Magnesium in PDB 4dlg: Ternary Structure of the Large Fragment of Taq Dna Polymerase

All present enzymatic activity of Ternary Structure of the Large Fragment of Taq Dna Polymerase:
2.7.7.7;

The structure of Ternary Structure of the Large Fragment of Taq Dna Polymerase, PDB code: 4dlg was solved by A.Marx, K.Diederichs, S.Obeid, B.Holzberger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.67 / 1.89
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	107.784, 107.784, 89.554, 90.00, 90.00, 120.00
R / Rfree (%)	21.4 / 25.2

The binding sites of Magnesium atom in the Ternary Structure of the Large Fragment of Taq Dna Polymerase (pdb code 4dlg). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Ternary Structure of the Large Fragment of Taq Dna Polymerase, PDB code: 4dlg:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Ternary Structure of the Large Fragment of Taq Dna Polymerase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Ternary Structure of the Large Fragment of Taq Dna Polymerase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg902 b:36.2 occ:1.00 O2G A:DCT901 1.9 40.5 1.0 O A:TYR611 1.9 19.7 1.0 OD1 A:ASP610 2.0 36.4 1.0 O2B A:DCT901 2.1 40.1 1.0 OD2 A:ASP785 2.1 35.0 1.0 O2A A:DCT901 2.2 28.7 1.0 CG A:ASP610 3.0 38.3 1.0 C A:TYR611 3.1 20.7 1.0 CG A:ASP785 3.2 28.6 1.0 MG A:MG903 3.2 29.3 1.0 PG A:DCT901 3.3 41.6 1.0 PB A:DCT901 3.3 41.5 1.0 OD2 A:ASP610 3.4 42.6 1.0 PA A:DCT901 3.6 34.0 1.0 O3B A:DCT901 3.7 39.1 1.0 OD1 A:ASP785 3.7 26.6 1.0 O A:HOH1221 3.7 30.8 1.0 N A:TYR611 3.9 19.0 1.0 O3A A:DCT901 3.9 49.8 1.0 CA A:TYR611 4.0 21.4 1.0 O1G A:DCT901 4.0 38.6 1.0 N A:SER612 4.1 22.5 1.0 O A:HOH1323 4.3 45.0 1.0 CB A:ASP610 4.3 31.1 1.0 C A:ASP610 4.3 21.7 1.0 O3G A:DCT901 4.3 38.1 1.0 CA A:SER612 4.3 28.6 1.0 C5' A:DCT901 4.4 37.4 1.0 CB A:ASP785 4.4 20.4 1.0 CB A:TYR611 4.4 23.8 1.0 N A:GLN613 4.4 27.4 1.0 O5' A:DCT901 4.5 34.5 1.0 O1B A:DCT901 4.5 38.5 1.0 O1A A:DCT901 4.6 30.4 1.0 O A:HOH1053 4.7 52.5 1.0 CG2 A:ILE614 4.7 33.1 1.0 CA A:ASP610 4.8 25.8 1.0 C A:SER612 4.8 26.7 1.0 O A:ASP785 4.8 21.9 1.0 O A:ASP610 4.8 23.0 1.0

Magnesium binding site 2 out of 2 in the Ternary Structure of the Large Fragment of Taq Dna Polymerase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Ternary Structure of the Large Fragment of Taq Dna Polymerase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg903 b:29.3 occ:1.00 O A:HOH1053 2.1 52.5 1.0 OD2 A:ASP610 2.2 42.6 1.0 OD1 A:ASP785 2.2 26.6 1.0 O2A A:DCT901 2.3 28.7 1.0 CG A:ASP610 2.9 38.3 1.0 OD1 A:ASP610 2.9 36.4 1.0 CG A:ASP785 3.0 28.6 1.0 OD2 A:ASP785 3.1 35.0 1.0 CD A:GLU786 3.2 24.2 0.5 MG A:MG902 3.2 36.2 1.0 PA A:DCT901 3.4 34.0 1.0 OE2 A:GLU786 3.4 24.5 0.5 CG A:GLU786 3.4 23.3 0.5 O A:HOH1323 3.5 45.0 1.0 C3' B:DOC112 3.5 24.3 1.0 OE1 A:GLU786 3.6 26.8 0.5 O1A A:DCT901 3.7 30.4 1.0 O5' A:DCT901 3.9 34.5 1.0 C5' A:DCT901 4.0 37.4 1.0 O2G A:DCT901 4.1 40.5 1.0 CB A:ASP610 4.3 31.1 1.0 CB A:ASP785 4.4 20.4 1.0 C4' B:DOC112 4.4 23.9 1.0 C5' B:DOC112 4.5 23.9 1.0 CB A:GLU786 4.5 22.3 0.5 OE1 A:GLU786 4.5 22.5 0.5 O A:ASP785 4.6 21.9 1.0 C A:ASP785 4.6 22.9 1.0 O2B A:DCT901 4.6 40.1 1.0 CB A:GLU786 4.7 22.1 0.5 NZ A:LYS831 4.7 55.4 1.0 C2' B:DOC112 4.8 23.9 1.0 O3A A:DCT901 4.8 49.8 1.0 N A:GLU786 4.9 21.6 0.5 O A:VAL783 4.9 20.8 1.0 N A:GLU786 4.9 21.6 0.5 CA A:ASP785 4.9 21.7 1.0 O A:TYR611 4.9 19.7 1.0 O5' B:DOC112 4.9 20.4 1.0

B.Holzberger, S.Obeid, W.Welte, K.Diederichs, A.Marx. Structural Insights Into the Potential of 4-Fluoroproline to Modulate Biophysical Properties of Protein Chem Sci V. 3 2924 2012.
DOI: 10.1039/C2SC20545A