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Magnesium in PDB 3rtv: Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with Natural Primer/Template Dna

Enzymatic activity of Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with Natural Primer/Template Dna

All present enzymatic activity of Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with Natural Primer/Template Dna:
2.7.7.7;

Protein crystallography data

The structure of Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with Natural Primer/Template Dna, PDB code: 3rtv was solved by A.Marx, K.Diederichs, K.Betz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.89 / 1.90
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 108.296, 108.296, 90.381, 90.00, 90.00, 120.00
R / Rfree (%) 16.2 / 20.2

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with Natural Primer/Template Dna (pdb code 3rtv). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with Natural Primer/Template Dna, PDB code: 3rtv:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 3rtv

Go back to Magnesium Binding Sites List in 3rtv
Magnesium binding site 1 out of 3 in the Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with Natural Primer/Template Dna


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 the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with Natural Primer/Template Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg833

b:25.9
occ:1.00
OD2 A:ASP785 2.1 21.8 1.0
O2G A:DCP1 2.1 22.9 1.0
O1A A:DCP1 2.2 19.0 1.0
OD1 A:ASP610 2.2 22.2 1.0
O A:TYR611 2.2 24.5 1.0
O2B A:DCP1 2.3 19.1 1.0
PB A:DCP1 3.2 24.1 1.0
CG A:ASP785 3.2 22.4 1.0
PA A:DCP1 3.3 21.5 1.0
CG A:ASP610 3.3 27.3 1.0
PG A:DCP1 3.3 26.4 1.0
C A:TYR611 3.4 22.5 1.0
OD1 A:ASP785 3.5 21.8 1.0
O3A A:DCP1 3.6 23.5 1.0
MG A:MG2 3.6 25.5 1.0
O3B A:DCP1 3.7 25.1 1.0
O A:HOH6 3.8 23.4 1.0
OD2 A:ASP610 3.9 25.5 1.0
N A:TYR611 4.0 20.8 1.0
C5' A:DCP1 4.0 21.1 1.0
O A:HOH188 4.0 29.5 1.0
CA A:TYR611 4.2 21.9 1.0
O5' A:DCP1 4.2 22.6 1.0
O1G A:DCP1 4.2 24.7 1.0
C A:ASP610 4.3 22.0 1.0
O3G A:DCP1 4.4 22.9 1.0
N A:SER612 4.4 23.9 1.0
N A:GLN613 4.4 22.6 1.0
O2A A:DCP1 4.4 19.9 1.0
O1B A:DCP1 4.5 21.8 1.0
CB A:ASP785 4.5 22.0 1.0
CA A:SER612 4.5 24.1 1.0
CB A:ASP610 4.5 23.5 1.0
CB A:TYR611 4.6 23.1 1.0
C A:SER612 4.7 25.5 1.0
N A:ILE614 4.7 24.1 1.0
CG2 A:ILE614 4.7 18.5 1.0
O A:ASP610 4.8 23.8 1.0
O A:ASP785 4.8 22.2 1.0
CA A:ASP610 4.9 22.4 1.0
O A:HOH842 4.9 24.1 1.0

Magnesium binding site 2 out of 3 in 3rtv

Go back to Magnesium Binding Sites List in 3rtv
Magnesium binding site 2 out of 3 in the Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with Natural Primer/Template Dna


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 the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with Natural Primer/Template Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2

b:25.5
occ:1.00
OD1 A:ASP785 2.3 21.8 1.0
O A:HOH840 2.4 23.5 1.0
O1A A:DCP1 2.4 19.0 1.0
O A:HOH842 2.4 24.1 1.0
OD2 A:ASP610 2.4 25.5 1.0
CG A:ASP610 3.2 27.3 1.0
OD1 A:ASP610 3.3 22.2 1.0
CG A:ASP785 3.3 22.4 1.0
PA A:DCP1 3.5 21.5 1.0
MG A:MG833 3.6 25.9 1.0
OD2 A:ASP785 3.6 21.8 1.0
C3' B:DDG112 3.6 21.4 1.0
O2A A:DCP1 3.7 19.9 1.0
O5' A:DCP1 3.9 22.6 1.0
O A:HOH188 4.0 29.5 1.0
C5' B:DDG112 4.2 22.1 1.0
CB A:GLU786 4.2 22.4 1.0
C4' B:DDG112 4.2 21.7 1.0
NZ A:LYS831 4.3 38.8 1.0
OE1 A:GLU786 4.3 34.4 1.0
C5' A:DCP1 4.3 21.1 1.0
O A:VAL783 4.4 21.4 1.0
CB A:ASP610 4.6 23.5 1.0
C A:ASP785 4.6 21.6 1.0
CB A:ASP785 4.7 22.0 1.0
O2G A:DCP1 4.7 22.9 1.0
O A:ASP785 4.7 22.2 1.0
N A:GLU786 4.8 21.5 1.0
N A:ASP785 4.8 19.3 1.0
O5' B:DDG112 4.8 22.5 1.0
O3A A:DCP1 4.9 23.5 1.0
C2' B:DDG112 4.9 20.5 1.0
OP1 B:DDG112 4.9 27.0 1.0
CA A:ASP785 4.9 20.4 1.0

Magnesium binding site 3 out of 3 in 3rtv

Go back to Magnesium Binding Sites List in 3rtv
Magnesium binding site 3 out of 3 in the Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with Natural Primer/Template Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with Natural Primer/Template Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1

b:56.9
occ:1.00
O C:HOH285 2.1 49.6 1.0
O B:HOH66 2.1 26.4 1.0
O B:HOH255 2.3 40.3 1.0
O B:HOH60 2.3 33.4 1.0
O B:HOH174 2.4 32.0 1.0
O C:HOH272 3.8 38.3 1.0
O C:HOH109 4.2 33.5 1.0
O6 B:DG108 4.3 24.5 1.0
O B:HOH161 4.3 43.2 1.0
N4 C:DC209 4.5 24.0 1.0
O6 B:DG107 4.6 23.9 1.0
N7 B:DG107 4.6 25.4 1.0
O B:HOH83 4.6 36.6 1.0
C5 B:DC106 4.8 30.3 1.0

Reference:

K.Betz, D.A.Malyshev, T.Lavergne, W.Welte, K.Diederichs, T.J.Dwyer, P.Ordoukhanian, F.E.Romesberg, A.Marx. Klentaq Polymerase Replicates Unnatural Base Pairs By Inducing A Watson-Crick Geometry. Nat.Chem.Biol. V. 8 612 2012.
ISSN: ISSN 1552-4450
PubMed: 22660438
DOI: 10.1038/NCHEMBIO.966
Page generated: Mon Dec 14 08:46:17 2020

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