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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: Tue Aug 12 20:22:45 2025

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