Atomistry » Magnesium » PDB 5ylu-5yve » 5yth
Atomistry »
  Magnesium »
    PDB 5ylu-5yve »
      5yth »

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 Sep 30 11:28:18 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy