Magnesium in PDB 5z3n: Structure of Large Fragment of Dna Polymerase I From Thermus Aquaticus Host-Guest Complex with the Unnatural Base 5FC Pair with Da

Enzymatic activity of Structure of Large Fragment of Dna Polymerase I From Thermus Aquaticus Host-Guest Complex with the Unnatural Base 5FC 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 5FC 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 5FC Pair with Da, PDB code: 5z3n 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) 93.48 / 1.91
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 107.947, 107.947, 90.121, 90.00, 90.00, 120.00
R / Rfree (%) 18.3 / 22.9

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 5FC Pair with Da (pdb code 5z3n). 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 5FC Pair with Da, PDB code: 5z3n:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 5z3n

Go back to Magnesium Binding Sites List in 5z3n
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 5FC 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 5FC Pair with Da within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg901

b:16.3
occ:1.00
O2B A:DGT903 2.0 14.7 1.0
OD2 A:ASP785 2.0 14.7 1.0
O A:TYR611 2.1 16.1 1.0
O1G A:DGT903 2.1 15.5 1.0
O2A A:DGT903 2.1 14.8 1.0
OD1 A:ASP610 2.1 14.7 1.0
PB A:DGT903 3.0 14.7 1.0
CG A:ASP785 3.1 13.7 1.0
C A:TYR611 3.3 16.6 1.0
CG A:ASP610 3.3 14.3 1.0
PA A:DGT903 3.3 14.5 1.0
PG A:DGT903 3.3 16.6 1.0
O3B A:DGT903 3.5 15.7 1.0
O3A A:DGT903 3.5 14.8 1.0
MG A:MG902 3.6 15.6 1.0
OD1 A:ASP785 3.6 13.0 1.0
O A:HOH1194 3.8 16.7 1.0
OD2 A:ASP610 3.8 13.8 1.0
N A:TYR611 4.0 15.0 1.0
C5' A:DGT903 4.1 13.8 1.0
O A:HOH1271 4.1 20.9 1.0
CA A:TYR611 4.1 16.0 1.0
O5' A:DGT903 4.2 13.9 1.0
O3G A:DGT903 4.2 16.1 1.0
N A:SER612 4.3 17.7 1.0
N A:GLN613 4.3 19.0 1.0
C A:ASP610 4.4 15.2 1.0
CB A:ASP785 4.4 13.4 1.0
O1B A:DGT903 4.4 15.1 1.0
O2G A:DGT903 4.4 15.9 1.0
CA A:SER612 4.5 18.6 1.0
CB A:ASP610 4.5 14.4 1.0
O1A A:DGT903 4.5 14.0 1.0
CB A:TYR611 4.5 15.9 1.0
C A:SER612 4.6 19.0 1.0
CG2 A:ILE614 4.7 15.2 1.0
N A:ILE614 4.8 17.6 1.0
O A:ASP610 4.8 16.2 1.0
CA A:ASP610 4.9 14.3 1.0
O A:ASP785 4.9 13.2 1.0
CB A:ILE614 5.0 16.1 1.0

Magnesium binding site 2 out of 3 in 5z3n

Go back to Magnesium Binding Sites List in 5z3n
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 5FC 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 5FC Pair with Da within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg902

b:15.6
occ:1.00
OD1 A:ASP785 2.2 13.0 1.0
OD2 A:ASP610 2.3 13.8 1.0
O A:HOH1090 2.3 13.8 1.0
O2A A:DGT903 2.4 14.8 1.0
O B:HOH318 2.6 14.0 1.0
CG A:ASP610 3.0 14.3 1.0
CG A:ASP785 3.1 13.7 1.0
OD1 A:ASP610 3.1 14.7 1.0
OD2 A:ASP785 3.4 14.7 1.0
PA A:DGT903 3.5 14.5 1.0
C3' B:DOC112 3.5 13.1 1.0
MG A:MG901 3.6 16.3 1.0
O1A A:DGT903 3.8 14.0 1.0
O A:HOH1271 3.9 20.9 1.0
O5' A:DGT903 4.0 13.9 1.0
C4' B:DOC112 4.1 12.9 1.0
CB A:GLU786 4.2 12.4 1.0
C5' B:DOC112 4.2 12.8 1.0
NZ A:LYS831 4.3 24.1 1.0
C5' A:DGT903 4.3 13.8 1.0
OE1 A:GLU786 4.3 13.2 1.0
O A:VAL783 4.4 10.9 1.0
CB A:ASP610 4.4 14.4 1.0
CB A:ASP785 4.5 13.4 1.0
C A:ASP785 4.6 12.5 1.0
O1G A:DGT903 4.6 15.5 1.0
O A:ASP785 4.7 13.2 1.0
N A:GLU786 4.7 12.0 1.0
C2' B:DOC112 4.7 13.0 1.0
N A:ASP785 4.8 11.8 1.0
O5' B:DOC112 4.9 12.5 1.0
O3A A:DGT903 4.9 14.8 1.0
CA A:ASP785 4.9 12.6 1.0
OP1 B:DOC112 5.0 13.4 1.0

Magnesium binding site 3 out of 3 in 5z3n

Go back to Magnesium Binding Sites List in 5z3n
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 5FC 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 5FC Pair with Da within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg201

b:32.2
occ:1.00
O B:HOH302 1.9 15.0 1.0
O B:HOH312 2.0 15.5 1.0
O C:HOH447 2.0 37.5 1.0
O B:HOH306 2.1 21.5 1.0
O B:HOH333 2.4 17.3 1.0
O6 B:DG108 4.1 14.6 1.0
O C:HOH437 4.1 21.5 1.0
O6 B:DG107 4.2 16.4 1.0
O B:HOH313 4.2 22.2 1.0
O B:HOH310 4.2 20.9 1.0
N7 B:DG107 4.3 17.1 1.0
O B:HOH327 4.3 27.3 1.0
N4 C:DC209 4.4 17.6 1.0
O C:HOH416 4.4 15.9 1.0
C5 B:DC106 4.4 21.6 1.0
C6 B:DC106 4.9 22.1 1.0
C6 B:DG107 4.9 16.3 1.0
C5 B:DG107 5.0 16.6 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 22:15:59 2020

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