Magnesium in PDB 5w6k: Structure of Mutant Taq Polymerase Incorporating Unnatural Base Pairs Z:P

All present enzymatic activity of Structure of Mutant Taq Polymerase Incorporating Unnatural Base Pairs Z:P:
2.7.7.7;

The structure of Structure of Mutant Taq Polymerase Incorporating Unnatural Base Pairs Z:P, PDB code: 5w6k was solved by I.Singh, M.M.Georgiadis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.98 / 2.34
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	109.306, 109.306, 90.871, 90.00, 90.00, 120.00
R / Rfree (%)	22.4 / 27.5

The binding sites of Magnesium atom in the Structure of Mutant Taq Polymerase Incorporating Unnatural Base Pairs Z:P (pdb code 5w6k). 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 Mutant Taq Polymerase Incorporating Unnatural Base Pairs Z:P, PDB code: 5w6k:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structure of Mutant Taq Polymerase Incorporating Unnatural Base Pairs Z:P


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Mutant Taq Polymerase Incorporating Unnatural Base Pairs Z:P within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg902 b:32.3 occ:1.00 O A:TYR611 1.9 35.6 1.0 O2B A:A5J901 2.0 32.5 1.0 O2G A:A5J901 2.1 34.0 1.0 O1A A:A5J901 2.2 32.3 1.0 OD1 A:ASP610 2.2 34.4 1.0 OD2 A:ASP785 2.2 27.2 1.0 PB A:A5J901 3.0 32.3 1.0 C A:TYR611 3.1 35.4 1.0 PG A:A5J901 3.2 34.8 1.0 CG A:ASP785 3.3 26.0 1.0 PA A:A5J901 3.4 32.4 1.0 CG A:ASP610 3.4 33.8 1.0 HA A:SER612 3.4 45.9 1.0 O3B A:A5J901 3.4 34.1 1.0 H5'2 A:A5J901 3.4 37.0 1.0 O3A A:A5J901 3.5 31.1 1.0 MG A:MG903 3.5 25.6 1.0 O A:HOH1023 3.6 17.6 1.0 H A:GLN613 3.8 47.5 1.0 OD1 A:ASP785 3.8 25.4 1.0 HG22 A:ILE614 3.8 41.7 1.0 H A:ILE614 3.9 45.2 1.0 OD2 A:ASP610 3.9 33.6 1.0 O1G A:A5J901 3.9 35.6 1.0 N A:SER612 4.0 36.6 1.0 O A:HOH1040 4.0 31.0 1.0 CA A:SER612 4.1 38.3 1.0 N A:TYR611 4.1 32.8 1.0 HB2 A:TYR611 4.1 39.8 1.0 CA A:TYR611 4.1 33.8 1.0 N A:GLN613 4.2 39.6 1.0 O1B A:A5J901 4.2 31.2 1.0 H A:TYR611 4.2 39.3 1.0 C5' A:A5J901 4.2 30.8 1.0 HB A:ILE614 4.2 41.8 1.0 O3G A:A5J901 4.3 34.8 1.0 O2A A:A5J901 4.3 31.2 1.0 O5' A:A5J901 4.3 30.5 1.0 C A:ASP610 4.4 33.2 1.0 C A:SER612 4.5 38.9 1.0 HZ2 A:LYS663 4.5 49.0 1.0 H5'1 A:A5J901 4.5 37.0 1.0 HG21 A:ILE614 4.5 41.7 1.0 CG2 A:ILE614 4.6 34.8 1.0 CB A:TYR611 4.6 33.2 1.0 HB2 A:ASP785 4.6 30.4 1.0 CB A:ASP610 4.6 33.2 1.0 CB A:ASP785 4.6 25.4 1.0 N A:ILE614 4.7 37.7 1.0 HB3 A:ASP610 4.7 39.8 1.0 HB3 A:TYR611 4.8 39.8 1.0 O A:ASP610 4.8 34.2 1.0 H A:SER612 4.8 43.9 1.0 CB A:ILE614 4.9 34.9 1.0 HA A:TYR611 4.9 40.5 1.0 CA A:ASP610 5.0 32.2 1.0 HB3 A:ASP785 5.0 30.4 1.0

Magnesium binding site 2 out of 2 in the Structure of Mutant Taq Polymerase Incorporating Unnatural Base Pairs Z:P


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Mutant Taq Polymerase Incorporating Unnatural Base Pairs Z:P within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg903 b:25.6 occ:1.00 OD1 A:ASP785 2.0 25.4 1.0 OD2 A:ASP610 2.1 33.6 1.0 O1A A:A5J901 2.3 32.3 1.0 O A:HOH1056 2.4 17.4 1.0 O A:HOH1028 2.6 27.0 1.0 H3'2 B:DOC112 2.8 35.2 1.0 CG A:ASP610 2.9 33.8 1.0 CG A:ASP785 2.9 26.0 1.0 OD1 A:ASP610 3.0 34.4 1.0 OD2 A:ASP785 3.2 27.2 1.0 PA A:A5J901 3.4 32.4 1.0 HB2 A:GLU786 3.5 33.1 1.0 O2A A:A5J901 3.5 31.2 1.0 MG A:MG902 3.5 32.3 1.0 C3' B:DOC112 3.8 29.3 1.0 H5' B:DOC112 3.8 36.6 1.0 H5'1 A:A5J901 3.8 37.0 1.0 O A:HOH1040 3.9 31.0 1.0 O5' A:A5J901 4.0 30.5 1.0 H3'1 B:DOC112 4.1 35.2 1.0 H5'2 A:A5J901 4.1 37.0 1.0 H4' B:DOC112 4.2 35.8 1.0 H A:ASP785 4.2 27.9 1.0 C5' A:A5J901 4.2 30.8 1.0 HB3 A:GLU786 4.2 33.1 1.0 CB A:GLU786 4.3 27.6 1.0 CB A:ASP610 4.3 33.2 1.0 CB A:ASP785 4.3 25.4 1.0 OE1 A:GLU786 4.4 29.8 1.0 C4' B:DOC112 4.4 29.8 1.0 O2G A:A5J901 4.4 34.0 1.0 C A:ASP785 4.5 24.9 1.0 HB2 A:ASP610 4.5 39.8 1.0 O A:ASP785 4.5 26.1 1.0 O A:VAL783 4.6 22.4 1.0 C5' B:DOC112 4.6 30.5 1.0 HB3 A:ASP785 4.7 30.4 1.0 HZ1 A:LYS831 4.7 44.7 1.0 N A:GLU786 4.7 26.4 1.0 H2'' B:DOC112 4.7 34.8 1.0 O3A A:A5J901 4.7 31.1 1.0 CA A:ASP785 4.8 24.4 1.0 HA A:ASP610 4.8 38.6 1.0 O2B A:A5J901 4.8 32.5 1.0 C2' B:DOC112 4.9 29.0 1.0 N A:ASP785 4.9 23.3 1.0 HB3 A:ASP610 4.9 39.8 1.0 HZ2 A:LYS663 4.9 49.0 1.0 O A:TYR611 4.9 35.6 1.0 HB2 A:ASP785 5.0 30.4 1.0

I.Singh, R.Laos, S.Hoshika, S.A.Benner, M.M.Georgiadis. Snapshots of An Evolved Dna Polymerase Pre- and Post-Incorporation of An Unnatural Nucleotide. Nucleic Acids Res. V. 46 7977 2018.
ISSN: ESSN 1362-4962
PubMed: 29986111
DOI: 10.1093/NAR/GKY552