Atomistry » Magnesium » PDB 5ske-5t19 » 5szt
Atomistry »
  Magnesium »
    PDB 5ske-5t19 »
      5szt »

Magnesium in PDB 5szt: Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with 7-(N-(10- Hydroxydecanoyl)-Aminopentenyl)-7-Deaza-2'-Datp

Enzymatic activity of Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with 7-(N-(10- Hydroxydecanoyl)-Aminopentenyl)-7-Deaza-2'-Datp

All present enzymatic activity of Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with 7-(N-(10- Hydroxydecanoyl)-Aminopentenyl)-7-Deaza-2'-Datp:
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 7-(N-(10- Hydroxydecanoyl)-Aminopentenyl)-7-Deaza-2'-Datp, PDB code: 5szt was solved by A.Hottin, K.Betz, A.Marx, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.95 / 1.80
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 108.425, 108.425, 90.615, 90.00, 90.00, 120.00
R / Rfree (%) 19.4 / 23

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 7-(N-(10- Hydroxydecanoyl)-Aminopentenyl)-7-Deaza-2'-Datp (pdb code 5szt). 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 7-(N-(10- Hydroxydecanoyl)-Aminopentenyl)-7-Deaza-2'-Datp, PDB code: 5szt:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 5szt

Go back to Magnesium Binding Sites List in 5szt
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 7-(N-(10- Hydroxydecanoyl)-Aminopentenyl)-7-Deaza-2'-Datp


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 7-(N-(10- Hydroxydecanoyl)-Aminopentenyl)-7-Deaza-2'-Datp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg901

b:34.2
occ:1.00
 O2G A:72J907 1.9 31.4 0.5
O3G A:72J907 2.0 31.4 0.5
OD2 A:ASP785 2.0 38.0 1.0
O1A A:72J907 2.0 32.2 0.5
O2B A:72J907 2.0 32.8 0.5
O1A A:72J907 2.0 32.3 0.5
O2B A:72J907 2.0 32.8 0.5
OD1 A:ASP610 2.1 39.5 1.0
O A:TYR611 2.2 48.6 1.0
CG A:ASP785 3.1 35.3 1.0
PB A:72J907 3.1 37.0 0.5
PB A:72J907 3.1 37.0 0.5
H6 A:72J907 3.2 39.6 0.5
H6 A:72J907 3.2 39.5 0.5
CG A:ASP610 3.2 38.8 1.0
PA A:72J907 3.2 34.0 0.5
PA A:72J907 3.3 33.8 0.5
PG A:72J907 3.3 39.9 0.5
PG A:72J907 3.3 39.6 0.5
C A:TYR611 3.4 47.8 1.0
O3A A:72J907 3.4 31.8 0.5
O3A A:72J907 3.5 32.0 0.5
O3B A:72J907 3.5 31.4 0.5
OD1 A:ASP785 3.5 37.6 1.0
O3B A:72J907 3.5 31.4 0.5
MG A:MG902 3.6 41.1 1.0
OD2 A:ASP610 3.7 37.4 1.0
O A:HOH1080 3.8 34.5 1.0
O A:HOH1145 3.9 39.2 1.0
HG22 A:ILE614 3.9 44.6 1.0
H A:GLN613 3.9 50.8 1.0
H A:ILE614 4.0 43.1 1.0
HA A:SER612 4.0 55.4 1.0
N A:TYR611 4.0 40.8 1.0
C5' A:72J907 4.1 33.0 0.5
C5' A:72J907 4.1 32.9 0.5
HB2 A:TYR611 4.1 46.1 1.0
H A:TYR611 4.1 49.0 1.0
O2G A:72J907 4.1 34.7 0.5
O5' A:72J907 4.2 29.6 0.5
O5' A:72J907 4.2 29.6 0.5
O1G A:72J907 4.2 34.6 0.5
CA A:TYR611 4.2 42.7 1.0
HZ1 A:LYS663 4.2 59.4 1.0
O3G A:72J907 4.3 33.4 0.5
C A:ASP610 4.4 34.2 1.0
CB A:ASP785 4.4 34.5 1.0
O2A A:72J907 4.4 31.8 0.5
O1G A:72J907 4.4 33.6 0.5
HB2 A:ASP785 4.4 41.4 1.0
N A:SER612 4.4 45.4 1.0
N A:GLN613 4.4 42.3 1.0
H5 A:72J907 4.4 39.6 0.5
O2A A:72J907 4.4 31.8 0.5
HB A:ILE614 4.4 45.8 1.0
H5 A:72J907 4.4 39.5 0.5
O1B A:72J907 4.5 32.7 0.5
O1B A:72J907 4.5 32.6 0.5
CB A:ASP610 4.5 37.0 1.0
CA A:SER612 4.6 46.2 1.0
CB A:TYR611 4.6 38.5 1.0
HG21 A:ILE614 4.6 44.6 1.0
CG2 A:ILE614 4.6 37.2 1.0
HB3 A:ASP610 4.7 44.4 1.0
C A:SER612 4.7 41.9 1.0
HB3 A:ASP785 4.8 41.4 1.0
O A:ASP610 4.8 38.1 1.0
HB3 A:TYR611 4.8 46.1 1.0
N A:ILE614 4.8 36.0 1.0
O A:ASP785 4.8 31.1 1.0
HA A:ASP610 4.9 40.5 1.0
CA A:ASP610 4.9 33.8 1.0
O A:HOH1084 5.0 37.8 1.0

Magnesium binding site 2 out of 3 in 5szt

Go back to Magnesium Binding Sites List in 5szt
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 7-(N-(10- Hydroxydecanoyl)-Aminopentenyl)-7-Deaza-2'-Datp


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 7-(N-(10- Hydroxydecanoyl)-Aminopentenyl)-7-Deaza-2'-Datp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg902

b:41.1
occ:1.00
 OD1 A:ASP785 2.2 37.6 1.0
O A:HOH1064 2.3 29.7 1.0
OD2 A:ASP610 2.3 37.4 1.0
O1A A:72J907 2.4 32.3 0.5
O1A A:72J907 2.4 32.2 0.5
O A:HOH1084 2.5 37.8 1.0
H3'2 B:DOC112 2.7 39.5 1.0
CG A:ASP610 3.1 38.8 1.0
CG A:ASP785 3.2 35.3 1.0
OD1 A:ASP610 3.2 39.5 1.0
PA A:72J907 3.4 33.8 0.5
PA A:72J907 3.4 34.0 0.5
HB2 A:GLU786 3.4 44.8 1.0
OD2 A:ASP785 3.5 38.0 1.0
C3' B:DOC112 3.5 32.9 1.0
MG A:MG901 3.6 34.2 1.0
H3'1 B:DOC112 3.6 39.5 1.0
H5' B:DOC112 3.7 40.9 1.0
O2A A:72J907 3.7 31.8 0.5
O2A A:72J907 3.7 31.8 0.5
O A:HOH1145 3.8 39.2 1.0
HZ1 A:LYS831 3.8 64.9 1.0
O5' A:72J907 3.9 29.6 0.5
O5' A:72J907 3.9 29.6 0.5
H5 A:72J907 4.0 39.5 0.5
H5 A:72J907 4.0 39.6 0.5
H4' B:DOC112 4.1 40.3 1.0
HB3 A:GLU786 4.1 44.8 1.0
H A:ASP785 4.2 36.4 1.0
HZ2 A:LYS831 4.2 64.9 1.0
C4' B:DOC112 4.2 33.6 1.0
CB A:GLU786 4.2 37.3 1.0
H6 A:72J907 4.2 39.5 0.5
H6 A:72J907 4.2 39.6 0.5
OE1 A:GLU786 4.3 36.0 1.0
C5' A:72J907 4.3 32.9 0.5
C5' A:72J907 4.3 33.0 0.5
C5' B:DOC112 4.3 34.1 1.0
NZ A:LYS831 4.4 54.1 1.0
CB A:ASP610 4.4 37.0 1.0
O A:VAL783 4.4 34.5 1.0
HZ3 A:LYS831 4.5 64.9 1.0
HB2 A:ASP610 4.5 44.4 1.0
CB A:ASP785 4.5 34.5 1.0
C A:ASP785 4.6 29.6 1.0
O3G A:72J907 4.6 31.4 0.5
O2G A:72J907 4.6 31.4 0.5
O A:ASP785 4.7 31.1 1.0
N A:GLU786 4.8 33.5 1.0
O3A A:72J907 4.8 32.0 0.5
C2' B:DOC112 4.8 31.5 1.0
HB3 A:ASP785 4.8 41.4 1.0
O3A A:72J907 4.8 31.8 0.5
HA A:ASP610 4.8 40.5 1.0
HZ1 A:LYS663 4.8 59.4 1.0
N A:ASP785 4.9 30.3 1.0
CA A:ASP785 4.9 29.9 1.0
H2'' B:DOC112 4.9 37.8 1.0
O5' B:DOC112 4.9 30.8 1.0

Magnesium binding site 3 out of 3 in 5szt

Go back to Magnesium Binding Sites List in 5szt
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 7-(N-(10- Hydroxydecanoyl)-Aminopentenyl)-7-Deaza-2'-Datp


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 7-(N-(10- Hydroxydecanoyl)-Aminopentenyl)-7-Deaza-2'-Datp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg201

b:52.2
occ:1.00
 O B:HOH313 2.2 44.1 1.0
O B:HOH301 2.2 48.9 1.0
O B:HOH322 2.2 49.4 1.0
O C:HOH430 2.2 52.0 1.0
O B:HOH323 2.2 48.5 1.0
O B:HOH315 2.2 47.4 1.0
O C:HOH406 3.9 38.6 1.0
O6 B:DG108 4.0 30.0 1.0
O C:HOH424 4.1 54.6 1.0
H42 C:DC209 4.2 36.5 1.0
O B:HOH307 4.2 40.6 1.0
H41 C:DC209 4.3 36.5 1.0
N7 B:DG107 4.5 30.5 1.0
H5 B:DC106 4.5 40.7 1.0
O6 B:DG107 4.5 30.4 1.0
N4 C:DC209 4.6 30.4 1.0
O B:HOH318 4.7 42.7 1.0
C5 B:DC106 5.0 33.9 1.0

Reference:

A.Hottin, K.Betz, K.Diederichs, A.Marx. Structural Basis For the Klentaq Dna Polymerase Catalysed Incorporation of Alkene- Versus Alkyne-Modified Nucleotides. Chemistry V. 23 2109 2017.
ISSN: ISSN 1521-3765
PubMed: 27901305
DOI: 10.1002/CHEM.201604515
Page generated: Mon Sep 30 04:42:33 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