Zinc in PDB 5arg: SMYD2 in Complex with Sgc Probe Bay-598

All present enzymatic activity of SMYD2 in Complex with Sgc Probe Bay-598:
2.1.1.43;

The structure of SMYD2 in Complex with Sgc Probe Bay-598, PDB code: 5arg was solved by R.C.Hillig, V.Badock, N.Barak, T.Stellfeld, E.Eggert, A.Ter Laak, J.Weiske, C.D.Christ, S.Koehr, D.Stoeckigt, J.Mowat, T.Mueller, A.E.Fernandez-Montalvan, I.V.Hartung, C.Stresemann, T.Brumby, H.Weinmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.72 / 1.99
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	52.343, 69.600, 131.115, 90.00, 90.00, 90.00
R / Rfree (%)	23 / 27.3

The structure of SMYD2 in Complex with Sgc Probe Bay-598 also contains other interesting chemical elements:

Fluorine	(F)	2 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Zinc atom in the SMYD2 in Complex with Sgc Probe Bay-598 (pdb code 5arg). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the SMYD2 in Complex with Sgc Probe Bay-598, PDB code: 5arg:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the SMYD2 in Complex with Sgc Probe Bay-598


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of SMYD2 in Complex with Sgc Probe Bay-598 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1003 b:50.0 occ:1.00 SG A:CYS267 2.3 65.0 1.0 SG A:CYS209 2.3 60.1 1.0 SG A:CYS264 2.4 68.5 1.0 SG A:CYS262 2.4 66.9 1.0 CB A:CYS267 2.7 71.6 1.0 CB A:CYS262 3.0 62.5 1.0 CB A:CYS209 3.0 56.7 1.0 CB A:CYS264 3.3 66.5 1.0 N A:CYS209 3.5 49.8 1.0 N A:CYS264 3.8 71.3 1.0 CA A:CYS209 3.9 48.8 1.0 N A:CYS267 3.9 71.3 1.0 CA A:CYS267 4.0 73.2 1.0 CA A:CYS264 4.1 70.1 1.0 CA A:CYS262 4.3 67.6 1.0 C A:CYS262 4.4 72.2 1.0 O A:CYS264 4.5 73.5 1.0 C A:CYS264 4.6 72.3 1.0 C A:SER208 4.6 48.4 1.0 NE2 A:HIS207 4.6 47.2 1.0 N A:GLU263 4.7 75.8 1.0 NH2 A:ARG250 4.7 57.3 1.0 O A:CYS262 4.8 73.5 1.0 CD2 A:HIS207 4.8 52.5 1.0 CB A:GLU266 4.9 60.2 1.0 CA A:SER208 4.9 50.8 1.0 C A:GLU266 4.9 68.6 1.0 C A:GLU263 5.0 78.6 1.0 C A:CYS209 5.0 46.5 1.0

Zinc binding site 2 out of 3 in the SMYD2 in Complex with Sgc Probe Bay-598


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of SMYD2 in Complex with Sgc Probe Bay-598 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1004 b:36.1 occ:1.00 SG A:CYS78 2.3 45.5 1.0 SG A:CYS74 2.3 47.0 1.0 SG A:CYS52 2.3 45.3 1.0 SG A:CYS55 2.4 45.2 1.0 CB A:CYS74 3.0 48.8 1.0 CB A:CYS52 3.2 38.0 1.0 CB A:CYS78 3.3 47.7 1.0 CB A:CYS55 3.5 38.5 1.0 N A:CYS74 3.7 48.1 1.0 N A:CYS55 3.9 34.6 1.0 CA A:CYS74 4.0 50.0 1.0 CA A:CYS55 4.3 33.4 1.0 CA A:CYS78 4.6 47.0 1.0 CA A:CYS52 4.6 35.8 1.0 CB A:TYR54 4.7 36.3 1.0 OG1 A:THR57 4.8 39.2 1.0 C A:TYR73 4.9 49.7 1.0 C A:TYR54 4.9 32.3 1.0 CB A:THR57 5.0 36.5 1.0 CD2 A:TYR54 5.0 39.9 1.0

Zinc binding site 3 out of 3 in the SMYD2 in Complex with Sgc Probe Bay-598


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of SMYD2 in Complex with Sgc Probe Bay-598 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1005 b:41.0 occ:0.80 NE2 A:HIS86 2.2 44.8 1.0 SG A:CYS68 2.2 56.1 1.0 SG A:CYS65 2.3 65.8 1.0 SG A:CYS90 2.4 61.7 1.0 CD2 A:HIS86 3.0 43.4 1.0 CB A:CYS65 3.2 68.4 1.0 CE1 A:HIS86 3.3 41.8 1.0 N A:CYS68 3.5 71.4 1.0 CB A:CYS68 3.5 66.8 1.0 CB A:CYS90 3.6 53.3 1.0 CB A:ARG67 3.9 71.6 1.0 CA A:CYS68 4.1 69.5 1.0 CG A:HIS86 4.2 38.5 1.0 ND1 A:HIS86 4.3 38.2 1.0 CA A:CYS90 4.3 49.4 1.0 C A:ARG67 4.5 71.5 1.0 CA A:CYS65 4.6 70.0 1.0 CA A:ARG67 4.6 73.3 1.0 N A:ARG67 4.7 75.2 1.0 CG A:ARG67 4.8 75.4 1.0 CZ3 A:TRP83 4.8 47.7 1.0 C A:CYS68 4.8 71.9 1.0 CD A:ARG67 4.8 78.0 1.0 C A:CYS65 4.9 72.7 1.0 CB A:ALA71 4.9 46.4 1.0 O A:CYS65 5.0 74.1 1.0 N A:LYS69 5.0 74.2 1.0

E.Eggert, R.C.Hillig, S.Kohr, D.Stockigt, J.Weiske, N.Barak, J.Mowat, T.Brumby, C.D.Christ, A.Ter Laak, T.Lang, A.E.Fernandez-Montalvan, V.Badock, H.Weinmann, I.V.Hartung, D.Barsyte-Lovejoy, M.Szewczyk, S.Kennedy, F.Li, M.Vedadi, P.J.Brown, V.Santhakumar, C.H.Arrowsmith, T.Stellfeld, C.Stresemann. Discovery and Characterization of A Highly Potent and Selective Aminopyrazoline-Based in Vivo Probe (Bay-598) For the Protein Lysine Methyltransferase SMYD2. J.Med.Chem. V. 59 4578 2016.
ISSN: ISSN 0022-2623
PubMed: 27075367
DOI: 10.1021/ACS.JMEDCHEM.5B01890