Magnesium in PDB 1tk8: T7 Dna Polymerase Ternary Complex with 8 Oxo Guanosine and Damp at the Elongation Site
Enzymatic activity of T7 Dna Polymerase Ternary Complex with 8 Oxo Guanosine and Damp at the Elongation Site
All present enzymatic activity of T7 Dna Polymerase Ternary Complex with 8 Oxo Guanosine and Damp at the Elongation Site:
2.7.7.7;
Protein crystallography data
The structure of T7 Dna Polymerase Ternary Complex with 8 Oxo Guanosine and Damp at the Elongation Site, PDB code: 1tk8
was solved by
L.G.Brieba,
B.F.Eichman,
R.J.Kokoska,
S.Doublie,
T.A.Kunkel,
T.Ellenberger,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
39.97 /
2.50
|
Space group
|
P 21 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
106.177,
215.710,
52.155,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
20.6 /
26.1
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the T7 Dna Polymerase Ternary Complex with 8 Oxo Guanosine and Damp at the Elongation Site
(pdb code 1tk8). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the
T7 Dna Polymerase Ternary Complex with 8 Oxo Guanosine and Damp at the Elongation Site, PDB code: 1tk8:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 1tk8
Go back to
Magnesium Binding Sites List in 1tk8
Magnesium binding site 1 out
of 4 in the T7 Dna Polymerase Ternary Complex with 8 Oxo Guanosine and Damp at the Elongation Site
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of T7 Dna Polymerase Ternary Complex with 8 Oxo Guanosine and Damp at the Elongation Site within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
T:Mg904
b:34.4
occ:1.00
|
O
|
T:HOH1221
|
2.1
|
26.3
|
1.0
|
O
|
T:HOH1487
|
2.1
|
16.5
|
1.0
|
O
|
T:HOH1222
|
2.3
|
26.0
|
1.0
|
O
|
T:HOH1489
|
2.3
|
26.4
|
1.0
|
O
|
T:HOH1488
|
2.4
|
28.6
|
1.0
|
O
|
T:HOH1257
|
2.7
|
49.5
|
1.0
|
O
|
T:HOH1246
|
4.0
|
26.0
|
1.0
|
O
|
T:HOH1070
|
4.0
|
30.2
|
1.0
|
N7
|
T:DG857
|
4.1
|
16.0
|
1.0
|
O
|
P:HOH1511
|
4.2
|
52.6
|
1.0
|
O6
|
T:DG858
|
4.2
|
9.8
|
1.0
|
O
|
T:HOH1352
|
4.3
|
30.3
|
1.0
|
N7
|
T:DG858
|
4.3
|
13.9
|
1.0
|
O
|
P:HOH1206
|
4.4
|
38.1
|
1.0
|
C8
|
T:DG857
|
4.6
|
17.4
|
1.0
|
O
|
T:HOH1387
|
4.6
|
39.7
|
1.0
|
O
|
T:HOH1086
|
4.6
|
26.0
|
1.0
|
O
|
T:HOH1362
|
4.6
|
37.5
|
1.0
|
N4
|
T:DC859
|
4.9
|
13.5
|
1.0
|
C5
|
T:DG857
|
5.0
|
17.7
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 1tk8
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Magnesium Binding Sites List in 1tk8
Magnesium binding site 2 out
of 4 in the T7 Dna Polymerase Ternary Complex with 8 Oxo Guanosine and Damp at the Elongation Site
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of T7 Dna Polymerase Ternary Complex with 8 Oxo Guanosine and Damp at the Elongation Site within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg901
b:24.6
occ:1.00
|
O1G
|
A:D3T823
|
1.9
|
24.0
|
1.0
|
O2B
|
A:D3T823
|
2.0
|
18.7
|
1.0
|
OD2
|
A:ASP654
|
2.1
|
20.5
|
1.0
|
O2A
|
A:D3T823
|
2.1
|
17.4
|
1.0
|
OD1
|
A:ASP475
|
2.2
|
30.8
|
1.0
|
O
|
A:ALA476
|
2.3
|
16.8
|
1.0
|
PG
|
A:D3T823
|
3.1
|
21.2
|
1.0
|
PB
|
A:D3T823
|
3.2
|
16.6
|
1.0
|
CG
|
A:ASP475
|
3.2
|
26.2
|
1.0
|
CG
|
A:ASP654
|
3.2
|
17.6
|
1.0
|
PA
|
A:D3T823
|
3.4
|
21.4
|
1.0
|
OD2
|
A:ASP475
|
3.5
|
28.8
|
1.0
|
O3B
|
A:D3T823
|
3.5
|
21.8
|
1.0
|
C
|
A:ALA476
|
3.5
|
17.4
|
1.0
|
MG
|
A:MG902
|
3.6
|
24.4
|
1.0
|
O3A
|
A:D3T823
|
3.7
|
20.7
|
1.0
|
OD1
|
A:ASP654
|
3.7
|
16.9
|
1.0
|
O2G
|
A:D3T823
|
3.8
|
20.0
|
1.0
|
O
|
A:HOH1531
|
3.9
|
32.4
|
1.0
|
O
|
A:HOH1530
|
4.0
|
28.6
|
1.0
|
N
|
A:ALA476
|
4.2
|
16.3
|
1.0
|
O3G
|
A:D3T823
|
4.3
|
20.5
|
1.0
|
N
|
A:GLY478
|
4.3
|
15.3
|
1.0
|
C5'
|
A:D3T823
|
4.3
|
22.8
|
1.0
|
CA
|
A:ALA476
|
4.4
|
17.9
|
1.0
|
O5'
|
A:D3T823
|
4.4
|
22.1
|
1.0
|
N
|
A:SER477
|
4.5
|
17.9
|
1.0
|
O1B
|
A:D3T823
|
4.5
|
19.6
|
1.0
|
CB
|
A:ASP654
|
4.5
|
14.4
|
1.0
|
O1A
|
A:D3T823
|
4.5
|
19.0
|
1.0
|
CA
|
A:SER477
|
4.6
|
17.1
|
1.0
|
CB
|
A:ASP475
|
4.6
|
20.4
|
1.0
|
C
|
A:ASP475
|
4.6
|
18.2
|
1.0
|
N
|
A:LEU479
|
4.8
|
17.0
|
1.0
|
C
|
A:SER477
|
4.8
|
14.9
|
1.0
|
CB
|
A:ALA476
|
4.8
|
16.9
|
1.0
|
O
|
A:ASP654
|
4.8
|
15.5
|
1.0
|
O
|
A:HOH1284
|
5.0
|
17.7
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 1tk8
Go back to
Magnesium Binding Sites List in 1tk8
Magnesium binding site 3 out
of 4 in the T7 Dna Polymerase Ternary Complex with 8 Oxo Guanosine and Damp at the Elongation Site
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of T7 Dna Polymerase Ternary Complex with 8 Oxo Guanosine and Damp at the Elongation Site within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg902
b:24.4
occ:1.00
|
OD1
|
A:ASP654
|
2.2
|
16.9
|
1.0
|
OD2
|
A:ASP475
|
2.3
|
28.8
|
1.0
|
O
|
A:HOH1008
|
2.4
|
14.0
|
1.0
|
O2A
|
A:D3T823
|
2.6
|
17.4
|
1.0
|
O
|
A:HOH1284
|
2.6
|
17.7
|
1.0
|
CG
|
A:ASP654
|
3.1
|
17.6
|
1.0
|
CG
|
A:ASP475
|
3.3
|
26.2
|
1.0
|
OD2
|
A:ASP654
|
3.4
|
20.5
|
1.0
|
C3'
|
P:2DA822
|
3.5
|
11.4
|
1.0
|
PA
|
A:D3T823
|
3.6
|
21.4
|
1.0
|
MG
|
A:MG901
|
3.6
|
24.6
|
1.0
|
OD1
|
A:ASP475
|
3.7
|
30.8
|
1.0
|
O
|
A:HOH1531
|
3.9
|
32.4
|
1.0
|
O5'
|
A:D3T823
|
4.0
|
22.1
|
1.0
|
O1A
|
A:D3T823
|
4.0
|
19.0
|
1.0
|
C4'
|
P:2DA822
|
4.1
|
11.2
|
1.0
|
C5'
|
A:D3T823
|
4.2
|
22.8
|
1.0
|
CB
|
A:GLU655
|
4.2
|
16.4
|
1.0
|
CE1
|
A:HIS704
|
4.3
|
40.4
|
1.0
|
C5'
|
P:2DA822
|
4.3
|
11.5
|
1.0
|
O1G
|
A:D3T823
|
4.3
|
24.0
|
1.0
|
C
|
A:ASP654
|
4.5
|
15.4
|
1.0
|
OE2
|
A:GLU655
|
4.5
|
20.8
|
1.0
|
CB
|
A:ASP654
|
4.5
|
14.4
|
1.0
|
O
|
A:ASP654
|
4.5
|
15.5
|
1.0
|
O
|
A:VAL652
|
4.5
|
14.0
|
1.0
|
C2'
|
P:2DA822
|
4.6
|
11.7
|
1.0
|
CB
|
A:ASP475
|
4.6
|
20.4
|
1.0
|
N
|
A:ASP654
|
4.7
|
13.2
|
1.0
|
N
|
A:GLU655
|
4.8
|
16.4
|
1.0
|
O5'
|
P:2DA822
|
4.8
|
15.4
|
1.0
|
CA
|
A:ASP654
|
4.8
|
14.5
|
1.0
|
NE2
|
A:HIS704
|
4.9
|
38.6
|
1.0
|
O2B
|
A:D3T823
|
5.0
|
18.7
|
1.0
|
O3A
|
A:D3T823
|
5.0
|
20.7
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 1tk8
Go back to
Magnesium Binding Sites List in 1tk8
Magnesium binding site 4 out
of 4 in the T7 Dna Polymerase Ternary Complex with 8 Oxo Guanosine and Damp at the Elongation Site
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of T7 Dna Polymerase Ternary Complex with 8 Oxo Guanosine and Damp at the Elongation Site within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg903
b:16.8
occ:1.00
|
OD1
|
A:ASP5
|
2.1
|
18.8
|
1.0
|
O
|
A:HOH1524
|
2.1
|
25.0
|
1.0
|
O
|
A:HOH1145
|
2.1
|
16.9
|
1.0
|
O
|
A:HOH1525
|
2.1
|
21.1
|
1.0
|
O
|
A:HOH1067
|
2.2
|
12.5
|
1.0
|
O
|
A:HOH1508
|
2.2
|
17.0
|
1.0
|
CG
|
A:ASP5
|
3.1
|
18.8
|
1.0
|
OD2
|
A:ASP5
|
3.5
|
19.3
|
1.0
|
OD2
|
A:ASP65
|
4.1
|
10.9
|
1.0
|
O
|
A:ILE6
|
4.1
|
16.2
|
1.0
|
O
|
A:HOH1026
|
4.1
|
17.5
|
1.0
|
OD1
|
A:ASP65
|
4.1
|
10.7
|
1.0
|
O
|
A:HOH1473
|
4.3
|
31.1
|
1.0
|
O
|
A:HIS59
|
4.3
|
10.5
|
1.0
|
O
|
A:HOH1251
|
4.3
|
35.1
|
1.0
|
OD2
|
A:ASP174
|
4.4
|
31.4
|
1.0
|
CB
|
A:ASP5
|
4.4
|
13.8
|
1.0
|
CG
|
A:ASP65
|
4.5
|
10.3
|
1.0
|
O
|
A:HOH1428
|
4.6
|
30.2
|
1.0
|
CE
|
A:MET107
|
4.7
|
24.4
|
1.0
|
N
|
A:ILE6
|
4.8
|
12.3
|
1.0
|
|
Reference:
L.G.Brieba,
B.F.Eichman,
R.J.Kokoska,
S.Doublie,
T.A.Kunkel,
T.Ellenberger.
Structural Basis For the Dual Coding Potential of 8-Oxoguanosine By A High-Fidelity Dna Polymerase. Embo J. V. 23 3452 2004.
ISSN: ISSN 0261-4189
PubMed: 15297882
DOI: 10.1038/SJ.EMBOJ.7600354
Page generated: Tue Aug 13 14:34:29 2024
|