Magnesium in PDB 5ytd: Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with the Natural Base Pair 5FC:Dgtp

All present enzymatic activity of Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with the Natural Base Pair 5FC:Dgtp:
2.7.7.7;

The structure of Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with the Natural Base Pair 5FC:Dgtp, PDB code: 5ytd 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)	94.32 / 2.00
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	108.909, 108.909, 90.539, 90.00, 90.00, 120.00
R / Rfree (%)	19.6 / 23.9

The binding sites of Magnesium atom in the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with the Natural Base Pair 5FC:Dgtp (pdb code 5ytd). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with the Natural Base Pair 5FC:Dgtp, PDB code: 5ytd:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with the Natural Base Pair 5FC:Dgtp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with the Natural Base Pair 5FC:Dgtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg902 b:41.4 occ:1.00 O A:TYR611 2.0 42.7 1.0 OD2 A:ASP785 2.0 43.9 1.0 O2G A:DGT901 2.0 68.9 1.0 OD1 A:ASP610 2.1 44.1 1.0 O2B A:DGT901 2.1 66.2 1.0 O2A A:DGT901 2.2 67.4 1.0 CG A:ASP785 3.1 42.7 1.0 C A:TYR611 3.2 43.8 1.0 CG A:ASP610 3.2 43.2 1.0 PB A:DGT901 3.2 66.5 1.0 PG A:DGT901 3.3 70.1 1.0 PA A:DGT901 3.5 66.6 1.0 OD1 A:ASP785 3.6 42.3 1.0 O3B A:DGT901 3.6 68.2 1.0 MG A:MG903 3.7 47.2 1.0 OD2 A:ASP610 3.7 44.2 1.0 O3A A:DGT901 3.8 66.7 1.0 O A:HOH1115 3.8 40.4 1.0 N A:TYR611 3.9 41.4 1.0 CA A:TYR611 4.0 43.4 1.0 O3G A:DGT901 4.0 72.8 1.0 O A:HOH1121 4.1 46.3 1.0 C5' A:DGT901 4.2 65.4 1.0 N A:SER612 4.2 45.4 1.0 C A:ASP610 4.2 42.1 1.0 O5' A:DGT901 4.3 65.9 1.0 CB A:ASP785 4.3 42.4 1.0 N A:GLN613 4.3 46.6 1.0 CA A:SER612 4.4 47.1 1.0 O1G A:DGT901 4.4 70.8 1.0 CB A:TYR611 4.4 43.6 1.0 CB A:ASP610 4.5 42.5 1.0 O1B A:DGT901 4.6 66.7 1.0 C A:SER612 4.6 47.0 1.0 O1A A:DGT901 4.7 68.1 1.0 O A:ASP610 4.7 42.3 1.0 CA A:ASP610 4.8 41.4 1.0 O A:ASP785 4.8 40.1 1.0 CG2 A:ILE614 4.8 42.1 1.0 N A:ILE614 4.9 44.0 1.0 O A:HOH1093 5.0 41.7 1.0

Magnesium binding site 2 out of 2 in the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with the Natural Base Pair 5FC:Dgtp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with the Natural Base Pair 5FC:Dgtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg903 b:47.2 occ:1.00 OD1 A:ASP785 2.2 42.3 1.0 O A:HOH1039 2.2 45.3 1.0 OD2 A:ASP610 2.2 44.2 1.0 O A:HOH1093 2.4 41.7 1.0 O2A A:DGT901 2.5 67.4 1.0 CG A:ASP610 3.0 43.2 1.0 CG A:ASP785 3.2 42.7 1.0 OD1 A:ASP610 3.2 44.1 1.0 OD2 A:ASP785 3.5 43.9 1.0 PA A:DGT901 3.5 66.6 1.0 C3' B:DOC112 3.6 39.5 1.0 MG A:MG902 3.7 41.4 1.0 O A:HOH1121 3.9 46.3 1.0 O1A A:DGT901 3.9 68.1 1.0 C5' B:DOC112 4.0 39.5 1.0 O5' A:DGT901 4.1 65.9 1.0 C4' B:DOC112 4.1 38.7 1.0 CB A:GLU786 4.1 43.9 1.0 O A:VAL783 4.4 38.8 1.0 C5' A:DGT901 4.4 65.4 1.0 NZ A:LYS831 4.4 57.6 1.0 CB A:ASP610 4.4 42.5 1.0 OE1 A:GLU786 4.4 48.9 1.0 O2G A:DGT901 4.5 68.9 1.0 CB A:ASP785 4.5 42.4 1.0 C A:ASP785 4.6 40.7 1.0 N A:GLU786 4.7 41.1 1.0 O A:ASP785 4.7 40.1 1.0 N A:ASP785 4.8 39.5 1.0 C2' B:DOC112 4.9 38.8 1.0 O5' B:DOC112 4.9 40.3 1.0 CA A:ASP785 4.9 41.7 1.0 OP1 B:DOC112 4.9 41.9 1.0 CA A:GLU786 5.0 41.8 1.0 O3A A:DGT901 5.0 66.7 1.0

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