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Magnesium in PDB 5e41: Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with 5-(N-(10- Hydroxydecanoyl)-Aminopentenyl)-2'-Deoxyuridine-Triphosphate

Enzymatic activity of Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with 5-(N-(10- Hydroxydecanoyl)-Aminopentenyl)-2'-Deoxyuridine-Triphosphate

All present enzymatic activity of Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with 5-(N-(10- Hydroxydecanoyl)-Aminopentenyl)-2'-Deoxyuridine-Triphosphate:
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 5-(N-(10- Hydroxydecanoyl)-Aminopentenyl)-2'-Deoxyuridine-Triphosphate, PDB code: 5e41 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) 46.67 / 1.80
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 107.774, 107.774, 89.614, 90.00, 90.00, 120.00
R / Rfree (%) 19.2 / 23.6

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 A Closed Ternary Complex with 5-(N-(10- Hydroxydecanoyl)-Aminopentenyl)-2'-Deoxyuridine-Triphosphate (pdb code 5e41). 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 A Closed Ternary Complex with 5-(N-(10- Hydroxydecanoyl)-Aminopentenyl)-2'-Deoxyuridine-Triphosphate, PDB code: 5e41:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 5e41

Go back to Magnesium Binding Sites List in 5e41
Magnesium binding site 1 out of 2 in the Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with 5-(N-(10- Hydroxydecanoyl)-Aminopentenyl)-2'-Deoxyuridine-Triphosphate


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 5-(N-(10- Hydroxydecanoyl)-Aminopentenyl)-2'-Deoxyuridine-Triphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg901

b:38.6
occ:1.00
OD1 A:ASP785 2.2 40.6 1.0
OD2 A:ASP610 2.4 39.0 1.0
O2A A:AUL903 2.4 34.3 1.0
O A:HOH1108 2.5 34.0 1.0
O A:HOH1054 2.6 43.5 1.0
H3'2 B:DOC112 2.7 49.2 1.0
CG A:ASP610 3.1 41.0 1.0
CG A:ASP785 3.1 39.7 1.0
OD1 A:ASP610 3.2 40.3 1.0
PA A:AUL903 3.4 34.7 1.0
OD2 A:ASP785 3.4 46.6 1.0
MG A:MG902 3.4 35.3 1.0
HB2 A:GLU786 3.5 46.9 1.0
H3'1 B:DOC112 3.5 49.2 1.0
C3' B:DOC112 3.5 41.0 1.0
O A:HOH1191 3.6 44.9 1.0
O1A A:AUL903 3.7 37.8 1.0
HZ1 A:LYS831 3.8 90.3 1.0
H5' B:DOC112 3.8 48.0 1.0
O5' A:AUL903 3.9 36.4 1.0
H36 A:AUL903 3.9 47.4 1.0
H4' B:DOC112 4.2 48.7 1.0
HB3 A:GLU786 4.2 46.9 1.0
C4' B:DOC112 4.2 40.6 1.0
H A:ASP785 4.2 39.4 1.0
CB A:GLU786 4.3 39.0 1.0
C5' A:AUL903 4.3 39.5 1.0
H35 A:AUL903 4.3 47.4 1.0
C5' B:DOC112 4.4 40.0 1.0
NZ A:LYS831 4.4 75.2 1.0
OE1 A:GLU786 4.4 39.6 1.0
O1G A:AUL903 4.5 33.2 1.0
HZ2 A:LYS831 4.5 90.3 1.0
CB A:ASP610 4.5 39.5 1.0
CB A:ASP785 4.5 34.1 1.0
HZ3 A:LYS831 4.5 90.3 1.0
O A:VAL783 4.5 32.3 1.0
C A:ASP785 4.6 37.2 1.0
HB2 A:ASP610 4.6 47.4 1.0
HZ1 A:LYS663 4.7 56.8 1.0
O A:ASP785 4.7 37.5 1.0
C2' B:DOC112 4.8 43.4 1.0
O3A A:AUL903 4.8 36.7 1.0
N A:GLU786 4.8 36.4 1.0
H2'' B:DOC112 4.8 52.1 1.0
HA A:ASP610 4.8 42.0 1.0
HB3 A:ASP785 4.9 40.9 1.0
O5' B:DOC112 4.9 36.9 1.0
CA A:ASP785 4.9 34.2 1.0
N A:ASP785 4.9 32.9 1.0
O1B A:AUL903 4.9 42.5 1.0

Magnesium binding site 2 out of 2 in 5e41

Go back to Magnesium Binding Sites List in 5e41
Magnesium binding site 2 out of 2 in the Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with 5-(N-(10- Hydroxydecanoyl)-Aminopentenyl)-2'-Deoxyuridine-Triphosphate


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 5-(N-(10- Hydroxydecanoyl)-Aminopentenyl)-2'-Deoxyuridine-Triphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg902

b:35.3
occ:1.00
OD2 A:ASP785 2.0 46.6 1.0
O2A A:AUL903 2.0 34.3 1.0
O1B A:AUL903 2.0 42.5 1.0
O1G A:AUL903 2.1 33.2 1.0
OD1 A:ASP610 2.1 40.3 1.0
O A:TYR611 2.2 37.8 1.0
CG A:ASP785 3.1 39.7 1.0
PB A:AUL903 3.2 39.2 1.0
H35 A:AUL903 3.2 47.4 1.0
CG A:ASP610 3.3 41.0 1.0
PA A:AUL903 3.3 34.7 1.0
C A:TYR611 3.4 40.9 1.0
PG A:AUL903 3.4 40.3 1.0
MG A:MG901 3.4 38.6 1.0
OD1 A:ASP785 3.5 40.6 1.0
O3A A:AUL903 3.6 36.7 1.0
O3B A:AUL903 3.7 38.2 1.0
HG22 A:ILE614 3.7 44.8 1.0
O A:HOH1115 3.8 35.8 1.0
OD2 A:ASP610 3.8 39.0 1.0
HA A:SER612 4.0 56.5 1.0
H A:GLN613 4.0 50.5 1.0
C5' A:AUL903 4.0 39.5 1.0
H A:ILE614 4.0 39.8 1.0
N A:TYR611 4.1 38.6 1.0
HB2 A:TYR611 4.1 46.1 1.0
O5' A:AUL903 4.1 36.4 1.0
O A:HOH1191 4.1 44.9 1.0
H A:TYR611 4.2 46.4 1.0
CA A:TYR611 4.2 38.4 1.0
H36 A:AUL903 4.2 47.4 1.0
O3G A:AUL903 4.2 41.5 1.0
HB2 A:ASP785 4.3 40.9 1.0
CB A:ASP785 4.3 34.1 1.0
N A:SER612 4.3 44.8 1.0
C A:ASP610 4.4 37.6 1.0
N A:GLN613 4.4 42.1 1.0
HB A:ILE614 4.5 43.1 1.0
O1A A:AUL903 4.5 37.8 1.0
O2G A:AUL903 4.5 37.0 1.0
H32 A:AUL903 4.5 43.6 1.0
HG21 A:ILE614 4.5 44.8 1.0
CG2 A:ILE614 4.5 37.3 1.0
CA A:SER612 4.5 47.1 1.0
O2B A:AUL903 4.5 38.5 1.0
CB A:ASP610 4.5 39.5 1.0
CB A:TYR611 4.6 38.5 1.0
HB3 A:TYR611 4.7 46.1 1.0
HB3 A:ASP610 4.7 47.4 1.0
C A:SER612 4.7 44.5 1.0
HB3 A:ASP785 4.7 40.9 1.0
O A:ASP785 4.8 37.5 1.0
N A:ILE614 4.8 33.1 1.0
O A:ASP610 4.8 38.5 1.0
HA A:ASP610 4.8 42.0 1.0
HZ1 A:LYS663 4.8 56.8 1.0
CA A:ASP610 4.9 35.0 1.0
CB A:ILE614 5.0 35.9 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 Dec 14 20:13:43 2020

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