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Magnesium in PDB 3pv8: Crystal Structure of Bacillus Dna Polymerase I Large Fragment Bound to Dna and Ddttp-Da in Closed Conformation

Enzymatic activity of Crystal Structure of Bacillus Dna Polymerase I Large Fragment Bound to Dna and Ddttp-Da in Closed Conformation

All present enzymatic activity of Crystal Structure of Bacillus Dna Polymerase I Large Fragment Bound to Dna and Ddttp-Da in Closed Conformation:
2.7.7.7;

Protein crystallography data

The structure of Crystal Structure of Bacillus Dna Polymerase I Large Fragment Bound to Dna and Ddttp-Da in Closed Conformation, PDB code: 3pv8 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) 88.42 / 1.52
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 93.890, 109.300, 150.420, 90.00, 90.00, 90.00
R / Rfree (%) 18.5 / 21.1

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Bacillus Dna Polymerase I Large Fragment Bound to Dna and Ddttp-Da in Closed Conformation (pdb code 3pv8). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Bacillus Dna Polymerase I Large Fragment Bound to Dna and Ddttp-Da in Closed Conformation, PDB code: 3pv8:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 3pv8

Go back to Magnesium Binding Sites List in 3pv8
Magnesium binding site 1 out of 2 in the Crystal Structure of Bacillus Dna Polymerase I Large Fragment Bound to Dna and Ddttp-Da in Closed 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 Ddttp-Da in Closed Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1

b:23.0
occ:1.00
OD2 A:ASP830 2.1 22.1 1.0
O2B A:D3T201 2.2 21.4 1.0
O2G A:D3T201 2.2 24.8 1.0
O2A A:D3T201 2.3 18.2 1.0
O A:TYR654 2.3 25.8 1.0
OD1 A:ASP653 2.4 28.7 0.5
PB A:D3T201 3.2 20.8 1.0
CG A:ASP830 3.2 26.1 1.0
PG A:D3T201 3.3 24.4 1.0
CG A:ASP653 3.3 33.2 0.5
PA A:D3T201 3.5 21.2 1.0
O3B A:D3T201 3.5 19.4 1.0
C A:TYR654 3.5 24.3 1.0
H5'2 A:D3T201 3.6 27.0 1.0
OD2 A:ASP653 3.6 35.0 0.5
OD1 A:ASP830 3.6 22.2 1.0
HB2 A:ASP653 3.7 34.0 0.5
O3A A:D3T201 3.7 20.5 1.0
HG22 A:ILE657 3.7 33.2 1.0
HA A:SER655 3.9 29.4 1.0
H A:ILE657 3.9 26.9 1.0
O A:HOH1785 4.0 28.8 1.0
H A:GLN656 4.1 26.7 1.0
HB2 A:TYR654 4.2 23.1 1.0
O3G A:D3T201 4.2 27.6 1.0
C5' A:D3T201 4.3 22.5 1.0
HB A:ILE657 4.3 27.0 1.0
N A:TYR654 4.3 24.2 1.0
O5' A:D3T201 4.4 18.7 1.0
H A:TYR654 4.4 29.0 1.0
HB2 A:ASP830 4.4 26.0 1.0
HG21 A:ILE657 4.4 33.2 1.0
CB A:ASP830 4.4 21.7 1.0
H5'1 A:D3T201 4.4 27.0 1.0
CA A:TYR654 4.4 22.7 1.0
O1G A:D3T201 4.4 22.0 1.0
N A:SER655 4.4 27.3 1.0
CG2 A:ILE657 4.5 27.7 1.0
N A:GLN656 4.5 22.3 1.0
CA A:SER655 4.5 24.5 1.0
O1B A:D3T201 4.5 23.8 1.0
O1A A:D3T201 4.6 17.2 1.0
CB A:ASP653 4.6 28.4 0.5
OD1 A:ASP653 4.6 40.4 0.5
O A:HOH1311 4.7 40.5 1.0
CB A:ASP653 4.7 27.7 0.5
C A:SER655 4.7 25.5 1.0
C A:ASP653 4.7 27.4 1.0
CB A:TYR654 4.7 19.3 1.0
N A:ILE657 4.8 22.4 1.0
O A:ASP830 4.8 24.5 1.0
HB3 A:ASP830 4.8 26.0 1.0
HB3 A:TYR654 4.8 23.1 1.0
HZ3 A:LYS706 4.8 31.4 1.0
CB A:ILE657 4.9 22.5 1.0
HB3 A:ASP653 5.0 33.3 0.5

Magnesium binding site 2 out of 2 in 3pv8

Go back to Magnesium Binding Sites List in 3pv8
Magnesium binding site 2 out of 2 in the Crystal Structure of Bacillus Dna Polymerase I Large Fragment Bound to Dna and Ddttp-Da in Closed Conformation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Bacillus Dna Polymerase I Large Fragment Bound to Dna and Ddttp-Da in Closed Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg2

b:14.4
occ:1.00
OD2 D:ASP830 2.0 12.8 1.0
O D:HOH1823 2.0 25.9 1.0
O2B D:D3T202 2.2 16.3 1.0
O2G D:D3T202 2.2 15.8 1.0
O D:TYR654 2.2 12.5 1.0
O2A D:D3T202 2.3 13.6 1.0
CG D:ASP830 3.1 11.6 1.0
PB D:D3T202 3.2 13.9 1.0
PG D:D3T202 3.4 16.9 1.0
C D:TYR654 3.5 10.9 1.0
PA D:D3T202 3.6 12.4 1.0
HA D:SER655 3.6 14.7 0.4
O D:HOH1820 3.6 30.8 1.0
O3B D:D3T202 3.6 12.4 1.0
H5'2 D:D3T202 3.6 10.7 1.0
OD1 D:ASP830 3.7 14.3 1.0
HA D:SER655 3.7 14.6 0.6
O3A D:D3T202 3.7 9.4 1.0
H D:GLN656 3.9 17.6 0.5
H D:GLN656 3.9 17.6 0.5
H D:ILE657 4.0 22.6 1.0
HG22 D:ILE657 4.0 24.9 1.0
HB2 D:ASP653 4.1 15.7 1.0
OD2 D:ASP653 4.1 24.7 1.0
HB D:ILE657 4.1 19.8 1.0
HB2 D:ASP830 4.2 10.3 1.0
CB D:ASP830 4.3 8.6 1.0
CA D:SER655 4.3 12.2 0.4
O3G D:D3T202 4.3 22.7 1.0
CA D:SER655 4.3 12.2 0.6
N D:SER655 4.3 11.3 1.0
HB2 D:TYR654 4.3 13.5 1.0
N D:GLN656 4.4 14.7 1.0
C5' D:D3T202 4.4 8.9 1.0
O D:HOH1690 4.4 30.9 1.0
O1G D:D3T202 4.4 13.1 1.0
O5' D:D3T202 4.4 10.8 1.0
O D:HOH902 4.5 29.9 1.0
HG21 D:ILE657 4.5 24.9 1.0
CA D:TYR654 4.5 9.4 1.0
H5'1 D:D3T202 4.5 10.7 1.0
CG2 D:ILE657 4.6 20.8 1.0
O1B D:D3T202 4.6 12.5 1.0
N D:TYR654 4.6 10.0 1.0
H D:TYR654 4.6 11.9 1.0
C D:SER655 4.6 11.1 1.0
HB3 D:ASP830 4.7 10.3 1.0
O1A D:D3T202 4.7 13.1 1.0
N D:ILE657 4.8 18.8 1.0
CB D:ILE657 4.8 16.5 1.0
CB D:TYR654 4.8 11.2 1.0
CB D:ASP653 4.9 13.1 1.0
HB3 D:TYR654 5.0 13.5 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: Thu Aug 15 09:45:20 2024

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