Magnesium in PDB 7m7p: Human Dna Pol Eta S113A with Da-Ended Primer and Dampnpp
Enzymatic activity of Human Dna Pol Eta S113A with Da-Ended Primer and Dampnpp
All present enzymatic activity of Human Dna Pol Eta S113A with Da-Ended Primer and Dampnpp:
2.7.7.7;
Protein crystallography data
The structure of Human Dna Pol Eta S113A with Da-Ended Primer and Dampnpp, PDB code: 7m7p
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)
|
31.51 /
1.80
|
Space group
|
P 61
|
Cell size a, b, c (Å), α, β, γ (°)
|
98.771,
98.771,
81.841,
90,
90,
120
|
R / Rfree (%)
|
20 /
24.3
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Human Dna Pol Eta S113A with Da-Ended Primer and Dampnpp
(pdb code 7m7p). 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 Da-Ended Primer and Dampnpp, PDB code: 7m7p:
Jump to Magnesium binding site number:
1;
2;
Magnesium binding site 1 out
of 2 in 7m7p
Go back to
Magnesium Binding Sites List in 7m7p
Magnesium binding site 1 out
of 2 in the Human Dna Pol Eta S113A with Da-Ended Primer and Dampnpp
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 Dampnpp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg502
b:8.1
occ:1.00
|
OD1
|
A:ASP115
|
2.0
|
6.5
|
1.0
|
OD1
|
A:ASP13
|
2.1
|
10.2
|
1.0
|
O1G
|
A:DZ4501
|
2.2
|
5.8
|
1.0
|
O1B
|
A:DZ4501
|
2.2
|
6.4
|
1.0
|
O
|
A:MET14
|
2.2
|
6.9
|
1.0
|
O1A
|
A:DZ4501
|
2.3
|
7.0
|
1.0
|
CG
|
A:ASP13
|
3.0
|
6.4
|
1.0
|
PB
|
A:DZ4501
|
3.1
|
7.2
|
1.0
|
CG
|
A:ASP115
|
3.2
|
4.8
|
1.0
|
PA
|
A:DZ4501
|
3.3
|
8.1
|
1.0
|
OD2
|
A:ASP13
|
3.4
|
13.6
|
1.0
|
PG
|
A:DZ4501
|
3.4
|
7.5
|
1.0
|
C
|
A:MET14
|
3.4
|
5.3
|
1.0
|
N3A
|
A:DZ4501
|
3.4
|
7.3
|
1.0
|
MG
|
A:MG503
|
3.5
|
9.3
|
1.0
|
O3B
|
A:DZ4501
|
3.6
|
6.6
|
1.0
|
OD2
|
A:ASP115
|
3.6
|
8.2
|
1.0
|
NZ
|
A:LYS231
|
3.8
|
8.4
|
1.0
|
N
|
A:MET14
|
3.9
|
4.6
|
1.0
|
O
|
A:HOH774
|
4.0
|
12.1
|
1.0
|
C5'
|
A:DZ4501
|
4.0
|
9.0
|
1.0
|
O2G
|
A:DZ4501
|
4.0
|
4.2
|
1.0
|
CA
|
A:MET14
|
4.2
|
7.8
|
1.0
|
O5'
|
A:DZ4501
|
4.2
|
8.2
|
1.0
|
O
|
A:HOH738
|
4.2
|
10.0
|
1.0
|
C
|
A:ASP13
|
4.3
|
6.5
|
1.0
|
CB
|
A:ASP13
|
4.3
|
7.9
|
1.0
|
CB
|
A:ASP115
|
4.4
|
5.6
|
1.0
|
N
|
A:ASP15
|
4.5
|
5.6
|
1.0
|
O2A
|
A:DZ4501
|
4.5
|
7.4
|
1.0
|
O2B
|
A:DZ4501
|
4.5
|
6.0
|
1.0
|
O3G
|
A:DZ4501
|
4.5
|
8.5
|
1.0
|
CE
|
A:LYS231
|
4.6
|
15.5
|
1.0
|
CB
|
A:MET14
|
4.6
|
7.9
|
1.0
|
N
|
A:CYS16
|
4.6
|
5.6
|
1.0
|
CA
|
A:ASP15
|
4.6
|
5.6
|
1.0
|
O
|
A:ASP13
|
4.7
|
5.7
|
1.0
|
CA
|
A:ASP13
|
4.7
|
6.1
|
1.0
|
N
|
A:PHE17
|
4.8
|
4.3
|
1.0
|
CB
|
A:PHE17
|
4.8
|
6.1
|
1.0
|
C
|
A:ASP15
|
4.8
|
6.7
|
1.0
|
O
|
A:ASP115
|
4.9
|
8.2
|
1.0
|
|
Magnesium binding site 2 out
of 2 in 7m7p
Go back to
Magnesium Binding Sites List in 7m7p
Magnesium binding site 2 out
of 2 in the Human Dna Pol Eta S113A with Da-Ended Primer and Dampnpp
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 Dampnpp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg503
b:9.3
occ:1.00
|
OD2
|
A:ASP13
|
2.1
|
13.6
|
1.0
|
OD2
|
A:ASP115
|
2.2
|
8.2
|
1.0
|
O
|
A:HOH738
|
2.2
|
10.0
|
1.0
|
O1A
|
A:DZ4501
|
2.2
|
7.0
|
1.0
|
OE2
|
A:GLU116
|
2.2
|
12.1
|
1.0
|
O3'
|
P:DA9
|
2.3
|
8.7
|
1.0
|
CG
|
A:ASP115
|
3.1
|
4.8
|
1.0
|
CG
|
A:ASP13
|
3.1
|
6.4
|
1.0
|
C3'
|
P:DA9
|
3.2
|
10.6
|
1.0
|
OD1
|
A:ASP115
|
3.3
|
6.5
|
1.0
|
CD
|
A:GLU116
|
3.3
|
15.8
|
1.0
|
PA
|
A:DZ4501
|
3.4
|
8.1
|
1.0
|
MG
|
A:MG502
|
3.5
|
8.1
|
1.0
|
OD1
|
A:ASP13
|
3.5
|
10.2
|
1.0
|
O2A
|
A:DZ4501
|
3.7
|
7.4
|
1.0
|
O5'
|
A:DZ4501
|
3.9
|
8.2
|
1.0
|
C4'
|
P:DA9
|
4.1
|
11.1
|
1.0
|
O
|
A:HOH685
|
4.1
|
20.0
|
1.0
|
OE1
|
A:GLU116
|
4.1
|
20.0
|
1.0
|
CB
|
A:GLU116
|
4.1
|
11.2
|
1.0
|
CG
|
A:GLU116
|
4.2
|
12.9
|
1.0
|
C5'
|
A:DZ4501
|
4.2
|
9.0
|
1.0
|
O
|
A:HOH774
|
4.2
|
12.1
|
1.0
|
O
|
P:HOH112
|
4.4
|
8.4
|
1.0
|
CB
|
A:ASP13
|
4.4
|
7.9
|
1.0
|
C2'
|
P:DA9
|
4.4
|
14.2
|
1.0
|
CB
|
A:ASP115
|
4.6
|
5.6
|
1.0
|
C
|
A:ASP115
|
4.6
|
8.6
|
1.0
|
O
|
A:ASP115
|
4.6
|
8.2
|
1.0
|
O1G
|
A:DZ4501
|
4.7
|
5.8
|
1.0
|
N3A
|
A:DZ4501
|
4.8
|
7.3
|
1.0
|
C5'
|
P:DA9
|
4.8
|
14.7
|
1.0
|
N
|
A:GLU116
|
4.8
|
7.0
|
1.0
|
O1B
|
A:DZ4501
|
4.9
|
6.4
|
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: Mon Jul 12 14:24:48 2021
|