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Magnesium in PDB 5nkl: Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with the Artificial Base Pair Dds-Dpxtp

Enzymatic activity of Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with the Artificial Base Pair Dds-Dpxtp

All present enzymatic activity of Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with the Artificial Base Pair Dds-Dpxtp:
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 the Artificial Base Pair Dds-Dpxtp, PDB code: 5nkl was solved by K.Betz, A.Marx, K.Diederichs, I.Hirao, M.Kimoto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.10 / 1.70
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 108.777, 108.777, 90.571, 90.00, 90.00, 120.00
R / Rfree (%) 18.1 / 23.7

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 the Artificial Base Pair Dds-Dpxtp (pdb code 5nkl). 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 the Artificial Base Pair Dds-Dpxtp, PDB code: 5nkl:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 5nkl

Go back to Magnesium Binding Sites List in 5nkl
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 the Artificial Base Pair Dds-Dpxtp


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 the Artificial Base Pair Dds-Dpxtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg901

b:46.1
occ:1.00
 H22 A:91T904 1.9 43.5 0.4
OD1 A:ASP785 2.2 40.0 1.0
O6 A:91R905 2.3 35.3 0.5
OD2 A:ASP610 2.3 57.6 1.0
O6 A:91T904 2.3 36.2 0.4
O A:HOH1006 2.4 41.6 1.0
O A:HOH1168 2.6 42.4 1.0
H3'2 B:DOC112 2.8 43.2 1.0
CG A:ASP610 3.1 54.7 1.0
CG A:ASP785 3.1 45.8 1.0
OD1 A:ASP610 3.2 51.6 1.0
HB2 A:GLU786 3.3 52.1 1.0
OD2 A:ASP785 3.3 42.3 1.0
P A:91R905 3.4 38.2 0.5
MG A:MG902 3.4 45.2 1.0
P A:91T904 3.5 38.8 0.4
H5' B:DOC112 3.5 39.8 1.0
H20 A:91R905 3.6 51.5 0.5
O7 A:91R905 3.8 42.6 0.5
O7 A:91T904 3.8 42.6 0.4
O A:HOH1054 3.8 46.0 1.0
C3' B:DOC112 3.8 36.0 1.0
O5 A:91T904 3.8 33.8 0.4
H16 A:91T904 3.8 42.8 0.4
HZ1 A:LYS831 3.8 86.8 1.0
O5 A:91R905 3.8 34.5 0.5
H15 A:91R905 3.9 42.5 0.5
H3'1 B:DOC112 4.1 43.2 1.0
HZ2 A:LYS831 4.1 86.8 1.0
HB3 A:GLU786 4.1 52.1 1.0
CB A:GLU786 4.1 43.4 1.0
HZ3 A:LYS831 4.2 86.8 1.0
H4' B:DOC112 4.2 41.7 1.0
H16 A:91R905 4.2 42.5 0.5
H A:ASP785 4.2 35.9 1.0
H15 A:91T904 4.2 42.8 0.4
OE1 A:GLU786 4.2 42.8 1.0
C13 A:91T904 4.2 35.7 0.4
C13 A:91R905 4.2 35.4 0.5
NZ A:LYS831 4.2 72.3 1.0
C4' B:DOC112 4.3 34.8 1.0
C5' B:DOC112 4.3 33.1 1.0
O A:VAL783 4.5 35.4 1.0
CB A:ASP785 4.5 33.3 1.0
O13 A:91T904 4.5 42.4 0.4
O14 A:91R905 4.5 42.9 0.5
CB A:ASP610 4.5 34.3 1.0
C A:ASP785 4.6 33.2 1.0
H17 A:91R905 4.7 51.1 0.5
HB2 A:ASP610 4.7 41.2 1.0
O A:ASP785 4.7 32.7 1.0
N A:GLU786 4.7 32.4 1.0
O8 A:91R905 4.8 42.6 0.5
HA A:ASP610 4.8 40.2 1.0
O8 A:91T904 4.8 42.5 0.4
HB3 A:ASP785 4.8 40.0 1.0
O5' B:DOC112 4.8 35.5 1.0
N A:ASP785 4.9 29.9 1.0
CA A:ASP785 4.9 37.0 1.0
O9 A:91T904 4.9 41.1 0.4
O9 A:91R905 4.9 41.8 0.5
H2'' B:DOC112 4.9 40.9 1.0
CA A:GLU786 5.0 34.4 1.0
C2' B:DOC112 5.0 34.1 1.0

Magnesium binding site 2 out of 2 in 5nkl

Go back to Magnesium Binding Sites List in 5nkl
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 the Artificial Base Pair Dds-Dpxtp


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 the Artificial Base Pair Dds-Dpxtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg902

b:45.2
occ:1.00
 H20 A:91R905 1.6 51.5 0.5
O14 A:91R905 2.0 42.9 0.5
OD1 A:ASP610 2.0 51.6 1.0
H22 A:91T904 2.0 43.5 0.4
OD2 A:ASP785 2.1 42.3 1.0
O13 A:91T904 2.1 42.4 0.4
O A:TYR611 2.1 42.3 1.0
O6 A:91T904 2.2 36.2 0.4
O6 A:91R905 2.2 35.3 0.5
O9 A:91R905 2.2 41.8 0.5
O9 A:91T904 2.2 41.1 0.4
CG A:ASP610 3.1 54.7 1.0
CG A:ASP785 3.2 45.8 1.0
P1 A:91R905 3.2 42.5 0.5
P1 A:91T904 3.2 43.4 0.4
P2 A:91R905 3.2 48.5 0.5
P2 A:91T904 3.3 48.1 0.4
H16 A:91R905 3.3 42.5 0.5
C A:TYR611 3.3 49.1 1.0
H15 A:91T904 3.3 42.8 0.4
P A:91R905 3.4 38.2 0.5
MG A:MG901 3.4 46.1 1.0
O11 A:91R905 3.5 41.6 0.5
O A:HOH1025 3.5 46.2 1.0
O11 A:91T904 3.5 42.1 0.4
P A:91T904 3.5 38.8 0.4
O8 A:91R905 3.6 42.6 0.5
OD1 A:ASP785 3.6 40.0 1.0
O8 A:91T904 3.7 42.5 0.4
OD2 A:ASP610 3.7 57.6 1.0
O A:HOH1054 3.8 46.0 1.0
HA A:SER612 3.9 63.6 1.0
H A:GLN613 3.9 56.4 1.0
N A:TYR611 4.0 35.9 1.0
HG22 A:ILE614 4.0 94.8 1.0
H A:TYR611 4.1 43.0 1.0
O12 A:91R905 4.1 51.9 0.5
C13 A:91T904 4.2 35.7 0.4
C13 A:91R905 4.2 35.4 0.5
O14 A:91T904 4.2 51.4 0.4
CA A:TYR611 4.2 44.4 1.0
O5 A:91T904 4.2 33.8 0.4
H A:ILE614 4.2 54.3 1.0
HB2 A:TYR611 4.2 47.4 1.0
O13 A:91R905 4.3 43.1 0.5
HZ3 A:LYS663 4.3 75.6 1.0
C A:ASP610 4.3 37.6 1.0
O5 A:91R905 4.3 34.5 0.5
N A:SER612 4.3 45.6 1.0
CB A:ASP610 4.3 34.3 1.0
N A:GLN613 4.4 47.0 1.0
HB2 A:ASP785 4.4 40.0 1.0
CB A:ASP785 4.4 33.3 1.0
O12 A:91T904 4.4 43.0 0.4
CA A:SER612 4.4 53.0 1.0
H16 A:91T904 4.4 42.8 0.4
HB3 A:ASP610 4.4 41.2 1.0
H15 A:91R905 4.5 42.5 0.5
H21 A:91T904 4.5 51.6 0.4
O7 A:91R905 4.5 42.6 0.5
O10 A:91R905 4.6 41.2 0.5
O7 A:91T904 4.6 42.6 0.4
O10 A:91T904 4.6 41.3 0.4
H20 A:91T904 4.6 61.7 0.4
H19 A:91R905 4.6 51.7 0.5
C A:SER612 4.7 44.1 1.0
CB A:TYR611 4.7 39.5 1.0
HA A:ASP610 4.7 40.2 1.0
CA A:ASP610 4.7 33.5 1.0
O A:ASP785 4.7 32.7 1.0
O A:ASP610 4.7 45.9 1.0
HB A:ILE614 4.7 60.2 1.0
HG21 A:ILE614 4.8 94.8 1.0
CG2 A:ILE614 4.8 79.0 1.0
HB3 A:ASP785 4.8 40.0 1.0
HB3 A:TYR611 4.9 47.4 1.0
O A:HOH1168 4.9 42.4 1.0

Reference:

K.Betz, M.Kimoto, K.Diederichs, I.Hirao, A.Marx. Structural Basis For Expansion of the Genetic Alphabet with An Artificial Nucleobase Pair. Angew. Chem. Int. Ed. Engl. V. 56 12000 2017.
ISSN: ESSN 1521-3773
PubMed: 28594080
DOI: 10.1002/ANIE.201704190
Page generated: Sun Sep 29 23:20:27 2024

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