Atomistry » Magnesium » PDB 3srf-3t2b » 3sv4
Atomistry »
  Magnesium »
    PDB 3srf-3t2b »
      3sv4 »

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: Thu Aug 15 11:10:50 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy