Magnesium in PDB 3px4: Crystal Structure of Bacillus Dna Polymerase I Large Fragment Bound to Dna and Ddctp-Da Mismatch (Wobble) in Ajar Conformation

Enzymatic activity of Crystal Structure of Bacillus Dna Polymerase I Large Fragment Bound to Dna and Ddctp-Da Mismatch (Wobble) in Ajar Conformation

All present enzymatic activity of Crystal Structure of Bacillus Dna Polymerase I Large Fragment Bound to Dna and Ddctp-Da Mismatch (Wobble) in Ajar Conformation:
2.7.7.7;

Protein crystallography data

The structure of Crystal Structure of Bacillus Dna Polymerase I Large Fragment Bound to Dna and Ddctp-Da Mismatch (Wobble) in Ajar Conformation, PDB code: 3px4 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) 71.10 / 1.58
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 93.680, 109.190, 150.460, 90.00, 90.00, 90.00
R / Rfree (%) 21.1 / 23.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Bacillus Dna Polymerase I Large Fragment Bound to Dna and Ddctp-Da Mismatch (Wobble) in Ajar Conformation (pdb code 3px4). 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 Dna and Ddctp-Da Mismatch (Wobble) in Ajar Conformation, PDB code: 3px4:

Magnesium binding site 1 out of 1 in 3px4

Go back to Magnesium Binding Sites List in 3px4
Magnesium binding site 1 out of 1 in the Crystal Structure of Bacillus Dna Polymerase I Large Fragment Bound to Dna and Ddctp-Da Mismatch (Wobble) in Ajar Conformation


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 Dna and Ddctp-Da Mismatch (Wobble) in Ajar Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1

b:29.2
occ:1.00
 O D:TYR654 2.7 14.9 1.0
O2G D:DCT202 2.8 31.3 1.0
OD2 D:ASP830 2.8 19.9 0.5
OD2 D:ASP830 2.9 21.0 0.5
O1A D:DCT202 2.9 27.2 1.0
O2B D:DCT202 2.9 20.9 1.0
OD2 D:ASP653 2.9 22.3 1.0
HB2 D:ASP653 3.4 12.0 1.0
HA D:SER655 3.5 10.9 1.0
O D:HOH891 3.6 18.2 1.0
HB2 D:ASP830 3.7 14.1 0.5
C D:TYR654 3.8 13.7 1.0
CG D:ASP830 3.8 10.6 0.5
O D:HOH1373 3.8 31.7 1.0
H D:GLN656 3.8 18.2 1.0
PB D:DCT202 3.9 18.6 1.0
CG D:ASP830 3.9 13.7 0.5
CG D:ASP653 3.9 15.9 1.0
PG D:DCT202 3.9 23.4 1.0
O D:HOH95 4.0 24.2 1.0
O3B D:DCT202 4.0 18.4 1.0
PA D:DCT202 4.0 22.0 1.0
CB D:ASP653 4.1 10.0 1.0
OD1 D:ASP830 4.2 11.1 0.5
CB D:ASP830 4.3 11.8 0.5
CA D:SER655 4.3 9.1 1.0
O3A D:DCT202 4.4 16.9 1.0
N D:SER655 4.5 12.4 1.0
HB3 D:ASP830 4.6 14.1 0.5
N D:GLN656 4.6 15.2 1.0
O2A D:DCT202 4.6 18.9 1.0
O D:HOH84 4.6 21.3 1.0
O3G D:DCT202 4.6 22.4 1.0
N D:TYR654 4.7 9.6 1.0
HB3 D:ASP653 4.7 12.0 1.0
H D:TYR654 4.8 11.4 1.0
CA D:TYR654 4.8 11.8 1.0
C D:ASP653 4.8 14.2 1.0
HB2 D:ASP830 4.9 12.1 0.5
OD1 D:ASP830 5.0 12.4 0.5
O D:ASP830 5.0 9.3 0.5

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 Dec 14 08:41:08 2020

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