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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

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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 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

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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

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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

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