Magnesium in PDB 5o7t: Crystal Structure of Klentaq Mutant M747K in A Closed Ternary Complex with A Dg:Dctp Base Pair

All present enzymatic activity of Crystal Structure of Klentaq Mutant M747K in A Closed Ternary Complex with A Dg:Dctp Base Pair:
2.7.7.7;

The structure of Crystal Structure of Klentaq Mutant M747K in A Closed Ternary Complex with A Dg:Dctp Base Pair, PDB code: 5o7t was solved by K.Betz, K.Diederichs, A.Marx, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.40 / 1.80
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	109.476, 109.476, 91.390, 90.00, 90.00, 120.00
R / Rfree (%)	17.7 / 23.5

The binding sites of Magnesium atom in the Crystal Structure of Klentaq Mutant M747K in A Closed Ternary Complex with A Dg:Dctp Base Pair (pdb code 5o7t). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Klentaq Mutant M747K in A Closed Ternary Complex with A Dg:Dctp Base Pair, PDB code: 5o7t:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of Klentaq Mutant M747K in A Closed Ternary Complex with A Dg:Dctp Base Pair


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Klentaq Mutant M747K in A Closed Ternary Complex with A Dg:Dctp Base Pair within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg901 b:37.8 occ:1.00 OD1 A:ASP610 2.0 39.3 1.0 O1G A:DCP903 2.1 37.8 1.0 OD2 A:ASP785 2.1 38.8 1.0 O1B A:DCP903 2.1 32.2 1.0 O A:TYR611 2.1 35.7 1.0 O1A A:DCP903 2.1 34.5 1.0 PB A:DCP903 3.1 38.2 1.0 CG A:ASP785 3.1 31.8 1.0 CG A:ASP610 3.2 42.1 1.0 H5'1 A:DCP903 3.2 40.9 1.0 C A:TYR611 3.3 37.5 1.0 PG A:DCP903 3.3 40.5 1.0 PA A:DCP903 3.4 37.7 1.0 MG A:MG902 3.5 47.6 1.0 OD1 A:ASP785 3.5 36.7 1.0 O3A A:DCP903 3.5 35.2 1.0 O3B A:DCP903 3.6 42.1 1.0 OD2 A:ASP610 3.7 42.8 1.0 O A:HOH1079 3.8 34.4 1.0 HG22 A:ILE614 3.9 48.0 1.0 N A:TYR611 3.9 47.2 1.0 O A:HOH1151 3.9 39.8 1.0 H A:TYR611 4.0 56.6 1.0 HA A:SER612 4.0 54.0 1.0 H A:ILE614 4.0 40.4 1.0 H A:GLN613 4.1 42.7 1.0 HB2 A:TYR611 4.1 49.4 1.0 C5' A:DCP903 4.1 34.0 1.0 CA A:TYR611 4.1 40.3 1.0 O5' A:DCP903 4.2 37.8 1.0 O2G A:DCP903 4.2 39.4 1.0 C A:ASP610 4.3 34.4 1.0 N A:SER612 4.3 41.9 1.0 HB A:ILE614 4.3 49.1 1.0 O3G A:DCP903 4.4 34.2 1.0 HZ2 A:LYS663 4.4 55.6 1.0 O2B A:DCP903 4.4 36.3 1.0 H5'2 A:DCP903 4.4 40.9 1.0 CB A:ASP610 4.4 47.2 1.0 CB A:ASP785 4.4 36.8 1.0 N A:GLN613 4.5 35.6 1.0 HB2 A:ASP785 4.5 44.2 1.0 O2A A:DCP903 4.5 35.6 1.0 CA A:SER612 4.5 45.0 1.0 HG21 A:ILE614 4.5 48.0 1.0 CG2 A:ILE614 4.6 40.0 1.0 HB3 A:ASP610 4.6 56.7 1.0 CB A:TYR611 4.6 41.1 1.0 C A:SER612 4.7 37.4 1.0 O A:ASP610 4.7 37.2 1.0 HB3 A:TYR611 4.8 49.4 1.0 N A:ILE614 4.8 33.6 1.0 CA A:ASP610 4.8 32.1 1.0 HA A:ASP610 4.8 38.5 1.0 HB3 A:ASP785 4.9 44.2 1.0 O A:ASP785 4.9 40.1 1.0 O A:HOH1141 4.9 36.3 1.0 CB A:ILE614 4.9 41.0 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of Klentaq Mutant M747K in A Closed Ternary Complex with A Dg:Dctp Base Pair


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Klentaq Mutant M747K in A Closed Ternary Complex with A Dg:Dctp Base Pair within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg902 b:47.6 occ:1.00 OD2 A:ASP610 2.1 42.8 1.0 OD1 A:ASP785 2.2 36.7 1.0 O1A A:DCP903 2.4 34.5 1.0 O A:HOH1039 2.4 34.6 1.0 O A:HOH1141 2.5 36.3 1.0 H3'1 B:DDG112 2.8 45.2 1.0 CG A:ASP610 2.9 42.1 1.0 OD1 A:ASP610 3.1 39.3 1.0 CG A:ASP785 3.1 31.8 1.0 HZ1 A:LYS831 3.4 53.0 1.0 HB2 A:GLU786 3.4 42.9 1.0 OD2 A:ASP785 3.4 38.8 1.0 PA A:DCP903 3.5 37.7 1.0 MG A:MG901 3.5 37.8 1.0 H5'' B:DDG112 3.6 48.8 1.0 O A:HOH1151 3.8 39.8 1.0 C3' B:DDG112 3.8 37.7 1.0 O2A A:DCP903 3.8 35.6 1.0 O5' A:DCP903 4.0 37.8 1.0 H3'2 B:DDG112 4.0 45.2 1.0 HB3 A:GLU786 4.0 42.9 1.0 H5'2 A:DCP903 4.0 40.9 1.0 CB A:GLU786 4.2 35.7 1.0 H A:ASP785 4.2 37.8 1.0 NZ A:LYS831 4.2 44.2 1.0 OE1 A:GLU786 4.2 39.5 1.0 H5'1 A:DCP903 4.3 40.9 1.0 CB A:ASP610 4.3 47.2 1.0 HZ2 A:LYS831 4.3 53.0 1.0 C5' A:DCP903 4.4 34.0 1.0 C5' B:DDG112 4.4 40.6 1.0 O A:VAL783 4.4 36.9 1.0 C4' B:DDG112 4.4 35.3 1.0 H4' B:DDG112 4.4 42.4 1.0 HB2 A:ASP610 4.4 56.7 1.0 CB A:ASP785 4.5 36.8 1.0 C A:ASP785 4.5 39.8 1.0 HZ3 A:LYS831 4.6 53.0 1.0 O1G A:DCP903 4.6 37.8 1.0 O A:ASP785 4.6 40.1 1.0 N A:GLU786 4.7 31.0 1.0 HA A:ASP610 4.7 38.5 1.0 O5' B:DDG112 4.8 31.6 1.0 O3A A:DCP903 4.8 35.2 1.0 HB3 A:ASP785 4.8 44.2 1.0 CA A:ASP785 4.9 36.9 1.0 N A:ASP785 4.9 31.5 1.0 HB3 A:ASP610 4.9 56.7 1.0 HZ2 A:LYS663 4.9 55.6 1.0 H A:GLU786 4.9 37.2 1.0 O1B A:DCP903 4.9 32.2 1.0 OP1 B:DDG112 5.0 37.1 1.0 CA A:GLU786 5.0 34.5 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of Klentaq Mutant M747K in A Closed Ternary Complex with A Dg:Dctp Base Pair


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Klentaq Mutant M747K in A Closed Ternary Complex with A Dg:Dctp Base Pair within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg201 b:52.1 occ:1.00 O B:HOH329 1.9 57.5 1.0 O B:HOH324 2.0 37.9 1.0 O B:HOH320 2.0 34.1 1.0 O B:HOH309 2.2 41.6 1.0 O B:HOH330 2.3 48.5 1.0 O C:HOH342 2.5 59.2 1.0 O C:HOH328 4.0 40.6 1.0 O C:HOH324 4.0 38.1 1.0 O6 B:DG108 4.2 36.4 1.0 H42 C:DC209 4.3 36.1 1.0 O B:HOH326 4.3 46.4 1.0 H41 C:DC209 4.3 36.1 1.0 O B:HOH310 4.3 38.5 1.0 H5 B:DC106 4.3 36.5 1.0 N7 B:DG107 4.4 39.4 1.0 O6 B:DG107 4.5 30.2 1.0 N4 C:DC209 4.6 30.1 1.0 C5 B:DC106 4.8 30.4 1.0

K.Betz, A.Nilforoushan, L.A.Wyss, K.Diederichs, S.J.Sturla, A.Marx. Structural Basis For the Selective Incorporation of An Artificial Nucleotide Opposite A Dna Adduct By A Dna Polymerase. Chem. Commun. (Camb.) V. 53 12704 2017.
ISSN: ESSN 1364-548X
PubMed: 29136072
DOI: 10.1039/C7CC07173F