Atomistry » Magnesium » PDB 5n78-5noj » 5nkl
Atomistry »
  Magnesium »
    PDB 5n78-5noj »
      5nkl »

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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy