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

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

All present enzymatic activity of Human Dna Polymerase Beta Complexed with Nicked Dna Containing A Mismatched Template Thymidine 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 Thymidine and Incoming Cytidine, PDB code: 1tva was solved by J.M.Krahn, W.A.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 / 2.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.600, 79.700, 54.600, 90.00, 106.40, 90.00
R / Rfree (%) 21.2 / 28.2

Other elements in 1tva:

The structure of Human Dna Polymerase Beta Complexed with Nicked Dna Containing A Mismatched Template Thymidine 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 Thymidine and Incoming Cytidine (pdb code 1tva). 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 Thymidine and Incoming Cytidine, PDB code: 1tva:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 1tva

Go back to Magnesium Binding Sites List in 1tva
Magnesium binding site 1 out of 2 in the Human Dna Polymerase Beta Complexed with Nicked Dna Containing A Mismatched Template Thymidine 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 Thymidine and Incoming Cytidine within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mg343

b:47.5
occ:1.00
 O A:HOH353 2.0 47.8 1.0
O A:HOH350 2.0 49.2 1.0
O A:HOH351 2.1 46.1 1.0
O P:HOH353 2.1 46.2 1.0
O A:HOH352 2.1 47.2 1.0
OP1 P:DC11 2.1 45.3 1.0
P P:DC11 3.2 42.5 1.0
O3' P:DC10 3.4 39.4 1.0
OD2 A:ASP192 3.4 31.6 1.0
O A:HOH381 3.6 45.1 1.0
OD1 A:ASP190 3.8 29.3 1.0
O5' P:DC11 3.8 45.0 1.0
OD2 A:ASP190 4.1 28.1 1.0
CG A:ASP192 4.3 28.5 1.0
CG A:ASP190 4.4 27.4 1.0
CB A:ASP192 4.4 23.2 1.0
O2 A:PO4344 4.4 45.3 1.0
O4 A:PO4344 4.5 43.3 1.0
OP2 P:DC11 4.6 40.5 1.0
C3' P:DC10 4.7 34.2 1.0
O1 A:PO4344 4.8 48.0 1.0
P A:PO4344 4.9 46.4 1.0

Magnesium binding site 2 out of 2 in 1tva

Go back to Magnesium Binding Sites List in 1tva
Magnesium binding site 2 out of 2 in the Human Dna Polymerase Beta Complexed with Nicked Dna Containing A Mismatched Template Thymidine 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 Thymidine and Incoming Cytidine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg345

b:37.7
occ:1.00
 O A:HOH357 2.1 29.5 1.0
O A:SER30 2.1 24.6 1.0
O A:HOH356 3.0 29.1 1.0
O A:HOH354 3.1 17.9 1.0
C A:SER30 3.3 20.8 1.0
O A:HOH355 3.3 31.2 1.0
CA A:SER30 3.9 19.2 1.0
CB A:SER30 4.2 20.3 1.0
O A:GLN31 4.3 22.0 1.0
N A:GLN31 4.4 21.9 1.0
C A:GLN31 4.5 21.2 1.0
CB A:GLN31 4.7 21.8 1.0
CA A:GLN31 4.8 20.3 1.0

Reference:

J.M.Krahn, W.A.Beard, S.H.Wilson. Structural Insights Into Dna Polymerase Beta Deterrents For Misincorporation Support 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: Tue Aug 13 14:39:53 2024

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