Magnesium in PDB 6paf: Co-Crystal Structure of Human SMYD3 with Isoxazole Amides Inhibitors

All present enzymatic activity of Co-Crystal Structure of Human SMYD3 with Isoxazole Amides Inhibitors:
2.1.1.43;

The structure of Co-Crystal Structure of Human SMYD3 with Isoxazole Amides Inhibitors, PDB code: 6paf was solved by P.A.Elkins, L.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.00 / 1.24
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.971, 65.991, 106.544, 90.00, 90.00, 90.00
R / Rfree (%)	17.2 / 18.8

The structure of Co-Crystal Structure of Human SMYD3 with Isoxazole Amides Inhibitors also contains other interesting chemical elements:

Zinc

(Zn)

3 atoms

The binding sites of Magnesium atom in the Co-Crystal Structure of Human SMYD3 with Isoxazole Amides Inhibitors (pdb code 6paf). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Co-Crystal Structure of Human SMYD3 with Isoxazole Amides Inhibitors, PDB code: 6paf:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Co-Crystal Structure of Human SMYD3 with Isoxazole Amides Inhibitors


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Co-Crystal Structure of Human SMYD3 with Isoxazole Amides Inhibitors within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg504 b:14.8 occ:1.00 O A:HOH822 2.0 17.9 1.0 O A:HOH832 2.0 16.6 1.0 O A:HOH1044 2.1 22.4 1.0 O A:HOH901 2.2 15.4 1.0 O A:HOH1060 4.1 30.6 1.0 O A:HOH607 4.1 16.1 1.0 O A:HOH722 4.2 11.5 1.0 O A:LEU129 4.2 8.8 1.0 OE2 A:GLU130 4.4 11.4 1.0 CA A:GLU130 4.5 8.0 1.0 O A:ASP128 4.5 10.5 1.0 O A:HOH904 4.7 24.2 1.0 N A:SER131 4.8 7.9 1.0 CD A:GLU130 4.8 9.8 1.0 C A:LEU129 4.8 7.7 1.0 OE1 A:GLU130 4.9 10.6 1.0 N A:GLU130 5.0 7.7 1.0

Magnesium binding site 2 out of 2 in the Co-Crystal Structure of Human SMYD3 with Isoxazole Amides Inhibitors


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Co-Crystal Structure of Human SMYD3 with Isoxazole Amides Inhibitors within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg505 b:13.6 occ:1.00 O A:HOH794 2.0 13.2 1.0 O A:HOH656 2.1 15.6 1.0 O A:HOH719 2.1 14.8 1.0 OE2 A:GLU130 4.1 11.4 1.0 O A:HOH1023 4.1 13.8 1.0 OE1 A:GLU130 4.1 10.6 1.0 OD1 A:ASN134 4.1 13.3 1.0 O A:HOH1060 4.2 30.6 1.0 OD1 A:ASN132 4.4 13.0 1.0 CD A:GLU130 4.4 9.8 1.0 CE A:LYS135 4.4 10.9 1.0 O A:HOH753 4.5 18.2 1.0 ND2 A:ASN134 4.6 14.6 1.0 CG A:ASN134 4.8 13.1 1.0 O A:HOH822 4.8 17.9 1.0 NZ A:LYS135 4.9 12.9 1.0

D.-S.Su, J.Qu, M.Schultz, C.W.Blackledge, H.Yu, J.Zeng, J.Burgess, A.Reif, M.Stern, R.Nagarajan, M.Baker Pappalardi, K.Wong, A.P.Graves, W.Bonnette, L.Wang, P.A.Elkins, B.Knapp-Reed, J.Carson, C.Mchugh, H.Mohammad, R.Kruger, J.Luengo, D.A.Heerding, C.L.Creasy. Discovery of Isoxazone Amides As Potent and Selective SMYD3 Inhibitors Acs Med.Chem.Lett. 2019.
ISSN: ISSN 1948-5875