Manganese in PDB 5j42: 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: 5j42 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)	42.07 / 1.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	61.054, 42.872, 109.054, 90.00, 94.05, 90.00
R / Rfree (%)	16 / 19.7

The binding sites of Manganese atom in the Crystal Structure of M2HTDP2-Cat in Complex with A Small Molecule Inhibitor (pdb code 5j42). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Crystal Structure of M2HTDP2-Cat in Complex with A Small Molecule Inhibitor, PDB code: 5j42:
Jump to Manganese binding site number: 1; 2;

Manganese 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 Manganese with other atoms in the Mn 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:Mn406 b:19.6 occ:1.00 O4 A:TLA403 2.1 22.1 1.0 OD1 A:ASP132 2.1 17.7 1.0 O A:HOH613 2.2 15.6 1.0 O3 A:TLA403 2.2 17.7 1.0 OE2 A:GLU162 2.3 24.5 1.0 O A:HOH530 2.4 20.7 1.0 C4 A:TLA403 2.9 23.1 1.0 CG A:ASP132 3.0 16.8 1.0 CD A:GLU162 3.0 23.7 1.0 C3 A:TLA403 3.1 18.7 1.0 OE1 A:GLU162 3.1 24.2 1.0 CB A:ASP132 3.8 16.8 1.0 NH2 B:ARG316 3.9 27.2 1.0 CA A:ASP132 3.9 17.3 1.0 OD2 A:ASP132 4.0 19.8 1.0 OD1 A:ASP358 4.1 19.9 1.0 O41 A:TLA403 4.1 26.6 1.0 OD2 A:ASP358 4.2 24.2 1.0 O A:HOH601 4.2 18.7 1.0 C2 A:TLA403 4.3 22.6 1.0 OD1 A:ASN130 4.4 17.3 1.0 O2 A:TLA403 4.4 25.1 1.0 CG A:GLU162 4.5 26.8 1.0 CG A:ASP358 4.5 21.9 1.0 CB A:LEU134 4.6 20.9 1.0 O B:HOH721 4.7 34.9 1.0 C A:ASP132 4.8 18.7 1.0 CD1 A:LEU134 4.8 25.3 1.0 CZ B:ARG316 4.8 26.4 1.0 N A:ASP132 4.9 17.6 1.0

Manganese 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 Manganese with other atoms in the Mn 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:Mn408 b:20.4 occ:1.00 OD1 B:ASP132 2.1 18.1 1.0 O41 B:TLA403 2.2 23.8 1.0 O3 B:TLA403 2.2 20.1 1.0 O B:HOH553 2.2 19.6 1.0 OE1 B:GLU162 2.2 19.2 1.0 O B:HOH647 2.2 19.6 1.0 C4 B:TLA403 3.0 23.9 1.0 CD B:GLU162 3.0 21.9 1.0 CG B:ASP132 3.0 18.2 1.0 OE2 B:GLU162 3.1 21.7 1.0 C3 B:TLA403 3.1 21.2 1.0 NH2 A:ARG316 3.6 29.5 1.0 OD2 B:ASP132 3.8 20.8 1.0 CB B:ASP132 3.9 19.6 1.0 CA B:ASP132 3.9 18.9 1.0 OD1 B:ASP358 4.1 18.9 1.0 O B:HOH594 4.2 26.1 1.0 O4 B:TLA403 4.2 24.8 1.0 C2 B:TLA403 4.3 23.1 1.0 OD2 B:ASP358 4.3 25.0 1.0 OD1 B:ASN130 4.4 20.5 1.0 O A:HOH623 4.4 29.4 1.0 O2 B:TLA403 4.5 24.3 1.0 CG B:GLU162 4.5 21.9 1.0 CG B:ASP358 4.6 22.3 1.0 CZ A:ARG316 4.7 30.2 1.0 CB B:LEU134 4.7 20.1 1.0 C B:ASP132 4.8 22.1 1.0 CD1 B:LEU134 4.8 25.4 1.0 N B:ASP132 4.8 18.2 1.0 NH1 A:ARG316 5.0 25.7 1.0 CB B:GLU162 5.0 24.1 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