Potassium in PDB 4mwo: Crystal Structure of Human Mitochondrial 5'(3')-Deoxyribonucleotidase in Complex with the Inhibitor Cpb-T

The structure of Crystal Structure of Human Mitochondrial 5'(3')-Deoxyribonucleotidase in Complex with the Inhibitor Cpb-T, PDB code: 4mwo was solved by P.Pachl, P.Rezacova, J.Brynda, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.90 / 1.67
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	73.974, 73.974, 105.950, 90.00, 90.00, 90.00
R / Rfree (%)	16.3 / 19.1

The binding sites of Potassium atom in the Crystal Structure of Human Mitochondrial 5'(3')-Deoxyribonucleotidase in Complex with the Inhibitor Cpb-T (pdb code 4mwo). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 2 binding sites of Potassium where determined in the Crystal Structure of Human Mitochondrial 5'(3')-Deoxyribonucleotidase in Complex with the Inhibitor Cpb-T, PDB code: 4mwo:
Jump to Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 in the Crystal Structure of Human Mitochondrial 5'(3')-Deoxyribonucleotidase in Complex with the Inhibitor Cpb-T


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Crystal Structure of Human Mitochondrial 5'(3')-Deoxyribonucleotidase in Complex with the Inhibitor Cpb-T within 5.0Å range: probe atom residue distance (Å) B Occ A:K303 b:26.0 occ:1.00 O A:ALA119 2.5 21.6 1.0 O A:HOH548 2.5 40.7 1.0 O A:LEU121 2.6 20.7 1.0 O A:THR124 2.6 19.5 1.0 O A:HOH534 2.6 28.7 1.0 O A:HOH532 2.9 30.2 1.0 C A:ALA119 3.7 20.5 1.0 C A:THR124 3.7 18.6 1.0 C A:LEU121 3.8 22.7 1.0 N A:THR124 4.1 20.9 1.0 N A:LEU121 4.1 21.6 1.0 O A:HOH409 4.1 24.1 1.0 C A:SER120 4.1 22.5 1.0 CA A:THR124 4.3 19.0 1.0 CA A:SER120 4.4 23.1 1.0 N A:SER120 4.5 20.2 1.0 CB A:THR124 4.5 19.2 1.0 O A:SER120 4.5 24.5 1.0 CA A:LEU121 4.6 22.2 1.0 CA A:ALA119 4.6 17.5 1.0 O A:HOH569 4.7 38.6 1.0 OD1 A:ASP125 4.8 22.4 1.0 N A:GLN122 4.8 26.2 1.0 O A:MET118 4.8 15.8 1.0 O A:HOH613 4.8 37.9 1.0 N A:ASP125 4.8 16.9 1.0 N A:ASN123 4.9 26.4 1.0 CA A:GLN122 4.9 28.8 1.0 C A:GLN122 5.0 26.7 1.0

Potassium binding site 2 out of 2 in the Crystal Structure of Human Mitochondrial 5'(3')-Deoxyribonucleotidase in Complex with the Inhibitor Cpb-T


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Crystal Structure of Human Mitochondrial 5'(3')-Deoxyribonucleotidase in Complex with the Inhibitor Cpb-T within 5.0Å range: probe atom residue distance (Å) B Occ A:K304 b:12.0 occ:1.00 O A:ASP43 2.3 12.3 1.0 O3 A:PO4302 2.3 5.5 0.4 OD1 A:ASP176 2.4 11.6 1.0 O A:HOH402 2.4 12.1 1.0 O A:HOH575 2.4 11.3 0.5 O3 A:GOL306 2.5 16.2 0.5 OD2 A:ASP41 2.5 18.8 1.0 O A:HOH576 2.5 16.0 0.4 OBC A:2E2301 2.6 17.2 0.6 CG A:ASP176 3.4 12.4 1.0 C A:ASP43 3.4 12.0 1.0 C3 A:GOL306 3.4 16.6 0.5 CG A:ASP41 3.5 14.3 1.0 OD1 A:ASP41 3.7 14.8 1.0 OD2 A:ASP176 3.7 13.5 1.0 P A:PO4302 3.8 5.9 0.4 PAA A:2E2301 3.9 18.5 0.6 OBA A:2E2301 4.1 18.8 0.6 CB A:ASP43 4.1 10.5 1.0 OD1 A:ASP175 4.2 11.3 1.0 CA A:ASP43 4.2 10.1 1.0 O2 A:PO4302 4.2 5.5 0.4 O A:HOH528 4.3 8.3 0.5 O A:HOH401 4.3 13.8 0.6 N A:ASP43 4.4 9.6 1.0 CE1 A:PHE75 4.4 16.3 1.0 N A:GLY44 4.4 11.0 1.0 CZ A:PHE75 4.6 15.7 1.0 CA A:GLY44 4.6 12.5 1.0 O1 A:PO4302 4.6 5.6 0.4 O4 A:PO4302 4.7 5.9 0.4 OBB A:2E2301 4.7 19.3 0.6 CB A:ASP176 4.7 11.7 1.0 O A:HOH578 4.7 19.9 0.5 N A:ASP176 4.7 11.2 1.0 C2 A:GOL306 4.8 17.2 0.5 CB A:ASP41 4.8 13.6 1.0 N A:ARG177 4.9 11.7 1.0 O A:HOH549 5.0 16.1 0.6 CG A:ASP175 5.0 12.2 1.0 CG2 A:VAL45 5.0 11.7 1.0

O.Simak, P.Pachl, M.Fabry, M.Budesinsky, T.Jandusik, A.Hnizda, R.Sklenickova, M.Petrova, V.Veverka, P.Rezacova, J.Brynda, I.Rosenberg. Conformationally Constrained Nucleoside Phosphonic Acids - Potent Inhibitors of Human Mitochondrial and Cytosolic 5'(3')-Nucleotidases. Org.Biomol.Chem. V. 12 7971 2014.
ISSN: ISSN 1477-0520
PubMed: 25178098
DOI: 10.1039/C4OB01332H