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Magnesium in PDB 5ytg: Structure of Large Fragment of Dna Polymerase I From Thermus Aquaticus Host-Guest Complex with the Unnatural Base I-Fc Pair with Da

Enzymatic activity of Structure of Large Fragment of Dna Polymerase I From Thermus Aquaticus Host-Guest Complex with the Unnatural Base I-Fc Pair with Da

All present enzymatic activity of Structure of Large Fragment of Dna Polymerase I From Thermus Aquaticus Host-Guest Complex with the Unnatural Base I-Fc Pair with Da:
2.7.7.7;

Protein crystallography data

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

Resolution Low / High (Å) 94.45 / 2.07
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 109.063, 109.063, 90.935, 90.00, 90.00, 120.00
R / Rfree (%) 19.8 / 25.2

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Large Fragment of Dna Polymerase I From Thermus Aquaticus Host-Guest Complex with the Unnatural Base I-Fc Pair with Da (pdb code 5ytg). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Structure of Large Fragment of Dna Polymerase I From Thermus Aquaticus Host-Guest Complex with the Unnatural Base I-Fc Pair with Da, PDB code: 5ytg:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 5ytg

Go back to Magnesium Binding Sites List in 5ytg
Magnesium binding site 1 out of 3 in the Structure of Large Fragment of Dna Polymerase I From Thermus Aquaticus Host-Guest Complex with the Unnatural Base I-Fc Pair with Da


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Large Fragment of Dna Polymerase I From Thermus Aquaticus Host-Guest Complex with the Unnatural Base I-Fc Pair with Da within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg902

b:71.6
occ:1.00
 O2B A:DGT901 1.9 43.2 1.0
OD2 A:ASP785 1.9 39.8 1.0
O A:TYR611 2.0 41.3 1.0
O3G A:DGT901 2.1 41.7 1.0
OD1 A:ASP610 2.1 38.9 1.0
O2A A:DGT901 2.2 40.6 1.0
CG A:ASP785 3.0 37.3 1.0
PB A:DGT901 3.1 41.2 1.0
C A:TYR611 3.2 40.6 1.0
CG A:ASP610 3.3 38.7 1.0
PG A:DGT901 3.4 43.7 1.0
OD1 A:ASP785 3.4 37.4 1.0
PA A:DGT901 3.5 39.6 1.0
O3B A:DGT901 3.6 41.7 1.0
O3A A:DGT901 3.7 40.1 1.0
N A:TYR611 3.8 38.0 1.0
O A:HOH1110 3.9 38.7 1.0
OD2 A:ASP610 3.9 38.8 1.0
CA A:TYR611 4.0 39.2 1.0
MG A:MG903 4.0 69.6 1.0
O A:HOH1122 4.1 43.4 1.0
C5' A:DGT901 4.1 38.4 1.0
O2G A:DGT901 4.1 43.8 1.0
N A:SER612 4.2 42.3 1.0
CB A:ASP785 4.3 36.5 1.0
C A:ASP610 4.3 38.6 1.0
O5' A:DGT901 4.3 38.4 1.0
N A:GLN613 4.3 44.1 1.0
CB A:TYR611 4.4 38.4 1.0
O1B A:DGT901 4.4 40.6 1.0
CA A:SER612 4.4 44.3 1.0
O1G A:DGT901 4.4 42.1 1.0
CB A:ASP610 4.5 39.0 1.0
O1A A:DGT901 4.6 37.9 1.0
C A:SER612 4.6 44.2 1.0
CG2 A:ILE614 4.7 36.5 1.0
O A:ASP610 4.8 39.8 1.0
O A:ASP785 4.8 35.6 1.0
N A:ILE614 4.8 39.6 1.0
CA A:ASP610 4.8 37.9 1.0
CB A:ILE614 5.0 37.8 1.0

Magnesium binding site 2 out of 3 in 5ytg

Go back to Magnesium Binding Sites List in 5ytg
Magnesium binding site 2 out of 3 in the Structure of Large Fragment of Dna Polymerase I From Thermus Aquaticus Host-Guest Complex with the Unnatural Base I-Fc Pair with Da


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Large Fragment of Dna Polymerase I From Thermus Aquaticus Host-Guest Complex with the Unnatural Base I-Fc Pair with Da within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg903

b:69.6
occ:1.00
 O A:HOH1012 1.9 35.8 1.0
OD1 A:ASP785 2.0 37.4 1.0
OD2 A:ASP610 2.5 38.8 1.0
O A:HOH1109 2.8 39.3 1.0
O2A A:DGT901 2.9 40.6 1.0
CG A:ASP785 3.1 37.3 1.0
CG A:ASP610 3.2 38.7 1.0
OD1 A:ASP610 3.4 38.9 1.0
C3' B:DOC112 3.6 35.3 1.0
OD2 A:ASP785 3.7 39.8 1.0
CB A:GLU786 3.8 39.3 1.0
PA A:DGT901 3.8 39.6 1.0
O A:VAL783 3.9 33.2 1.0
MG A:MG902 4.0 71.6 1.0
O1A A:DGT901 4.0 37.9 1.0
C5' B:DOC112 4.1 36.2 1.0
C4' B:DOC112 4.1 35.2 1.0
OE1 A:GLU786 4.1 43.7 1.0
C A:ASP785 4.2 35.9 1.0
O5' A:DGT901 4.3 38.4 1.0
O A:HOH1122 4.3 43.4 1.0
CB A:ASP785 4.3 36.5 1.0
N A:GLU786 4.4 36.1 1.0
N A:ASP785 4.4 33.6 1.0
C5' A:DGT901 4.5 38.4 1.0
O A:ASP785 4.5 35.6 1.0
CA A:ASP785 4.5 35.4 1.0
CB A:ASP610 4.5 39.0 1.0
NZ A:LYS831 4.6 52.6 1.0
CA A:GLU786 4.7 37.7 1.0
CG A:GLU786 4.8 41.7 1.0
CD A:GLU786 4.8 43.5 1.0
C2' B:DOC112 4.8 34.5 1.0
O5' B:DOC112 4.9 36.3 1.0
OP1 B:DOC112 5.0 36.5 1.0

Magnesium binding site 3 out of 3 in 5ytg

Go back to Magnesium Binding Sites List in 5ytg
Magnesium binding site 3 out of 3 in the Structure of Large Fragment of Dna Polymerase I From Thermus Aquaticus Host-Guest Complex with the Unnatural Base I-Fc Pair with Da


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Large Fragment of Dna Polymerase I From Thermus Aquaticus Host-Guest Complex with the Unnatural Base I-Fc Pair with Da within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg201

b:81.3
occ:1.00
 O B:HOH313 1.7 39.4 1.0
O B:HOH324 2.2 41.6 1.0
O B:HOH306 2.3 34.2 1.0
O B:HOH302 2.4 41.7 1.0
N7 B:DG107 4.2 32.6 1.0
O C:HOH315 4.3 34.5 1.0
O6 B:DG108 4.4 31.2 1.0
O B:HOH304 4.4 39.7 1.0
O B:HOH314 4.5 46.3 1.0
O6 B:DG107 4.5 30.9 1.0
C5 B:DC106 4.6 35.2 1.0
O C:HOH324 4.6 41.7 1.0
O B:HOH311 4.7 47.1 1.0
N4 C:DC209 4.9 30.1 1.0
C6 B:DC106 4.9 35.4 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: Wed Aug 13 01:05:30 2025

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