Magnesium in PDB 7m7u: Human Dna Pol Eta S113A with Dt-Ended Primer and Datp: in Crystallo Reaction For 480S
Enzymatic activity of Human Dna Pol Eta S113A with Dt-Ended Primer and Datp: in Crystallo Reaction For 480S
All present enzymatic activity of Human Dna Pol Eta S113A with Dt-Ended Primer and Datp: in Crystallo Reaction For 480S:
2.7.7.7;
Protein crystallography data
The structure of Human Dna Pol Eta S113A with Dt-Ended Primer and Datp: in Crystallo Reaction For 480S, PDB code: 7m7u
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)
|
29.47 /
1.94
|
Space group
|
P 61
|
Cell size a, b, c (Å), α, β, γ (°)
|
98.215,
98.215,
81.728,
90,
90,
120
|
R / Rfree (%)
|
17.9 /
22.2
|
Other elements in 7m7u:
The structure of Human Dna Pol Eta S113A with Dt-Ended Primer and Datp: in Crystallo Reaction For 480S also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Human Dna Pol Eta S113A with Dt-Ended Primer and Datp: in Crystallo Reaction For 480S
(pdb code 7m7u). 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 Dt-Ended Primer and Datp: in Crystallo Reaction For 480S, PDB code: 7m7u:
Jump to Magnesium binding site number:
1;
2;
Magnesium binding site 1 out
of 2 in 7m7u
Go back to
Magnesium Binding Sites List in 7m7u
Magnesium binding site 1 out
of 2 in the Human Dna Pol Eta S113A with Dt-Ended Primer and Datp: in Crystallo Reaction For 480S
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 Dt-Ended Primer and Datp: in Crystallo Reaction For 480S within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg502
b:22.8
occ:0.50
|
CA
|
A:CA501
|
0.0
|
23.0
|
0.2
|
O1B
|
A:DTP507
|
2.1
|
21.9
|
0.5
|
O
|
A:MET14
|
2.1
|
20.3
|
1.0
|
OD2
|
A:ASP115
|
2.2
|
21.9
|
0.7
|
O
|
A:HOH865
|
2.2
|
18.4
|
0.5
|
OD1
|
A:ASP13
|
2.2
|
23.3
|
0.7
|
O3G
|
A:DTP507
|
2.3
|
21.0
|
0.5
|
O2A
|
A:DTP507
|
2.7
|
22.1
|
0.5
|
OD1
|
A:ASP13
|
2.8
|
22.2
|
0.3
|
MG
|
A:MG503
|
3.1
|
22.2
|
0.3
|
OD2
|
A:ASP13
|
3.1
|
26.7
|
0.3
|
PB
|
A:DTP507
|
3.1
|
20.4
|
0.5
|
CG
|
A:ASP13
|
3.2
|
22.4
|
0.3
|
PG
|
A:DTP507
|
3.3
|
22.6
|
0.5
|
C
|
A:MET14
|
3.3
|
17.5
|
1.0
|
CG
|
A:ASP13
|
3.3
|
23.9
|
0.7
|
CG
|
A:ASP115
|
3.4
|
21.2
|
0.7
|
O3B
|
A:DTP507
|
3.5
|
21.3
|
0.5
|
O3A
|
A:DTP507
|
3.6
|
21.4
|
0.5
|
O2G
|
A:DTP507
|
3.6
|
21.9
|
0.5
|
PA
|
A:DTP507
|
3.6
|
27.0
|
0.5
|
OD2
|
A:ASP115
|
3.7
|
18.5
|
0.3
|
O
|
A:HOH617
|
3.7
|
21.8
|
1.0
|
N
|
A:MET14
|
3.9
|
13.9
|
1.0
|
OD1
|
A:ASP115
|
4.0
|
23.0
|
0.7
|
C5'
|
A:DTP507
|
4.0
|
23.1
|
0.5
|
OD2
|
A:ASP13
|
4.1
|
33.9
|
0.7
|
CG
|
A:ASP115
|
4.1
|
22.3
|
0.3
|
C
|
A:ASP13
|
4.2
|
19.4
|
0.3
|
CA
|
A:MET14
|
4.2
|
16.4
|
1.0
|
O
|
A:ASP115
|
4.2
|
18.9
|
0.3
|
C
|
A:ASP13
|
4.2
|
19.0
|
0.7
|
N
|
A:CYS16
|
4.2
|
19.8
|
1.0
|
CB
|
A:ASP115
|
4.3
|
19.2
|
0.3
|
N
|
A:ASP15
|
4.3
|
15.2
|
1.0
|
O5'
|
A:DTP507
|
4.3
|
23.4
|
0.5
|
CA
|
A:ASP15
|
4.3
|
17.4
|
1.0
|
CB
|
A:ASP13
|
4.3
|
21.1
|
0.7
|
O
|
A:HOH688
|
4.3
|
27.0
|
0.3
|
CB
|
A:ASP13
|
4.4
|
21.1
|
0.3
|
C
|
A:ASP15
|
4.4
|
18.8
|
1.0
|
O2B
|
A:DTP507
|
4.5
|
19.1
|
0.5
|
CB
|
A:ASP115
|
4.5
|
19.9
|
0.7
|
O
|
A:ASP13
|
4.6
|
18.7
|
0.3
|
CA
|
A:ASP13
|
4.6
|
19.9
|
0.7
|
CA
|
A:ASP13
|
4.6
|
19.9
|
0.3
|
O1G
|
A:DTP507
|
4.6
|
25.0
|
0.5
|
O
|
A:ASP13
|
4.6
|
17.9
|
0.7
|
N
|
A:PHE17
|
4.6
|
14.9
|
1.0
|
CB
|
A:MET14
|
4.7
|
19.1
|
1.0
|
O
|
A:ASP115
|
4.8
|
19.2
|
0.7
|
OD1
|
A:ASP115
|
4.9
|
18.6
|
0.3
|
O1A
|
A:DTP507
|
4.9
|
25.2
|
0.5
|
CA
|
A:CYS16
|
4.9
|
17.7
|
1.0
|
CB
|
A:PHE17
|
5.0
|
14.3
|
1.0
|
|
Magnesium binding site 2 out
of 2 in 7m7u
Go back to
Magnesium Binding Sites List in 7m7u
Magnesium binding site 2 out
of 2 in the Human Dna Pol Eta S113A with Dt-Ended Primer and Datp: in Crystallo Reaction For 480S
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 Dt-Ended Primer and Datp: in Crystallo Reaction For 480S within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg503
b:22.2
occ:0.30
|
OD2
|
A:ASP13
|
2.0
|
26.7
|
0.3
|
O2A
|
A:DTP507
|
2.2
|
22.1
|
0.5
|
O
|
A:HOH688
|
2.3
|
27.0
|
0.3
|
OD1
|
A:ASP115
|
2.3
|
23.0
|
0.7
|
OD1
|
A:ASP13
|
2.4
|
23.3
|
0.7
|
OD2
|
A:ASP115
|
2.8
|
21.9
|
0.7
|
O3'
|
P:DT8
|
2.8
|
24.7
|
0.5
|
CG
|
A:ASP115
|
2.9
|
21.2
|
0.7
|
OD1
|
A:ASP115
|
2.9
|
18.6
|
0.3
|
CG
|
A:ASP13
|
3.0
|
23.9
|
0.7
|
OE2
|
A:GLU116
|
3.0
|
38.1
|
1.0
|
CG
|
A:ASP115
|
3.0
|
22.3
|
0.3
|
OD2
|
A:ASP13
|
3.1
|
33.9
|
0.7
|
CA
|
A:CA501
|
3.1
|
23.0
|
0.2
|
MG
|
A:MG502
|
3.1
|
22.8
|
0.5
|
CG
|
A:ASP13
|
3.2
|
22.4
|
0.3
|
O
|
A:ASP115
|
3.2
|
18.9
|
0.3
|
OD2
|
A:ASP115
|
3.2
|
18.5
|
0.3
|
PA
|
A:DTP507
|
3.6
|
27.0
|
0.5
|
C3'
|
P:DT8
|
3.6
|
26.1
|
0.5
|
OD1
|
A:ASP13
|
3.8
|
22.2
|
0.3
|
CB
|
A:GLU116
|
3.8
|
22.0
|
1.0
|
C
|
A:ASP115
|
3.9
|
19.8
|
0.3
|
CB
|
A:ASP115
|
3.9
|
19.2
|
0.3
|
CD
|
A:GLU116
|
4.0
|
28.6
|
1.0
|
O5'
|
A:DTP507
|
4.0
|
23.4
|
0.5
|
C5'
|
A:DTP507
|
4.1
|
23.1
|
0.5
|
CG
|
A:GLU116
|
4.2
|
25.3
|
1.0
|
O
|
A:ASP115
|
4.2
|
19.2
|
0.7
|
O3G
|
A:DTP507
|
4.2
|
21.0
|
0.5
|
O
|
A:HOH865
|
4.3
|
18.4
|
0.5
|
CB
|
A:ASP115
|
4.3
|
19.9
|
0.7
|
C
|
A:ASP115
|
4.3
|
22.0
|
0.7
|
CB
|
A:ASP13
|
4.3
|
21.1
|
0.3
|
O1A
|
A:DTP507
|
4.3
|
25.2
|
0.5
|
CB
|
A:ASP13
|
4.4
|
21.1
|
0.7
|
O1B
|
A:DTP507
|
4.5
|
21.9
|
0.5
|
CA
|
A:ASP115
|
4.5
|
18.7
|
0.3
|
C4'
|
P:DT8
|
4.6
|
27.3
|
0.5
|
N
|
A:GLU116
|
4.6
|
18.4
|
1.0
|
CA
|
A:GLU116
|
4.6
|
19.1
|
1.0
|
O3A
|
A:DTP507
|
4.6
|
21.4
|
0.5
|
CA
|
A:ASP13
|
4.7
|
19.9
|
0.3
|
CA
|
A:ASP13
|
4.7
|
19.9
|
0.7
|
CA
|
A:ASP115
|
4.8
|
18.5
|
0.7
|
C2'
|
P:DT8
|
4.8
|
26.7
|
0.5
|
O
|
A:MET14
|
4.9
|
20.3
|
1.0
|
NZ
|
A:LYS224
|
4.9
|
26.6
|
0.7
|
C4'
|
P:DT8
|
5.0
|
27.4
|
0.5
|
O3'
|
P:DT8
|
5.0
|
25.8
|
0.5
|
|
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 00:20:58 2024
|