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Magnesium in PDB 3syz: Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in An Open Binary Complex with Dnam As Templating Nucleobase

Enzymatic activity of Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in An Open Binary Complex with Dnam As Templating Nucleobase

All present enzymatic activity of Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in An Open Binary Complex with Dnam As Templating Nucleobase:
2.7.7.7;

Protein crystallography data

The structure of Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in An Open Binary Complex with Dnam As Templating Nucleobase, PDB code: 3syz was solved by K.Betz, K.Diederichs, A.Marx, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.54 / 1.95
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 108.529, 108.529, 90.524, 90.00, 90.00, 120.00
R / Rfree (%) 16 / 20.1

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 An Open Binary Complex with Dnam As Templating Nucleobase (pdb code 3syz). 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 the Large Fragment of Dna Polymerase I From Thermus Aquaticus in An Open Binary Complex with Dnam As Templating Nucleobase, PDB code: 3syz:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 3syz

Go back to Magnesium Binding Sites List in 3syz
Magnesium binding site 1 out of 2 in the Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in An Open Binary Complex with Dnam As Templating Nucleobase


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 An Open Binary Complex with Dnam As Templating Nucleobase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg837

b:64.1
occ:1.00
 O A:HOH856 2.2 44.2 1.0
O A:HOH857 2.2 46.0 1.0
O A:HOH860 2.2 54.5 1.0
O A:HOH858 2.2 52.6 1.0
O A:HOH859 2.2 57.0 1.0
OE2 A:GLU786 3.7 47.9 1.0
OD1 A:ASP610 3.8 50.2 0.8
HB2 A:ASP610 3.9 36.1 0.2
HB3 A:ASP610 3.9 32.8 0.8
O A:HOH246 4.1 42.2 1.0
H3'2 B:DOC112 4.2 35.2 1.0
HG2 A:GLU786 4.4 49.5 1.0
OD1 A:ASP785 4.4 32.7 1.0
OD2 A:ASP785 4.4 36.9 1.0
H3'1 B:DOC112 4.5 35.2 1.0
O A:TYR611 4.7 31.5 1.0
CB A:ASP610 4.7 30.1 0.2
CG A:ASP610 4.7 36.8 0.8
H5' B:DOC112 4.7 35.9 1.0
CD A:GLU786 4.7 39.9 1.0
CB A:ASP610 4.7 27.3 0.8
OD2 A:ASP610 4.8 27.6 0.2
CG A:ASP785 4.8 26.6 1.0
C3' B:DOC112 4.8 29.3 1.0
HB3 A:ASP610 4.9 36.1 0.2
CG A:ASP610 4.9 25.6 0.2

Magnesium binding site 2 out of 2 in 3syz

Go back to Magnesium Binding Sites List in 3syz
Magnesium binding site 2 out of 2 in the Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in An Open Binary Complex with Dnam As Templating Nucleobase


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 An Open Binary Complex with Dnam As Templating Nucleobase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1

b:45.5
occ:1.00
 O B:HOH2 2.2 34.5 1.0
O B:HOH5 2.2 41.5 1.0
O B:HOH6 2.2 48.1 1.0
O B:HOH113 2.2 46.6 1.0
O C:HOH220 2.2 57.4 1.0
O B:HOH3 2.2 30.5 1.0
H11 C:GOL5 3.5 62.0 1.0
HO1 C:GOL5 4.1 46.9 1.0
O6 B:DG108 4.1 28.3 1.0
O B:HOH224 4.2 40.2 1.0
O1 C:GOL5 4.3 39.1 1.0
O C:HOH83 4.3 35.5 1.0
C1 C:GOL5 4.3 51.7 1.0
N7 B:DG107 4.4 29.4 1.0
O6 B:DG107 4.5 26.3 1.0
O B:HOH62 4.5 37.3 1.0
N4 C:DC209 4.5 27.6 1.0
H2 C:GOL5 4.6 69.8 1.0
C5 B:DC106 4.7 34.5 1.0
O B:HOH225 4.8 49.8 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 Aug 11 03:16:39 2025

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