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Magnesium in PDB 1tv9: Human Dna Polymerase Beta Complexed with Nicked Dna Containing A Mismatched Template Adenine and Incoming Cytidine

Enzymatic activity of Human Dna Polymerase Beta Complexed with Nicked Dna Containing A Mismatched Template Adenine and Incoming Cytidine

All present enzymatic activity of Human Dna Polymerase Beta Complexed with Nicked Dna Containing A Mismatched Template Adenine and Incoming Cytidine:
2.7.7.7;

Protein crystallography data

The structure of Human Dna Polymerase Beta Complexed with Nicked Dna Containing A Mismatched Template Adenine and Incoming Cytidine, PDB code: 1tv9 was solved by J.M.Krahn, W.M.Beard, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.680, 79.650, 54.670, 90.00, 106.77, 90.00
R / Rfree (%) 17.9 / 23.9

Other elements in 1tv9:

The structure of Human Dna Polymerase Beta Complexed with Nicked Dna Containing A Mismatched Template Adenine and Incoming Cytidine also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Human Dna Polymerase Beta Complexed with Nicked Dna Containing A Mismatched Template Adenine and Incoming Cytidine (pdb code 1tv9). 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 Polymerase Beta Complexed with Nicked Dna Containing A Mismatched Template Adenine and Incoming Cytidine, PDB code: 1tv9:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 1tv9

Go back to Magnesium Binding Sites List in 1tv9
Magnesium binding site 1 out of 2 in the Human Dna Polymerase Beta Complexed with Nicked Dna Containing A Mismatched Template Adenine and Incoming Cytidine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human Dna Polymerase Beta Complexed with Nicked Dna Containing A Mismatched Template Adenine and Incoming Cytidine within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mg786

b:23.6
occ:1.00
 O A:HOH1350 2.0 24.7 1.0
O P:HOH791 2.0 28.5 1.0
OP1 P:DC11 2.0 26.3 1.0
O A:HOH1349 2.0 26.6 1.0
O P:HOH788 2.0 19.9 1.0
O A:HOH1348 2.0 26.1 1.0
P P:DC11 3.3 22.6 1.0
O3' P:DC10 3.6 19.5 1.0
OD2 A:ASP192 3.9 22.7 1.0
O4 A:PO4792 4.1 30.8 1.0
OD1 A:ASP190 4.1 20.6 1.0
O A:HOH891 4.3 26.1 1.0
OP2 P:DC11 4.3 20.2 1.0
OD2 A:ASP190 4.3 19.4 1.0
O P:HOH108 4.3 24.3 1.0
O5' P:DC11 4.4 23.1 1.0
CB A:ASP192 4.4 17.8 1.0
C5' P:DC11 4.5 23.2 1.0
O2 A:PO4792 4.5 34.1 1.0
O3 A:PO4792 4.5 36.2 1.0
CG A:ASP192 4.6 20.9 1.0
P A:PO4792 4.6 34.9 1.0
CA A:GLY179 4.7 12.9 1.0
CG A:ASP190 4.7 17.3 1.0
O A:PHE272 4.7 20.3 1.0
O3' P:DC11 4.8 21.1 1.0
C3' P:DC11 4.8 22.3 1.0
O P:HOH451 4.9 45.4 1.0
C3' P:DC10 5.0 22.1 1.0

Magnesium binding site 2 out of 2 in 1tv9

Go back to Magnesium Binding Sites List in 1tv9
Magnesium binding site 2 out of 2 in the Human Dna Polymerase Beta Complexed with Nicked Dna Containing A Mismatched Template Adenine and Incoming Cytidine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human Dna Polymerase Beta Complexed with Nicked Dna Containing A Mismatched Template Adenine and Incoming Cytidine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg781

b:26.8
occ:1.00
 OG A:SER171 2.3 19.8 1.0
O A:HOH847 2.3 21.6 1.0
O A:HOH972 2.4 33.0 1.0
O A:HOH901 2.5 27.3 1.0
O A:HOH996 2.8 34.9 1.0
CB A:SER171 3.4 17.5 1.0
N A:SER171 4.0 19.0 1.0
O A:HOH930 4.3 29.9 1.0
CA A:SER171 4.3 19.3 1.0
O A:HOH824 4.4 18.4 1.0
O A:HOH1299 4.6 68.7 1.0
OD1 A:ASP170 4.9 21.4 1.0

Reference:

J.M.Krahn, W.M.Beard, S.H.Wilson. Structural Insights Into Dna Polymerase Beta Deterrents For Misincorporation Support of An Induced-Fit Mechanism For Fidelity Structure V. 12 1823 2004.
ISSN: ISSN 0969-2126
PubMed: 15458631
DOI: 10.1016/J.STR.2004.08.001
Page generated: Sun Aug 10 04:58:22 2025

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