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Magnesium in PDB 1l3t: Crystal Structure of Bacillus Dna Polymerase I Fragment Product Complex with 10 Base Pairs of Duplex Dna Following Addition of A Single Dttp Residue

Enzymatic activity of Crystal Structure of Bacillus Dna Polymerase I Fragment Product Complex with 10 Base Pairs of Duplex Dna Following Addition of A Single Dttp Residue

All present enzymatic activity of Crystal Structure of Bacillus Dna Polymerase I Fragment Product Complex with 10 Base Pairs of Duplex Dna Following Addition of A Single Dttp Residue:
2.7.7.7;

Protein crystallography data

The structure of Crystal Structure of Bacillus Dna Polymerase I Fragment Product Complex with 10 Base Pairs of Duplex Dna Following Addition of A Single Dttp Residue, PDB code: 1l3t was solved by S.J.Johnson, J.S.Taylor, L.S.Beese, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.06 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 87.530, 93.356, 106.229, 90.00, 90.00, 90.00
R / Rfree (%) 20.6 / 23.1

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Bacillus Dna Polymerase I Fragment Product Complex with 10 Base Pairs of Duplex Dna Following Addition of A Single Dttp Residue (pdb code 1l3t). 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 Fragment Product Complex with 10 Base Pairs of Duplex Dna Following Addition of A Single Dttp Residue, PDB code: 1l3t:

Magnesium binding site 1 out of 1 in 1l3t

Go back to Magnesium Binding Sites List in 1l3t
Magnesium binding site 1 out of 1 in the Crystal Structure of Bacillus Dna Polymerase I Fragment Product Complex with 10 Base Pairs of Duplex Dna Following Addition of A Single Dttp Residue


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 Fragment Product Complex with 10 Base Pairs of Duplex Dna Following Addition of A Single Dttp Residue within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg920

b:28.5
occ:1.00
 OD1 A:ASP653 2.7 18.5 1.0
O A:TYR654 2.8 14.3 1.0
O B:HOH2842 2.9 36.4 1.0
O A:HOH2525 3.0 25.6 1.0
OD2 A:ASP830 3.0 16.3 1.0
O A:HOH2541 3.3 27.9 1.0
CG A:ASP653 3.6 17.8 1.0
O A:HOH2660 3.7 27.0 1.0
O A:HOH2512 3.7 14.7 1.0
CB A:ASP653 3.9 16.4 1.0
CG A:ASP830 3.9 17.0 1.0
C A:TYR654 4.0 15.1 1.0
O A:HOH2812 4.0 31.9 1.0
O A:HOH2836 4.2 37.7 1.0
OD1 A:ASP830 4.3 16.1 1.0
O B:HOH2707 4.4 33.4 1.0
O B:HOH2816 4.4 32.2 1.0
O A:HOH2645 4.5 34.6 1.0
N A:TYR654 4.6 14.3 1.0
CA A:SER655 4.6 15.9 1.0
C A:ASP653 4.6 14.4 1.0
N A:SER655 4.7 15.3 1.0
OD2 A:ASP653 4.8 17.9 1.0
CA A:ASP653 4.9 15.0 1.0
N A:GLN656 4.9 15.6 1.0
CA A:TYR654 4.9 14.1 1.0

Reference:

S.J.Johnson, J.S.Taylor, L.S.Beese. Processive Dna Synthesis Observed in A Polymerase Crystal Suggests A Mechanism For the Prevention of Frameshift Mutations Proc.Natl.Acad.Sci.Usa V. 100 3895 2003.
ISSN: ISSN 0027-8424
PubMed: 12649320
DOI: 10.1073/PNAS.0630532100
Page generated: Tue Aug 13 08:25:55 2024

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