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Magnesium in PDB 5ytf: Structure of Large Fragment of Dna Polymerase I From Thermus Aquaticus Host-Guest Complex with the Unnatural Base M-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 M-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 M-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 M-Fc Pair with Da, PDB code: 5ytf 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) 93.26 / 1.98
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 107.690, 107.690, 90.319, 90.00, 90.00, 120.00
R / Rfree (%) 18.1 / 23.3

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 M-Fc Pair with Da (pdb code 5ytf). 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 M-Fc Pair with Da, PDB code: 5ytf:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 5ytf

Go back to Magnesium Binding Sites List in 5ytf
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 M-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 M-Fc Pair with Da within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg901

b:26.2
occ:1.00
 O2B A:DGT903 2.0 25.2 1.0
O3G A:DGT903 2.1 26.9 1.0
O2A A:DGT903 2.1 23.2 1.0
O A:TYR611 2.1 23.6 1.0
OD2 A:ASP785 2.1 23.0 1.0
OD1 A:ASP610 2.2 24.0 1.0
PB A:DGT903 3.1 25.9 1.0
CG A:ASP785 3.1 22.7 1.0
PG A:DGT903 3.3 27.8 1.0
CG A:ASP610 3.3 24.0 1.0
C A:TYR611 3.3 24.2 1.0
PA A:DGT903 3.3 23.8 1.0
OD1 A:ASP785 3.4 22.6 1.0
O3A A:DGT903 3.5 24.4 1.0
MG A:MG902 3.5 24.9 1.0
O3B A:DGT903 3.5 27.1 1.0
O A:HOH1103 3.7 31.4 1.0
OD2 A:ASP610 3.7 23.4 1.0
O A:HOH1074 3.9 24.6 1.0
N A:TYR611 4.0 22.9 1.0
C5' A:DGT903 4.0 22.8 1.0
CA A:TYR611 4.1 23.6 1.0
O5' A:DGT903 4.2 22.2 1.0
O1G A:DGT903 4.2 28.3 1.0
N A:SER612 4.3 24.9 1.0
O2G A:DGT903 4.3 28.9 1.0
C A:ASP610 4.3 23.8 1.0
N A:GLN613 4.4 26.3 1.0
O1B A:DGT903 4.4 25.5 1.0
CB A:ASP785 4.4 21.7 1.0
CA A:SER612 4.5 26.0 1.0
O1A A:DGT903 4.5 23.0 1.0
CB A:TYR611 4.6 23.9 1.0
CB A:ASP610 4.6 24.4 1.0
CG2 A:ILE614 4.6 24.0 1.0
C A:SER612 4.7 26.0 1.0
O A:ASP610 4.7 23.4 1.0
N A:ILE614 4.8 24.8 1.0
O A:HOH1122 4.9 23.2 1.0
O A:ASP785 4.9 20.4 1.0
CA A:ASP610 4.9 23.6 1.0
CB A:ILE614 5.0 24.3 1.0

Magnesium binding site 2 out of 3 in 5ytf

Go back to Magnesium Binding Sites List in 5ytf
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 M-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 M-Fc Pair with Da within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg902

b:24.9
occ:1.00
 OD2 A:ASP610 2.2 23.4 1.0
OD1 A:ASP785 2.3 22.6 1.0
O A:HOH1063 2.3 24.7 1.0
O2A A:DGT903 2.4 23.2 1.0
O A:HOH1122 2.5 23.2 1.0
CG A:ASP610 3.0 24.0 1.0
OD1 A:ASP610 3.1 24.0 1.0
CG A:ASP785 3.3 22.7 1.0
PA A:DGT903 3.5 23.8 1.0
MG A:MG901 3.5 26.2 1.0
OD2 A:ASP785 3.6 23.0 1.0
O A:HOH1103 3.7 31.4 1.0
C3' B:DOC112 3.7 22.3 1.0
O1A A:DGT903 3.9 23.0 1.0
O5' A:DGT903 4.0 22.2 1.0
NZ A:LYS831 4.2 34.2 1.0
CB A:GLU786 4.2 22.5 1.0
C5' B:DOC112 4.3 22.6 1.0
C5' A:DGT903 4.3 22.8 1.0
CB A:ASP610 4.3 24.4 1.0
OE1 A:GLU786 4.3 24.4 1.0
C4' B:DOC112 4.4 22.0 1.0
O A:VAL783 4.5 20.6 1.0
O3G A:DGT903 4.6 26.9 1.0
CB A:ASP785 4.6 21.7 1.0
C A:ASP785 4.6 20.9 1.0
O A:ASP785 4.7 20.4 1.0
N A:GLU786 4.8 20.8 1.0
O5' B:DOC112 4.8 23.9 1.0
O3A A:DGT903 4.9 24.4 1.0
C2' B:DOC112 4.9 22.3 1.0
CA A:ASP785 4.9 21.4 1.0
N A:ASP785 5.0 20.8 1.0
CA A:GLU786 5.0 21.3 1.0

Magnesium binding site 3 out of 3 in 5ytf

Go back to Magnesium Binding Sites List in 5ytf
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 M-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 M-Fc Pair with Da within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg201

b:35.3
occ:1.00
 O B:HOH303 1.9 26.7 1.0
O B:HOH308 2.0 28.2 1.0
O B:HOH306 2.0 28.5 1.0
O C:HOH330 2.0 42.6 1.0
O B:HOH325 2.1 40.1 1.0
O B:HOH326 2.2 28.4 1.0
O6 B:DG108 3.9 24.4 1.0
O B:HOH307 4.0 30.2 1.0
N7 B:DG107 4.2 25.3 1.0
O C:HOH317 4.2 33.4 1.0
O6 B:DG107 4.2 22.4 1.0
O C:HOH310 4.2 33.1 1.0
O B:HOH317 4.4 38.8 1.0
N4 C:DC209 4.5 23.2 1.0
C5 B:DC106 4.5 27.5 1.0
C6 B:DG108 4.9 24.1 1.0
C6 B:DG107 4.9 23.6 1.0
C5 B:DG107 4.9 24.7 1.0
C6 B:DC106 5.0 28.5 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 Sep 30 11:27:45 2024

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