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Magnesium in PDB 3auo: Dna Polymerase X From Thermus Thermophilus HB8 Ternary Complex with 1- Nt Gapped Dna and Ddgtp

Enzymatic activity of Dna Polymerase X From Thermus Thermophilus HB8 Ternary Complex with 1- Nt Gapped Dna and Ddgtp

All present enzymatic activity of Dna Polymerase X From Thermus Thermophilus HB8 Ternary Complex with 1- Nt Gapped Dna and Ddgtp:
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase X From Thermus Thermophilus HB8 Ternary Complex with 1- Nt Gapped Dna and Ddgtp, PDB code: 3auo was solved by S.Nakane, N.Nakagawa, R.Masui, S.Kuramitsu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 95.445, 96.941, 143.428, 90.00, 90.00, 90.00
R / Rfree (%) 24.1 / 29.3

Other elements in 3auo:

The structure of Dna Polymerase X From Thermus Thermophilus HB8 Ternary Complex with 1- Nt Gapped Dna and Ddgtp also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Dna Polymerase X From Thermus Thermophilus HB8 Ternary Complex with 1- Nt Gapped Dna and Ddgtp (pdb code 3auo). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Dna Polymerase X From Thermus Thermophilus HB8 Ternary Complex with 1- Nt Gapped Dna and Ddgtp, PDB code: 3auo:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 3auo

Go back to Magnesium Binding Sites List in 3auo
Magnesium binding site 1 out of 4 in the Dna Polymerase X From Thermus Thermophilus HB8 Ternary Complex with 1- Nt Gapped Dna and Ddgtp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Dna Polymerase X From Thermus Thermophilus HB8 Ternary Complex with 1- Nt Gapped Dna and Ddgtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg577

b:13.9
occ:1.00
 O2B A:DG3576 1.9 13.2 1.0
OD2 A:ASP200 2.0 16.3 1.0
O1G A:DG3576 2.1 13.0 1.0
OD1 A:ASP198 2.1 16.5 1.0
O1A A:DG3576 2.2 12.7 1.0
PB A:DG3576 3.0 13.0 1.0
CG A:ASP200 3.1 16.3 1.0
PG A:DG3576 3.1 11.3 1.0
CG A:ASP198 3.3 16.2 1.0
PA A:DG3576 3.4 13.4 1.0
O3B A:DG3576 3.4 11.8 1.0
OG A:SER188 3.5 18.3 1.0
O3A A:DG3576 3.5 13.1 1.0
O3G A:DG3576 3.6 11.8 1.0
OD1 A:ASP200 3.6 15.7 1.0
OD2 A:ASP198 3.8 16.8 1.0
N A:SER188 4.0 18.6 1.0
O A:HOH610 4.0 10.7 1.0
O A:ASP198 4.1 16.4 1.0
C5' A:DG3576 4.2 12.1 1.0
N A:ASP198 4.3 15.8 1.0
MG A:MG578 4.3 31.0 1.0
CA A:GLY187 4.3 19.0 1.0
O5' A:DG3576 4.3 12.6 1.0
C A:ASP198 4.4 16.0 1.0
CB A:ASP200 4.4 16.7 1.0
O1B A:DG3576 4.4 13.0 1.0
O2G A:DG3576 4.5 11.8 1.0
CB A:ASP198 4.5 16.0 1.0
CB A:SER188 4.5 18.2 1.0
O2A A:DG3576 4.5 12.9 1.0
CA A:ASP198 4.7 15.9 1.0
C A:GLY187 4.7 18.9 1.0
N A:ASP200 4.9 16.5 1.0
CA A:SER188 4.9 18.4 1.0
N A:LEU199 5.0 16.0 1.0
N A:GLY197 5.0 15.3 1.0

Magnesium binding site 2 out of 4 in 3auo

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Magnesium binding site 2 out of 4 in the Dna Polymerase X From Thermus Thermophilus HB8 Ternary Complex with 1- Nt Gapped Dna and Ddgtp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Dna Polymerase X From Thermus Thermophilus HB8 Ternary Complex with 1- Nt Gapped Dna and Ddgtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg578

b:31.0
occ:1.00
 OD2 A:ASP243 2.6 19.7 1.0
OD2 A:ASP198 2.6 16.8 1.0
O1A A:DG3576 2.7 12.7 1.0
OD1 A:ASP200 3.0 15.7 1.0
O2A A:DG3576 3.3 12.9 1.0
PA A:DG3576 3.3 13.4 1.0
CG A:ASP198 3.3 16.2 1.0
C3' D:DDG29 3.5 21.9 1.0
C5' D:DDG29 3.6 22.4 1.0
OD1 A:ASP198 3.6 16.5 1.0
CG A:ASP243 3.7 19.7 1.0
C4' D:DDG29 3.8 22.1 1.0
O5' A:DG3576 3.9 12.6 1.0
CG A:ASP200 4.1 16.3 1.0
NE2 A:GLN241 4.1 19.1 1.0
O5' D:DDG29 4.2 23.5 1.0
MG A:MG577 4.3 13.9 1.0
OD2 A:ASP200 4.3 16.3 1.0
OP1 D:DDG29 4.4 22.8 1.0
C5' A:DG3576 4.4 12.1 1.0
CB A:ASP198 4.5 16.0 1.0
O1G A:DG3576 4.5 13.0 1.0
OD1 A:ASP243 4.5 21.2 1.0
CB A:ASP243 4.6 18.9 1.0
O3A A:DG3576 4.8 13.1 1.0
CD A:GLN241 4.8 19.2 1.0
C2' D:DDG29 4.9 21.5 1.0
P D:DDG29 4.9 24.9 1.0

Magnesium binding site 3 out of 4 in 3auo

Go back to Magnesium Binding Sites List in 3auo
Magnesium binding site 3 out of 4 in the Dna Polymerase X From Thermus Thermophilus HB8 Ternary Complex with 1- Nt Gapped Dna and Ddgtp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Dna Polymerase X From Thermus Thermophilus HB8 Ternary Complex with 1- Nt Gapped Dna and Ddgtp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg577

b:17.4
occ:1.00
 O2B B:DG3576 2.2 10.8 1.0
OD1 B:ASP198 2.5 18.7 1.0
O1G B:DG3576 2.6 11.9 1.0
OD2 B:ASP200 2.6 17.4 1.0
O B:ASP198 2.9 17.4 1.0
OG B:SER188 2.9 16.2 1.0
O B:HOH619 3.1 17.3 1.0
O1A B:DG3576 3.3 9.6 1.0
PG B:DG3576 3.4 12.1 1.0
O3G B:DG3576 3.4 9.6 1.0
PB B:DG3576 3.6 11.1 1.0
N B:SER188 3.6 16.7 1.0
C B:ASP198 3.6 17.3 1.0
CG B:ASP198 3.6 17.9 1.0
CG B:ASP200 3.6 17.0 1.0
O3B B:DG3576 3.8 11.5 1.0
N B:ASP198 3.9 16.8 1.0
CB B:SER188 4.1 16.4 1.0
CA B:GLY187 4.2 17.6 1.0
CA B:ASP198 4.2 17.1 1.0
OD1 B:ASP200 4.3 17.3 1.0
CA B:SER188 4.4 16.3 1.0
C B:GLY187 4.4 17.2 1.0
OD2 B:ASP198 4.5 18.5 1.0
N B:LEU199 4.5 17.3 1.0
O3A B:DG3576 4.5 10.7 1.0
PA B:DG3576 4.5 11.4 1.0
N B:ASP200 4.5 17.4 1.0
CB B:ASP198 4.5 17.2 1.0
CB B:ASP200 4.6 17.2 1.0
N B:GLY197 4.6 15.9 1.0
CA B:LEU199 4.7 17.4 1.0
O1B B:DG3576 4.7 10.4 1.0
N B:ALA189 4.8 15.5 1.0
CB B:VAL196 4.8 15.0 1.0
O2G B:DG3576 4.8 12.7 1.0
C B:LEU199 4.9 17.5 1.0
C B:GLY197 5.0 16.5 1.0

Magnesium binding site 4 out of 4 in 3auo

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Magnesium binding site 4 out of 4 in the Dna Polymerase X From Thermus Thermophilus HB8 Ternary Complex with 1- Nt Gapped Dna and Ddgtp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Dna Polymerase X From Thermus Thermophilus HB8 Ternary Complex with 1- Nt Gapped Dna and Ddgtp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg578

b:24.9
occ:1.00
 O1A B:DG3576 2.6 9.6 1.0
OD2 B:ASP198 2.8 18.5 1.0
OD2 B:ASP243 3.0 27.4 1.0
O2A B:DG3576 3.1 9.8 1.0
PA B:DG3576 3.2 11.4 1.0
OD1 B:ASP200 3.3 17.3 1.0
CG B:ASP198 3.3 17.9 1.0
C3' E:DDG29 3.5 23.9 1.0
OD1 B:ASP198 3.5 18.7 1.0
C5' E:DDG29 3.6 24.3 1.0
O5' B:DG3576 3.7 11.7 1.0
C4' E:DDG29 3.8 24.1 1.0
CG B:ASP243 3.9 25.4 1.0
CG B:ASP200 4.2 17.0 1.0
C5' B:DG3576 4.3 12.4 1.0
NE2 B:GLN241 4.3 24.3 1.0
O5' E:DDG29 4.3 25.3 1.0
OD2 B:ASP200 4.3 17.4 1.0
O1G B:DG3576 4.5 11.9 1.0
CB B:ASP198 4.5 17.2 1.0
OD1 B:ASP243 4.6 26.5 1.0
OP1 E:DDG29 4.7 25.5 1.0
CB B:ASP243 4.7 24.4 1.0
O3A B:DG3576 4.7 10.7 1.0
C2' E:DDG29 4.9 23.3 1.0

Reference:

S.Nakane, H.Ishikawa, N.Nakagawa, S.Kuramitsu, R.Masui. The Structural Basis of the Kinetic Mechanism of A Gap-Filling X-Family Dna Polymerase That Binds Mg(2+)-Dntp Before Binding to Dna. J.Mol.Biol. V. 417 179 2012.
ISSN: ISSN 0022-2836
PubMed: 22306405
DOI: 10.1016/J.JMB.2012.01.025
Page generated: Wed Aug 14 08:46:23 2024

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