Magnesium in PDB 5ytc: Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with the Unnatural Base M-Fc Pair with Datp in the Active Site

Enzymatic activity of Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with the Unnatural Base M-Fc Pair with Datp in the Active Site

All present enzymatic activity of Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with the Unnatural Base M-Fc Pair with Datp in the Active Site:
2.7.7.7;

Protein crystallography data

The structure of Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with the Unnatural Base M-Fc Pair with Datp in the Active Site, PDB code: 5ytc was solved by H.Zeng, M.Mondal, R.Y.Song, J.Zhang, B.Xia, C.Q.Yi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 94.30 / 2.28
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 108.886, 108.886, 90.533, 90.00, 90.00, 120.00
R / Rfree (%) 19.4 / 25.8

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with the Unnatural Base M-Fc Pair with Datp in the Active Site (pdb code 5ytc). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with the Unnatural Base M-Fc Pair with Datp in the Active Site, PDB code: 5ytc:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 5ytc

Go back to Magnesium Binding Sites List in 5ytc
Magnesium binding site 1 out of 2 in the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with the Unnatural Base M-Fc Pair with Datp in the Active Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with the Unnatural Base M-Fc Pair with Datp in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg903

b:52.9
occ:1.00
 O A:HOH1001 2.2 46.2 1.0
OD2 A:ASP610 2.2 31.1 1.0
OD1 A:ASP785 2.4 29.1 1.0
O1A A:DTP902 2.4 47.2 1.0
CG A:ASP610 3.0 30.6 1.0
OE1 A:GLU786 3.1 30.9 1.0
OD1 A:ASP610 3.1 32.5 1.0
O A:HOH1127 3.2 43.9 1.0
CG A:ASP785 3.3 29.8 1.0
OD2 A:ASP785 3.4 32.6 1.0
PA A:DTP902 3.5 46.6 1.0
O2A A:DTP902 3.6 47.3 1.0
C3' B:DOC113 3.8 22.8 1.0
C5' B:DOC113 4.0 22.1 1.0
O5' A:DTP902 4.1 44.2 1.0
CD A:GLU786 4.1 30.5 1.0
C4' B:DOC113 4.2 22.1 1.0
CB A:GLU786 4.3 28.1 1.0
CB A:ASP610 4.5 29.8 1.0
CG A:GLU786 4.5 28.4 1.0
O5' B:DOC113 4.5 21.9 1.0
O3G A:DTP902 4.5 48.0 1.0
C5' A:DTP902 4.6 43.6 1.0
CB A:ASP785 4.7 28.1 1.0
C A:ASP785 4.7 26.7 1.0
NZ A:LYS831 4.7 43.4 1.0
N A:GLU786 4.8 25.9 1.0
O A:ASP785 4.8 27.4 1.0
O3A A:DTP902 4.9 46.5 1.0
OP1 B:DOC113 4.9 23.1 1.0
O A:VAL783 4.9 21.2 1.0

Magnesium binding site 2 out of 2 in 5ytc

Go back to Magnesium Binding Sites List in 5ytc
Magnesium binding site 2 out of 2 in the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with the Unnatural Base M-Fc Pair with Datp in the Active Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with the Unnatural Base M-Fc Pair with Datp in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg201

b:37.7
occ:1.00
 O B:HOH324 2.0 32.4 1.0
O C:HOH329 2.0 31.0 1.0
O B:HOH301 2.2 22.6 1.0
O B:HOH303 2.2 22.0 1.0
O B:HOH325 2.3 32.5 1.0
O B:HOH307 2.4 18.4 1.0
O B:HOH310 4.1 43.1 1.0
O C:HOH309 4.1 23.2 1.0
O C:HOH307 4.2 28.1 1.0
O6 B:DG108 4.3 21.4 1.0
N7 B:DG107 4.6 16.1 1.0
N4 C:DC209 4.7 20.5 1.0
O6 B:DG107 4.7 15.9 1.0
O B:HOH315 4.7 17.4 1.0
C5 B:DC106 4.8 19.1 1.0

Reference:

H.Zeng, M.Mondal, R.Song, J.Zhang, B.Xia, M.Liu, C.Zhu, B.He, Y.Q.Gao, C.Yi. Unnatural Cytosine Bases Recognized As Thymines By Dna Polymerases By the Formation of the Watson-Crick Geometry. Angew. Chem. Int. Ed. Engl. V. 58 130 2019.
ISSN: ESSN 1521-3773
PubMed: 30407705
DOI: 10.1002/ANIE.201807845
Page generated: Mon Dec 14 22:14:28 2020

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