Magnesium in PDB 5fv7: Human FEN1 in Complex with An N-Hydroxyurea Compound

The structure of Human FEN1 in Complex with An N-Hydroxyurea Compound, PDB code: 5fv7 was solved by J.C.Exell, M.J.Thompson, L.D.Finger, S.K.Shaw, W.M.Abbott, C.Mcwhirter, J.E.Debreczeni, C.D.Jones, J.W.M.Nissink, T.A.Ward, C.W.L.Sioberg, D.M.Molina, S.T.Durant, J.A.Grasby, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	65.29 / 2.84
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	43.339, 50.193, 66.945, 102.06, 94.01, 90.74
R / Rfree (%)	23.4 / 30

The binding sites of Magnesium atom in the Human FEN1 in Complex with An N-Hydroxyurea Compound (pdb code 5fv7). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Human FEN1 in Complex with An N-Hydroxyurea Compound, PDB code: 5fv7:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Human FEN1 in Complex with An N-Hydroxyurea Compound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human FEN1 in Complex with An N-Hydroxyurea Compound within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1339 b:45.4 occ:1.00 OE1 A:GLU160 2.2 35.8 1.0 O23 A:R3Z1341 2.3 41.7 1.0 O19 A:R3Z1341 2.5 43.0 1.0 N20 A:R3Z1341 3.2 43.7 1.0 C18 A:R3Z1341 3.2 44.4 1.0 CD A:GLU160 3.3 35.6 1.0 OD1 A:ASP86 3.3 39.5 1.0 OD1 A:ASP34 3.4 37.9 1.0 OD2 A:ASP34 3.6 36.4 1.0 OD2 A:ASP86 3.6 41.4 1.0 OE2 A:GLU160 3.8 36.0 1.0 CG A:ASP34 3.9 36.4 1.0 CG A:ASP86 3.9 40.4 1.0 CG A:GLU158 3.9 39.7 1.0 N A:GLU160 4.0 35.9 1.0 N A:ALA159 4.1 37.6 1.0 OD2 A:ASP179 4.2 37.2 1.0 CB A:ALA159 4.3 36.7 1.0 CB A:GLU160 4.4 35.1 1.0 CG A:GLU160 4.4 35.1 1.0 CB A:SER36 4.5 39.8 1.0 C21 A:R3Z1341 4.5 44.6 1.0 MG A:MG1340 4.5 23.9 1.0 CA A:ALA159 4.6 37.3 1.0 C17 A:R3Z1341 4.6 45.0 1.0 OE2 A:GLU158 4.6 40.2 1.0 C A:ALA159 4.8 37.0 1.0 C A:GLU158 4.8 38.5 1.0 CA A:GLU160 4.8 35.3 1.0 CD A:GLU158 4.8 40.4 1.0 CB A:GLU158 4.9 39.3 1.0 O22 A:R3Z1341 4.9 46.5 1.0

Magnesium binding site 2 out of 4 in the Human FEN1 in Complex with An N-Hydroxyurea Compound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human FEN1 in Complex with An N-Hydroxyurea Compound within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1340 b:23.9 occ:1.00 OE2 A:GLU160 2.1 36.0 1.0 OD2 A:ASP179 2.2 37.2 1.0 O22 A:R3Z1341 2.3 46.5 1.0 O23 A:R3Z1341 2.6 41.7 1.0 OD1 A:ASP181 2.7 37.1 1.0 OD2 A:ASP181 2.8 36.6 1.0 CD A:GLU160 3.0 35.6 1.0 CG A:ASP181 3.2 36.7 1.0 OE2 A:GLU158 3.2 40.2 1.0 CG A:ASP179 3.2 37.2 1.0 C21 A:R3Z1341 3.2 44.6 1.0 N20 A:R3Z1341 3.3 43.7 1.0 OD1 A:ASP179 3.4 38.0 1.0 N A:GLY2 3.7 39.9 1.0 OE1 A:GLU160 3.7 35.8 1.0 CG A:GLU160 3.9 35.1 1.0 CD A:GLU158 4.1 40.4 1.0 N12 A:R3Z1341 4.4 46.2 1.0 MG A:MG1339 4.5 45.4 1.0 CB A:ASP179 4.6 36.9 1.0 CG A:GLU158 4.6 39.7 1.0 CE2 A:PHE185 4.6 35.1 1.0 C18 A:R3Z1341 4.6 44.4 1.0 CB A:ASP181 4.6 36.3 1.0 C8 A:R3Z1341 4.9 46.9 1.0 OE1 A:GLU158 5.0 40.9 1.0 CA A:GLY2 5.0 39.6 1.0

Magnesium binding site 3 out of 4 in the Human FEN1 in Complex with An N-Hydroxyurea Compound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Human FEN1 in Complex with An N-Hydroxyurea Compound within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1336 b:30.8 occ:1.00 OE1 B:GLU160 1.9 44.8 1.0 O19 B:R3Z1338 2.4 42.0 1.0 O23 B:R3Z1338 2.4 36.0 1.0 CD B:GLU160 3.0 44.5 1.0 C18 B:R3Z1338 3.1 40.9 1.0 N20 B:R3Z1338 3.2 39.0 1.0 OE2 B:GLU160 3.5 45.3 1.0 OD2 B:ASP34 3.5 42.4 1.0 OD1 B:ASP34 3.7 43.4 1.0 OD1 B:ASP86 3.9 48.3 1.0 OD2 B:ASP179 3.9 44.8 1.0 OD2 B:ASP86 4.0 50.1 1.0 CG B:ASP34 4.1 41.9 1.0 CG B:GLU160 4.3 43.7 1.0 N B:GLU160 4.3 43.9 1.0 MG B:MG1337 4.4 22.9 1.0 CG B:ASP86 4.4 49.6 1.0 CB B:GLU160 4.4 42.5 1.0 CG B:GLU158 4.4 49.2 1.0 C17 B:R3Z1338 4.5 41.5 1.0 C21 B:R3Z1338 4.5 38.5 1.0 N B:ALA159 4.6 46.3 1.0 CB B:ALA159 4.8 43.6 1.0 CB B:SER36 4.9 46.8 1.0 O22 B:R3Z1338 5.0 37.1 1.0 CA B:GLU160 5.0 43.4 1.0

Magnesium binding site 4 out of 4 in the Human FEN1 in Complex with An N-Hydroxyurea Compound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Human FEN1 in Complex with An N-Hydroxyurea Compound within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1337 b:22.9 occ:1.00 O22 B:R3Z1338 2.0 37.1 1.0 O23 B:R3Z1338 2.2 36.0 1.0 OD2 B:ASP179 2.5 44.8 1.0 OE2 B:GLU160 2.6 45.3 1.0 OD2 B:ASP181 2.8 42.7 1.0 C21 B:R3Z1338 2.8 38.5 1.0 N20 B:R3Z1338 2.9 39.0 1.0 OD1 B:ASP181 3.0 42.5 1.0 CG B:ASP181 3.3 42.8 1.0 CG B:ASP179 3.4 43.6 1.0 CD B:GLU160 3.4 44.5 1.0 OD1 B:ASP179 3.6 43.9 1.0 N B:GLY2 3.6 47.5 1.0 OD2 B:ASP233 3.8 55.2 1.0 OE1 B:GLU160 3.8 44.8 1.0 N12 B:R3Z1338 4.1 39.5 1.0 C18 B:R3Z1338 4.2 40.9 1.0 OE1 B:GLU158 4.3 49.8 1.0 MG B:MG1336 4.4 30.8 1.0 CG B:GLU160 4.6 43.7 1.0 CG B:ASP233 4.6 55.2 1.0 CD B:GLU158 4.6 50.5 1.0 CA B:GLY2 4.7 46.8 1.0 CB B:ASP181 4.7 43.7 1.0 C11 B:R3Z1338 4.8 38.4 1.0 CB B:ASP179 4.8 43.1 1.0 C8 B:R3Z1338 4.8 38.6 1.0 O19 B:R3Z1338 4.8 42.0 1.0 CG B:GLU158 5.0 49.2 1.0

J.C.Exell, M.J.Thompson, L.D.Finger, S.K.Shaw, W.M.Abbott, C.Mcwhirter, J.E.Debreczeni, C.D.Jones, J.W.M.Nissink, T.A.Ward, C.W.L.Sioberg, D.M.Molina, S.T.Durant, J.A.Grasby. Cellular Active N-Hydroxyurea FEN1 Inhibitors Block Substrate Entry to the Active Site Nat.Chem.Biol. V. 12 815 2016.
ISSN: ISSN 1552-4450
PubMed: 27526030
DOI: 10.1038/NCHEMBIO.2148