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Magnesium in PDB 3sv4: Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in An Open Binary Complex with Dt 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 Dt 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 Dt 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 Dt As Templating Nucleobase, PDB code: 3sv4 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) 46.93 / 1.99
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 108.388, 108.388, 90.467, 90.00, 90.00, 120.00
R / Rfree (%) 17.9 / 21.6

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 Dt As Templating Nucleobase (pdb code 3sv4). 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 An Open Binary Complex with Dt As Templating Nucleobase, PDB code: 3sv4:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 3sv4

Go back to Magnesium Binding Sites List in 3sv4
Magnesium binding site 1 out of 3 in the Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in An Open Binary Complex with Dt 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 Dt As Templating Nucleobase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg7

b:77.8
occ:1.00
 O A:HOH885 2.2 43.9 1.0
O A:HOH888 2.2 63.9 1.0
O A:HOH889 2.2 66.8 1.0
O A:HOH887 2.2 69.8 1.0
O A:HOH886 2.2 76.4 1.0
OE2 A:GLU786 3.7 49.0 1.0
O A:HOH256 3.9 43.2 1.0
OD2 A:ASP785 4.0 44.8 1.0
HB3 A:ASP610 4.1 50.5 1.0
H3'1 B:DOC112 4.2 35.7 1.0
H3'2 B:DOC112 4.3 35.7 1.0
OD1 A:ASP785 4.4 33.4 1.0
HG2 A:GLU786 4.5 50.8 1.0
CG A:ASP785 4.6 30.7 1.0
C3' B:DOC112 4.7 29.7 1.0
CD A:GLU786 4.7 48.7 1.0
H5' B:DOC112 4.8 38.4 1.0
O A:TYR611 4.9 40.7 1.0
CB A:ASP610 4.9 42.1 1.0
O A:HOH872 4.9 43.3 1.0
HB2 A:ASP610 5.0 50.5 1.0
CG A:GLU786 5.0 42.4 1.0

Magnesium binding site 2 out of 3 in 3sv4

Go back to Magnesium Binding Sites List in 3sv4
Magnesium binding site 2 out of 3 in the Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in An Open Binary Complex with Dt 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 Dt As Templating Nucleobase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg7

b:44.9
occ:1.00
 O B:HOH5 2.2 30.2 1.0
O B:HOH4 2.2 42.1 1.0
O B:HOH6 2.2 41.6 1.0
O B:HOH2 2.2 47.6 1.0
O C:HOH218 2.2 62.3 1.0
O B:HOH115 2.2 39.7 1.0
O B:HOH78 4.1 41.1 1.0
O6 B:DG108 4.1 27.9 1.0
O C:HOH219 4.1 46.4 1.0
O C:HOH44 4.1 32.8 1.0
O B:HOH241 4.2 40.5 1.0
O B:HOH60 4.4 33.5 1.0
O6 B:DG107 4.4 28.0 1.0
O A:HOH255 4.4 43.9 1.0
N7 B:DG107 4.4 34.3 1.0
N4 C:DC209 4.5 26.6 1.0
C5 B:DC106 4.6 36.9 1.0

Magnesium binding site 3 out of 3 in 3sv4

Go back to Magnesium Binding Sites List in 3sv4
Magnesium binding site 3 out of 3 in the Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in An Open Binary Complex with Dt As Templating Nucleobase


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 An Open Binary Complex with Dt As Templating Nucleobase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg7

b:60.1
occ:1.00
 O C:HOH1 2.2 61.4 1.0
O C:HOH221 2.2 63.4 1.0
O B:HOH119 2.2 84.6 1.0
O C:HOH222 2.2 51.4 1.0
O C:HOH4 2.2 58.1 1.0
O C:HOH223 2.2 79.0 1.0
O6 C:DG214 3.8 50.4 1.0
N7 C:DG213 4.0 54.0 1.0
O6 C:DG213 4.3 58.2 1.0
N7 C:DG214 4.7 49.9 1.0
C7 C:DT212 4.7 37.4 1.0
C5 C:DG213 4.8 50.0 1.0
C6 C:DG214 4.8 50.7 1.0
C6 C:DG213 4.9 49.5 1.0
N6 B:DA102 5.0 51.5 1.0
C8 C:DG213 5.0 53.3 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 Aug 11 03:15:34 2025

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