29.9
|
0.5
|
C
|
A:ASP15
|
4.7
|
18.8
|
1.0
|
O3'
|
P:A8
|
4.7
|
29.9
|
0.6
|
N
|
A:PHE17
|
4.7
|
12.7
|
1.0
|
O
|
A:ASP13
|
4.8
|
15.6
|
0.7
|
CA
|
A:ASP13
|
4.8
|
19.8
|
0.7
|
O1A
|
A:DTP506
|
4.8
|
27.2
|
0.4
|
CA
|
A:ASP13
|
4.8
|
19.6
|
0.3
|
O
|
A:ASP13
|
4.8
|
15.7
|
0.3
|
O
|
A:ASP115
|
4.9
|
18.2
|
1.0
|
CB
|
A:MET14
|
4.9
|
18.4
|
1.0
|
OP2
|
P:DA9
|
5.0
|
27.3
|
0.5
|
CA
|
A:CYS16
|
5.0
|
20.4
|
1.0
|
|
Magnesium binding site 2 out
of 2 in 7m8a
Go back to
Magnesium Binding Sites List in 7m8a
Magnesium binding site 2 out
of 2 in the Human Dna Pol Eta S113A with Ra-Ended Primer and Datp: in Crystallo Reaction For 40 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 Ra-Ended Primer and Datp: in Crystallo Reaction For 40 S within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg508
b:26.5
occ:0.30
|
OD1
|
A:ASP13
|
2.1
|
28.2
|
0.3
|
O2A
|
A:DTP506
|
2.1
|
23.0
|
0.4
|
OP1
|
P:DA9
|
2.1
|
23.0
|
0.5
|
O3'
|
P:A8
|
2.3
|
29.9
|
0.6
|
O
|
A:HOH733
|
2.3
|
38.4
|
1.0
|
OD1
|
A:ASP115
|
2.5
|
26.1
|
1.0
|
O3'
|
P:A8
|
2.5
|
29.9
|
0.5
|
OD2
|
A:ASP115
|
2.7
|
32.3
|
1.0
|
OE2
|
A:GLU116
|
2.7
|
39.3
|
0.5
|
OE2
|
A:GLU116
|
2.7
|
39.3
|
0.5
|
OD1
|
A:ASP13
|
2.8
|
22.6
|
0.7
|
P
|
P:DA9
|
2.9
|
24.6
|
0.5
|
CG
|
A:ASP115
|
2.9
|
31.3
|
1.0
|
CA
|
A:CA501
|
3.0
|
24.3
|
0.3
|
MG
|
A:MG502
|
3.0
|
24.4
|
0.6
|
OD2
|
A:ASP13
|
3.1
|
37.4
|
0.7
|
CG
|
A:ASP13
|
3.2
|
23.8
|
0.3
|
CG
|
A:ASP13
|
3.3
|
26.5
|
0.7
|
PA
|
A:DTP506
|
3.4
|
25.7
|
0.4
|
CD
|
A:GLU116
|
3.6
|
34.7
|
0.5
|
CD
|
A:GLU116
|
3.6
|
34.6
|
0.5
|
C3'
|
P:A8
|
3.7
|
32.2
|
0.6
|
C3'
|
P:A8
|
3.8
|
32.2
|
0.5
|
CG
|
A:GLU116
|
3.8
|
30.9
|
0.5
|
CG
|
A:GLU116
|
3.8
|
30.9
|
0.5
|
OD2
|
A:ASP13
|
3.8
|
23.3
|
0.3
|
O5'
|
P:DA9
|
3.9
|
25.1
|
0.5
|
C5'
|
P:DA9
|
4.0
|
24.5
|
0.5
|
C5'
|
A:DTP506
|
4.0
|
24.8
|
0.4
|
O5'
|
A:DTP506
|
4.0
|
25.0
|
0.4
|
OP2
|
P:DA9
|
4.0
|
27.3
|
0.5
|
O1A
|
A:DTP506
|
4.0
|
27.2
|
0.4
|
C4'
|
P:A8
|
4.1
|
33.4
|
0.5
|
O5
|
A:DPO507
|
4.1
|
21.1
|
0.4
|
O3G
|
A:DTP506
|
4.2
|
22.6
|
0.4
|
C4'
|
P:A8
|
4.2
|
33.7
|
0.6
|
CB
|
A:GLU116
|
4.2
|
29.1
|
1.0
|
O1
|
A:DPO507
|
4.3
|
18.7
|
0.4
|
C5'
|
P:A8
|
4.4
|
33.1
|
0.5
|
CB
|
A:ASP115
|
4.4
|
16.2
|
1.0
|
CB
|
A:ASP13
|
4.4
|
20.1
|
0.3
|
O1B
|
A:DTP506
|
4.4
|
18.6
|
0.4
|
O3A
|
A:DTP506
|
4.5
|
24.5
|
0.4
|
O
|
A:ASP115
|
4.5
|
18.2
|
1.0
|
C5'
|
P:A8
|
4.5
|
32.9
|
0.6
|
O2'
|
P:A8
|
4.6
|
35.1
|
0.6
|
O2'
|
P:A8
|
4.6
|
34.9
|
0.5
|
C
|
A:ASP115
|
4.6
|
22.1
|
1.0
|
CB
|
A:ASP13
|
4.7
|
19.5
|
0.7
|
C2'
|
P:A8
|
4.7
|
32.3
|
0.6
|
C2'
|
P:A8
|
4.8
|
32.0
|
0.5
|
OE1
|
A:GLU116
|
4.8
|
34.9
|
0.5
|
OE1
|
A:GLU116
|
4.8
|
34.9
|
0.5
|
O
|
A:HOH605
|
4.8
|
40.4
|
1.0
|
N
|
A:GLU116
|
4.9
|
18.9
|
1.0
|
|
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 00:24:04 2024
|