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Magnesium in PDB 3tap: Crystal Structure of Bacillus Dna Polymerase I Large Fragment Bound to Duplex Dna with Cytosine-Adenine Mismatch at (N-3) Position

Enzymatic activity of Crystal Structure of Bacillus Dna Polymerase I Large Fragment Bound to Duplex Dna with Cytosine-Adenine Mismatch at (N-3) Position

All present enzymatic activity of Crystal Structure of Bacillus Dna Polymerase I Large Fragment Bound to Duplex Dna with Cytosine-Adenine Mismatch at (N-3) Position:
2.7.7.7;

Protein crystallography data

The structure of Crystal Structure of Bacillus Dna Polymerase I Large Fragment Bound to Duplex Dna with Cytosine-Adenine Mismatch at (N-3) Position, PDB code: 3tap was solved by W.Wang, L.S.Beese, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.72 / 1.66
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 87.660, 93.270, 105.700, 90.00, 90.00, 90.00
R / Rfree (%) 17.6 / 20.2

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Bacillus Dna Polymerase I Large Fragment Bound to Duplex Dna with Cytosine-Adenine Mismatch at (N-3) Position (pdb code 3tap). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Crystal Structure of Bacillus Dna Polymerase I Large Fragment Bound to Duplex Dna with Cytosine-Adenine Mismatch at (N-3) Position, PDB code: 3tap:

Magnesium binding site 1 out of 1 in 3tap

Go back to Magnesium Binding Sites List in 3tap
Magnesium binding site 1 out of 1 in the Crystal Structure of Bacillus Dna Polymerase I Large Fragment Bound to Duplex Dna with Cytosine-Adenine Mismatch at (N-3) Position


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Bacillus Dna Polymerase I Large Fragment Bound to Duplex Dna with Cytosine-Adenine Mismatch at (N-3) Position within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1

b:32.6
occ:1.00
 OD1 A:ASP653 2.8 22.9 1.0
O A:TYR654 2.9 18.7 1.0
O A:HOH1096 3.0 24.8 1.0
OD2 A:ASP830 3.1 23.3 1.0
O A:HOH209 3.2 29.7 1.0
HB2 A:ASP653 3.2 18.3 1.0
O A:HOH952 3.7 28.9 1.0
CG A:ASP653 3.7 23.3 1.0
O A:HOH72 3.8 17.0 1.0
HA A:SER655 3.8 16.2 1.0
CB A:ASP653 3.9 15.3 1.0
CG A:ASP830 4.0 23.7 1.0
O B:HOH570 4.0 45.3 1.0
C A:TYR654 4.0 15.0 1.0
O A:HOH207 4.1 29.9 1.0
H A:GLN656 4.2 14.9 1.0
OD1 A:ASP830 4.3 20.2 1.0
O A:HOH1035 4.3 48.7 1.0
O A:HOH1095 4.3 32.4 1.0
O A:HOH1159 4.3 41.2 1.0
HB3 A:ASP653 4.5 18.3 1.0
CA A:SER655 4.7 13.5 1.0
N A:TYR654 4.8 12.1 1.0
C A:ASP653 4.8 16.8 1.0
N A:SER655 4.8 12.9 1.0
OD2 A:ASP653 4.9 19.6 1.0
H A:TYR654 4.9 14.5 1.0
N A:GLN656 5.0 12.4 1.0
HB2 A:ASP830 5.0 18.2 1.0
CA A:ASP653 5.0 12.5 1.0

Reference:

W.Wang, H.W.Hellinga, L.S.Beese. Structural Evidence For the Rare Tautomer Hypothesis of Spontaneous Mutagenesis. Proc.Natl.Acad.Sci.Usa V. 108 17644 2011.
ISSN: ISSN 0027-8424
PubMed: 22006298
DOI: 10.1073/PNAS.1114496108
Page generated: Mon Aug 11 03:51:50 2025

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