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

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 Dg

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 Dg:
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 Dg, PDB code: 5yth 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) 94.63 / 2.53
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 109.273, 109.273, 91.119, 90.00, 90.00, 120.00
R / Rfree (%) 20.4 / 27.5

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 Dg (pdb code 5yth). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 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 Dg, PDB code: 5yth:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 5yth

Go back to Magnesium Binding Sites List in 5yth
Magnesium binding site 1 out of 2 in the Structure of Large Fragment of Dna Polymerase I From Thermus Aquaticus Host-Guest Complex with the Unnatural Base M-Fc Pair with Dg


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 Dg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg902

b:48.1
occ:1.00
 O3G A:DGT901 1.9 56.6 1.0
O2B A:DGT901 1.9 56.8 1.0
OD2 A:ASP785 2.0 45.8 1.0
O A:TYR611 2.1 52.4 1.0
O2A A:DGT901 2.1 56.1 1.0
OD1 A:ASP610 2.2 52.4 1.0
PB A:DGT901 3.0 56.2 1.0
CG A:ASP785 3.1 44.7 1.0
PG A:DGT901 3.2 57.5 1.0
C A:TYR611 3.3 53.4 1.0
PA A:DGT901 3.3 55.3 1.0
CG A:ASP610 3.3 51.8 1.0
O3B A:DGT901 3.5 56.8 1.0
OD1 A:ASP785 3.6 43.4 1.0
O3A A:DGT901 3.6 55.4 1.0
MG A:MG903 3.8 64.2 1.0
OD2 A:ASP610 3.8 51.5 1.0
O A:HOH1026 3.9 49.6 1.0
O A:HOH1020 4.0 43.9 1.0
C5' A:DGT901 4.0 57.0 1.0
N A:TYR611 4.1 51.8 1.0
O1G A:DGT901 4.1 59.7 1.0
CA A:TYR611 4.1 52.7 1.0
N A:GLN613 4.1 55.0 1.0
O5' A:DGT901 4.2 55.9 1.0
O2G A:DGT901 4.2 57.8 1.0
N A:SER612 4.2 55.2 1.0
CG2 A:ILE614 4.3 49.1 1.0
CA A:SER612 4.3 56.1 1.0
O1B A:DGT901 4.4 56.6 1.0
CB A:ASP785 4.4 44.4 1.0
C A:SER612 4.4 55.9 1.0
C A:ASP610 4.5 52.5 1.0
O1A A:DGT901 4.5 55.6 1.0
N A:ILE614 4.5 52.2 1.0
CB A:TYR611 4.5 51.9 1.0
CB A:ASP610 4.6 52.2 1.0
CB A:ILE614 4.7 50.5 1.0
O A:ASP610 4.9 54.0 1.0
O A:ASP785 4.9 45.8 1.0

Magnesium binding site 2 out of 2 in 5yth

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


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 Dg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg903

b:64.2
occ:1.00
 O A:HOH1022 2.0 37.2 1.0
OD2 A:ASP610 2.2 51.5 1.0
O2A A:DGT901 2.3 56.1 1.0
O B:HOH201 2.4 43.9 1.0
OD1 A:ASP785 2.4 43.4 1.0
PA A:DGT901 3.1 55.3 1.0
CG A:ASP610 3.2 51.8 1.0
O1A A:DGT901 3.2 55.6 1.0
C3' B:DOC112 3.4 47.8 1.0
CG A:ASP785 3.4 44.7 1.0
OD1 A:ASP610 3.4 52.4 1.0
O A:HOH1020 3.6 43.9 1.0
O5' A:DGT901 3.7 55.9 1.0
OD2 A:ASP785 3.7 45.8 1.0
MG A:MG902 3.8 48.1 1.0
NZ A:LYS831 3.8 56.2 1.0
C4' B:DOC112 4.1 47.4 1.0
C5' A:DGT901 4.1 57.0 1.0
C5' B:DOC112 4.2 47.5 1.0
OE1 A:GLU786 4.3 48.5 1.0
CB A:GLU786 4.4 46.9 1.0
O A:VAL783 4.5 43.4 1.0
CB A:ASP610 4.5 52.2 1.0
C2' B:DOC112 4.5 47.6 1.0
O3G A:DGT901 4.6 56.6 1.0
O3A A:DGT901 4.6 55.4 1.0
OP1 B:DOC112 4.7 48.0 1.0
O5' B:DOC112 4.7 47.1 1.0
CB A:ASP785 4.8 44.4 1.0
C A:ASP785 4.8 44.6 1.0
N A:GLU786 5.0 44.5 1.0
O A:ASP785 5.0 45.8 1.0
O2B A:DGT901 5.0 56.8 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 22:14:33 2020

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