Magnesium in PDB 7m81: Human Dna Pol Eta with Da-Ended Primer and Datp: in Crystallo Reaction For 100 S
Enzymatic activity of Human Dna Pol Eta with Da-Ended Primer and Datp: in Crystallo Reaction For 100 S
All present enzymatic activity of Human Dna Pol Eta with Da-Ended Primer and Datp: in Crystallo Reaction For 100 S:
2.7.7.7;
Protein crystallography data
The structure of Human Dna Pol Eta with Da-Ended Primer and Datp: in Crystallo Reaction For 100 S, PDB code: 7m81
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)
|
30.16 /
2.05
|
Space group
|
P 61
|
Cell size a, b, c (Å), α, β, γ (°)
|
99.147,
99.147,
81.761,
90,
90,
120
|
R / Rfree (%)
|
17.1 /
22.6
|
Other elements in 7m81:
The structure of Human Dna Pol Eta with Da-Ended Primer and Datp: in Crystallo Reaction For 100 S also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Human Dna Pol Eta with Da-Ended Primer and Datp: in Crystallo Reaction For 100 S
(pdb code 7m81). 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 with Da-Ended Primer and Datp: in Crystallo Reaction For 100 S, PDB code: 7m81:
Jump to Magnesium binding site number:
1;
2;
3;
Magnesium binding site 1 out
of 3 in 7m81
Go back to
Magnesium Binding Sites List in 7m81
Magnesium binding site 1 out
of 3 in the Human Dna Pol Eta with Da-Ended Primer and Datp: in Crystallo Reaction For 100 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 with Da-Ended Primer and Datp: in Crystallo Reaction For 100 S within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg501
b:36.9
occ:0.40
|
OP1
|
P:DA9
|
1.9
|
34.2
|
0.6
|
OD1
|
A:ASP13
|
1.9
|
34.1
|
0.5
|
O2A
|
A:DTP506
|
1.9
|
34.1
|
0.5
|
O
|
A:HOH736
|
2.0
|
38.5
|
1.0
|
OE2
|
A:GLU116
|
2.2
|
55.5
|
1.0
|
OD2
|
A:ASP13
|
2.6
|
43.2
|
0.6
|
P
|
P:DA9
|
2.7
|
36.0
|
0.6
|
OD1
|
A:ASP13
|
2.7
|
30.4
|
0.6
|
O3'
|
P:DA8
|
2.7
|
23.4
|
0.6
|
CG
|
A:ASP13
|
2.9
|
30.0
|
0.5
|
OD1
|
A:ASP115
|
2.9
|
37.2
|
1.0
|
CG
|
A:ASP13
|
2.9
|
31.6
|
0.6
|
MG
|
A:MG503
|
3.2
|
23.5
|
0.7
|
CA
|
A:CA502
|
3.2
|
23.7
|
0.3
|
PA
|
A:DTP506
|
3.3
|
37.8
|
0.5
|
OD2
|
A:ASP13
|
3.4
|
22.6
|
0.5
|
CD
|
A:GLU116
|
3.4
|
67.4
|
1.0
|
O3'
|
P:DA8
|
3.4
|
39.6
|
0.5
|
O
|
A:HOH704
|
3.5
|
41.2
|
1.0
|
OP2
|
P:DA9
|
3.5
|
32.1
|
0.6
|
OD2
|
A:ASP115
|
3.6
|
32.3
|
1.0
|
CG
|
A:ASP115
|
3.6
|
38.4
|
1.0
|
C3'
|
P:DA8
|
3.8
|
39.3
|
0.5
|
O1A
|
A:DTP506
|
3.8
|
30.5
|
0.5
|
C3'
|
P:DA8
|
4.0
|
41.5
|
0.6
|
O5'
|
P:DA9
|
4.1
|
35.1
|
0.6
|
OE1
|
A:GLU116
|
4.1
|
69.7
|
1.0
|
CB
|
A:ASP13
|
4.1
|
26.5
|
0.5
|
O5'
|
A:DTP506
|
4.2
|
34.5
|
0.5
|
O5
|
A:DPO507
|
4.2
|
24.4
|
0.6
|
CB
|
A:GLU116
|
4.3
|
28.5
|
1.0
|
O3G
|
A:DTP506
|
4.3
|
24.5
|
0.5
|
CB
|
A:ASP13
|
4.3
|
25.9
|
0.6
|
NZ
|
A:LYS224
|
4.3
|
26.8
|
0.6
|
CG
|
A:GLU116
|
4.3
|
50.7
|
1.0
|
O3A
|
A:DTP506
|
4.3
|
26.4
|
0.5
|
C5'
|
P:DA8
|
4.3
|
40.0
|
0.5
|
C4'
|
P:DA8
|
4.4
|
37.7
|
0.5
|
C4'
|
P:DA8
|
4.4
|
37.8
|
0.6
|
C5'
|
P:DA9
|
4.4
|
30.4
|
0.6
|
C5'
|
A:DTP506
|
4.5
|
30.1
|
0.5
|
OG
|
A:SER113
|
4.6
|
41.7
|
1.0
|
C5'
|
P:DA8
|
4.6
|
40.2
|
0.6
|
O1
|
A:DPO507
|
4.6
|
23.9
|
0.6
|
O2
|
A:DPO507
|
4.7
|
26.6
|
0.6
|
O1B
|
A:DTP506
|
4.8
|
23.2
|
0.5
|
O
|
A:ASP115
|
4.9
|
27.0
|
1.0
|
|
Magnesium binding site 2 out
of 3 in 7m81
Go back to
Magnesium Binding Sites List in 7m81
Magnesium binding site 2 out
of 3 in the Human Dna Pol Eta with Da-Ended Primer and Datp: in Crystallo Reaction For 100 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 with Da-Ended Primer and Datp: in Crystallo Reaction For 100 S within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg503
b:23.5
occ:0.70
|
CA
|
A:CA502
|
0.0
|
23.7
|
0.3
|
O5
|
A:DPO507
|
2.1
|
24.4
|
0.6
|
O1
|
A:DPO507
|
2.1
|
23.9
|
0.6
|
O3G
|
A:DTP506
|
2.2
|
24.5
|
0.5
|
O1B
|
A:DTP506
|
2.2
|
23.2
|
0.5
|
OD1
|
A:ASP13
|
2.3
|
30.4
|
0.6
|
OD2
|
A:ASP13
|
2.3
|
22.6
|
0.5
|
O
|
A:MET14
|
2.3
|
22.9
|
1.0
|
OD2
|
A:ASP115
|
2.4
|
32.3
|
1.0
|
OP1
|
P:DA9
|
2.4
|
34.2
|
0.6
|
O2A
|
A:DTP506
|
2.5
|
34.1
|
0.5
|
CG
|
A:ASP13
|
2.9
|
30.0
|
0.5
|
OD1
|
A:ASP13
|
3.0
|
34.1
|
0.5
|
PB
|
A:DTP506
|
3.0
|
28.6
|
0.5
|
P1
|
A:DPO507
|
3.2
|
28.3
|
0.6
|
CG
|
A:ASP13
|
3.2
|
31.6
|
0.6
|
MG
|
A:MG501
|
3.2
|
36.9
|
0.4
|
O3A
|
A:DTP506
|
3.3
|
26.4
|
0.5
|
P2
|
A:DPO507
|
3.3
|
30.8
|
0.6
|
PG
|
A:DTP506
|
3.3
|
30.6
|
0.5
|
PA
|
A:DTP506
|
3.4
|
37.8
|
0.5
|
CG
|
A:ASP115
|
3.4
|
38.4
|
1.0
|
O3B
|
A:DTP506
|
3.4
|
28.2
|
0.5
|
O2
|
A:DPO507
|
3.4
|
26.6
|
0.6
|
O4
|
A:DPO507
|
3.4
|
28.0
|
0.6
|
OD2
|
A:ASP13
|
3.5
|
43.2
|
0.6
|
C
|
A:MET14
|
3.5
|
21.3
|
1.0
|
O
|
A:HOH704
|
3.7
|
41.2
|
1.0
|
P
|
P:DA9
|
3.8
|
36.0
|
0.6
|
OD1
|
A:ASP115
|
3.8
|
37.2
|
1.0
|
O2G
|
A:DTP506
|
4.0
|
26.2
|
0.5
|
O7
|
A:DPO507
|
4.0
|
26.1
|
0.6
|
C5'
|
A:DTP506
|
4.1
|
30.1
|
0.5
|
N
|
A:MET14
|
4.2
|
14.7
|
1.0
|
NZ
|
A:LYS231
|
4.2
|
35.7
|
1.0
|
C5'
|
P:DA9
|
4.2
|
30.4
|
0.6
|
O5'
|
A:DTP506
|
4.3
|
34.5
|
0.5
|
CB
|
A:ASP13
|
4.4
|
26.5
|
0.5
|
O
|
A:HOH736
|
4.4
|
38.5
|
1.0
|
N
|
A:CYS16
|
4.4
|
22.2
|
1.0
|
O6
|
A:DPO507
|
4.4
|
28.8
|
0.6
|
O5'
|
P:DA9
|
4.4
|
35.1
|
0.6
|
O2B
|
A:DTP506
|
4.4
|
27.8
|
0.5
|
CA
|
A:MET14
|
4.4
|
22.6
|
1.0
|
C
|
A:ASP13
|
4.4
|
21.3
|
0.6
|
C
|
A:ASP13
|
4.5
|
21.4
|
0.5
|
N
|
A:ASP15
|
4.5
|
21.7
|
1.0
|
CB
|
A:ASP13
|
4.5
|
25.9
|
0.6
|
O3
|
A:DPO507
|
4.5
|
27.9
|
0.6
|
CA
|
A:ASP15
|
4.5
|
28.6
|
1.0
|
OP2
|
P:DA9
|
4.5
|
32.1
|
0.6
|
O1G
|
A:DTP506
|
4.6
|
29.1
|
0.5
|
O1A
|
A:DTP506
|
4.6
|
30.5
|
0.5
|
C
|
A:ASP15
|
4.7
|
30.0
|
1.0
|
CB
|
A:ASP115
|
4.7
|
22.7
|
1.0
|
N
|
A:PHE17
|
4.8
|
19.6
|
1.0
|
O
|
A:ASP13
|
4.9
|
24.2
|
0.6
|
CA
|
A:ASP13
|
4.9
|
21.1
|
0.6
|
O3'
|
P:DA8
|
4.9
|
23.4
|
0.6
|
CA
|
A:ASP13
|
4.9
|
21.1
|
0.5
|
CB
|
A:MET14
|
4.9
|
27.7
|
1.0
|
O
|
A:ASP13
|
4.9
|
24.2
|
0.5
|
CE
|
A:LYS231
|
5.0
|
49.8
|
1.0
|
|
Magnesium binding site 3 out
of 3 in 7m81
Go back to
Magnesium Binding Sites List in 7m81
Magnesium binding site 3 out
of 3 in the Human Dna Pol Eta with Da-Ended Primer and Datp: in Crystallo Reaction For 100 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 with Da-Ended Primer and Datp: in Crystallo Reaction For 100 S within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
P:Mg101
b:39.2
occ:0.55
|
NH1
|
A:ARG61
|
2.2
|
23.4
|
0.5
|
O2
|
A:DPO507
|
2.2
|
26.6
|
0.6
|
O
|
A:HOH649
|
2.2
|
36.5
|
1.0
|
O
|
A:HOH696
|
2.3
|
40.9
|
1.0
|
O3A
|
A:DTP506
|
2.4
|
26.4
|
0.5
|
O1A
|
A:DTP506
|
2.4
|
30.5
|
0.5
|
OP2
|
P:DA9
|
2.6
|
32.1
|
0.6
|
O
|
A:HOH704
|
2.9
|
41.2
|
1.0
|
PA
|
A:DTP506
|
3.0
|
37.8
|
0.5
|
CZ
|
A:ARG61
|
3.2
|
26.5
|
0.5
|
NH2
|
A:ARG61
|
3.4
|
17.0
|
0.5
|
P1
|
A:DPO507
|
3.6
|
28.3
|
0.6
|
PB
|
A:DTP506
|
3.6
|
28.6
|
0.5
|
O
|
A:HOH833
|
3.7
|
40.1
|
1.0
|
O
|
A:HOH881
|
3.7
|
43.2
|
1.0
|
P
|
P:DA9
|
3.8
|
36.0
|
0.6
|
O3B
|
A:DTP506
|
3.8
|
28.2
|
0.5
|
O6
|
A:DPO507
|
3.8
|
28.8
|
0.6
|
NH1
|
A:ARG61
|
3.9
|
26.7
|
0.6
|
NE
|
A:ARG61
|
3.9
|
40.3
|
0.6
|
O4
|
A:DPO507
|
3.9
|
28.0
|
0.6
|
O2A
|
A:DTP506
|
4.0
|
34.1
|
0.5
|
O1G
|
A:DTP506
|
4.0
|
29.1
|
0.5
|
O5'
|
A:DTP506
|
4.1
|
34.5
|
0.5
|
O2B
|
A:DTP506
|
4.2
|
27.8
|
0.5
|
OP1
|
P:DA9
|
4.2
|
34.2
|
0.6
|
CZ
|
A:ARG61
|
4.2
|
36.0
|
0.6
|
O3
|
A:DPO507
|
4.3
|
27.9
|
0.6
|
O5'
|
P:DA9
|
4.3
|
35.1
|
0.6
|
PG
|
A:DTP506
|
4.3
|
30.6
|
0.5
|
O3G
|
A:DTP506
|
4.3
|
24.5
|
0.5
|
O
|
P:HOH207
|
4.3
|
43.6
|
1.0
|
P2
|
A:DPO507
|
4.4
|
30.8
|
0.6
|
O5
|
A:DPO507
|
4.4
|
24.4
|
0.6
|
NE
|
A:ARG61
|
4.4
|
32.4
|
0.5
|
O1
|
A:DPO507
|
4.6
|
23.9
|
0.6
|
O
|
A:HOH630
|
4.7
|
24.9
|
1.0
|
O
|
A:HOH736
|
4.7
|
38.5
|
1.0
|
O1B
|
A:DTP506
|
4.8
|
23.2
|
0.5
|
CD
|
A:ARG61
|
4.9
|
39.0
|
0.6
|
C8
|
A:DTP506
|
5.0
|
32.6
|
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 00:21:19 2024
|