Magnesium in PDB 5j3z: Crystal Structure of M2HTDP2-Cat in Complex with A Small Molecule Inhibitor

The structure of Crystal Structure of M2HTDP2-Cat in Complex with A Small Molecule Inhibitor, PDB code: 5j3z was solved by P.Hornyak, L.H.Pearl, K.W.Caldecott, A.W.Oliver, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.81 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	61.010, 42.800, 108.760, 90.00, 94.15, 90.00
R / Rfree (%)	17.3 / 20.2

The binding sites of Magnesium atom in the Crystal Structure of M2HTDP2-Cat in Complex with A Small Molecule Inhibitor (pdb code 5j3z). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of M2HTDP2-Cat in Complex with A Small Molecule Inhibitor, PDB code: 5j3z:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of M2HTDP2-Cat in Complex with A Small Molecule Inhibitor


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 M2HTDP2-Cat in Complex with A Small Molecule Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:34.8 occ:1.00 O A:HOH502 2.1 30.7 1.0 OD1 A:ASP132 2.2 18.9 1.0 O A:HOH535 2.4 25.5 1.0 O A:HOH501 2.6 27.7 1.0 O A:HOH510 2.6 14.3 1.0 O A:HOH715 2.7 51.0 1.0 OE1 A:GLU162 2.8 23.2 1.0 CG A:ASP132 3.2 19.5 1.0 CD A:GLU162 3.3 32.0 1.0 OE2 A:GLU162 3.4 24.1 1.0 NH2 B:ARG316 3.7 29.8 1.0 CA A:ASP132 3.8 12.5 1.0 CB A:ASP132 3.9 14.0 1.0 O A:HOH563 4.0 38.4 1.0 OD2 A:ASP132 4.0 24.1 1.0 O2 A:GOL403 4.0 45.4 1.0 OD1 A:ASP358 4.4 19.2 1.0 O3 A:GOL403 4.4 38.2 1.0 OD2 A:ASP358 4.5 23.9 1.0 OD1 A:ASN130 4.6 14.6 1.0 C A:ASP132 4.6 16.5 1.0 CG A:GLU162 4.6 23.1 1.0 CG A:ASP358 4.8 20.9 1.0 CZ B:ARG316 4.8 44.0 1.0 O A:HOH608 4.9 76.6 1.0 O A:HOH579 4.9 0.9 1.0 N A:ASP132 4.9 12.7 1.0 CB A:GLU162 5.0 14.0 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of M2HTDP2-Cat in Complex with A Small Molecule Inhibitor


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 M2HTDP2-Cat in Complex with A Small Molecule Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:28.0 occ:1.00 O B:HOH531 2.1 94.2 1.0 OE1 B:GLU162 2.3 28.1 1.0 OD1 B:ASP132 2.3 17.9 1.0 O B:HOH508 2.4 16.5 1.0 O B:HOH669 2.5 22.4 1.0 CD B:GLU162 3.0 36.0 1.0 OE2 B:GLU162 3.0 27.7 1.0 CG B:ASP132 3.1 19.3 1.0 O B:HOH745 3.1 83.1 1.0 CA B:ASP132 3.8 13.2 1.0 CB B:ASP132 3.8 15.0 1.0 NH2 A:ARG316 3.9 29.4 1.0 OD2 B:ASP132 3.9 24.2 1.0 OXT B:ACT412 4.1 36.4 1.0 O A:HOH747 4.2 34.2 1.0 OD1 B:ASP358 4.3 18.7 1.0 CG B:GLU162 4.4 22.3 1.0 OD1 B:ASN130 4.5 15.9 1.0 CH3 B:ACT412 4.6 39.4 1.0 C B:ASP132 4.7 17.8 1.0 OD2 B:ASP358 4.7 28.0 1.0 CZ A:ARG316 4.8 43.9 1.0 N B:ASP132 4.8 12.7 1.0 CG B:ASP358 4.8 22.4 1.0 C B:ACT412 4.9 39.3 1.0 CB B:LEU134 4.9 20.3 1.0 O A:HOH722 4.9 42.1 1.0 CB B:GLU162 4.9 13.7 1.0 NH1 A:ARG316 5.0 21.9 1.0 CD1 B:LEU134 5.0 25.2 1.0

P.Hornyak, T.Askwith, S.Walker, E.Komulainen, M.Paradowski, L.E.Pennicott, E.J.Bartlett, N.C.Brissett, A.Raoof, M.Watson, A.M.Jordan, D.J.Ogilvie, S.E.Ward, J.R.Atack, L.H.Pearl, K.W.Caldecott, A.W.Oliver. Mode of Action of Dna-Competitive Small Molecule Inhibitors of Tyrosyl Dna Phosphodiesterase 2. Biochem.J. V. 473 1869 2016.
ISSN: ESSN 1470-8728
PubMed: 27099339
DOI: 10.1042/BCJ20160180