Magnesium in PDB 5yte: Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with with Natural Dt:Datp Base Pair

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

The structure of Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with with Natural Dt:Datp Base Pair, PDB code: 5yte 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)	94.54 / 2.21
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	109.169, 109.169, 91.003, 90.00, 90.00, 120.00
R / Rfree (%)	18.4 / 23.8

The binding sites of Magnesium atom in the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with with Natural Dt:Datp Base Pair (pdb code 5yte). 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 with Natural Dt:Datp Base Pair, PDB code: 5yte:
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 with Natural Dt:Datp Base Pair


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 with Natural Dt:Datp Base Pair within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg902 b:52.8 occ:1.00 OD1 A:ASP785 2.3 38.3 1.0 O A:HOH1065 2.3 49.4 1.0 OD2 A:ASP610 2.4 43.8 1.0 O1A A:DTP901 2.4 48.4 1.0 OD1 A:ASP610 3.0 44.8 1.0 CG A:ASP610 3.0 43.5 1.0 CG A:ASP785 3.2 38.9 1.0 OD2 A:ASP785 3.4 41.2 1.0 PA A:DTP901 3.5 47.5 1.0 MG A:MG903 3.6 41.3 1.0 O A:HOH1103 3.7 42.3 1.0 C3' B:DOC112 3.7 35.2 1.0 O2A A:DTP901 3.8 48.4 1.0 O5' A:DTP901 4.0 45.7 1.0 CB A:GLU786 4.1 40.0 1.0 C4' B:DOC112 4.3 35.0 1.0 OE1 A:GLU786 4.3 44.8 1.0 CB A:ASP610 4.4 41.6 1.0 C5' B:DOC112 4.5 35.2 1.0 NZ A:LYS831 4.5 49.3 1.0 O A:VAL783 4.5 31.8 1.0 C5' A:DTP901 4.5 45.1 1.0 C A:ASP785 4.6 37.1 1.0 CB A:ASP785 4.6 37.6 1.0 N A:GLU786 4.6 37.0 1.0 O1G A:DTP901 4.6 50.0 1.0 O A:ASP785 4.7 38.4 1.0 CA A:GLU786 4.9 38.4 1.0 O5' B:DOC112 4.9 34.3 1.0 C2' B:DOC112 4.9 34.6 1.0 OP1 B:DOC112 4.9 36.0 1.0 CA A:ASP785 5.0 36.3 1.0 O3A A:DTP901 5.0 47.4 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 with Natural Dt:Datp Base Pair


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 with Natural Dt:Datp Base Pair within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg903 b:41.3 occ:1.00 O A:TYR611 1.9 39.6 1.0 OD2 A:ASP785 2.1 41.2 1.0 O1G A:DTP901 2.1 50.0 1.0 OD1 A:ASP610 2.1 44.8 1.0 O1B A:DTP901 2.2 45.9 1.0 O1A A:DTP901 2.3 48.4 1.0 C A:TYR611 3.1 40.7 1.0 CG A:ASP785 3.2 38.9 1.0 CG A:ASP610 3.3 43.5 1.0 PB A:DTP901 3.4 47.5 1.0 PG A:DTP901 3.4 50.4 1.0 PA A:DTP901 3.6 47.5 1.0 MG A:MG902 3.6 52.8 1.0 OD1 A:ASP785 3.7 38.3 1.0 N A:TYR611 3.8 38.9 1.0 O3B A:DTP901 3.8 47.9 1.0 O A:HOH1131 3.9 41.3 1.0 O3A A:DTP901 3.9 47.4 1.0 O A:HOH1103 3.9 42.3 1.0 OD2 A:ASP610 3.9 43.8 1.0 CA A:TYR611 3.9 39.6 1.0 N A:SER612 4.1 43.5 1.0 C A:ASP610 4.1 40.1 1.0 O2G A:DTP901 4.3 51.3 1.0 C5' A:DTP901 4.3 45.1 1.0 CA A:SER612 4.3 44.9 1.0 O5' A:DTP901 4.3 45.7 1.0 N A:GLN613 4.3 44.7 1.0 CB A:ASP785 4.4 37.6 1.0 CB A:TYR611 4.4 38.8 1.0 O3G A:DTP901 4.5 51.1 1.0 CB A:ASP610 4.5 41.6 1.0 O A:ASP610 4.6 41.1 1.0 C A:SER612 4.6 44.9 1.0 O2B A:DTP901 4.7 45.4 1.0 O2A A:DTP901 4.7 48.4 1.0 O A:ASP785 4.7 38.4 1.0 CA A:ASP610 4.7 40.0 1.0 CG2 A:ILE614 4.9 39.7 1.0 N A:ILE614 5.0 42.0 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