Zinc in PDB 6yuh: Crystal Structure of SMYD3 with Diperodon R Enantiomer Bound to Allosteric Site

All present enzymatic activity of Crystal Structure of SMYD3 with Diperodon R Enantiomer Bound to Allosteric Site:
2.1.1.354;

The structure of Crystal Structure of SMYD3 with Diperodon R Enantiomer Bound to Allosteric Site, PDB code: 6yuh was solved by D.Cederfelt, V.O.Talibov, D.Dobritzsch, U.H.Danielson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	52.30 / 1.93
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.142, 66.284, 105.949, 90, 90, 90
R / Rfree (%)	18.6 / 23

The binding sites of Zinc atom in the Crystal Structure of SMYD3 with Diperodon R Enantiomer Bound to Allosteric Site (pdb code 6yuh). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of SMYD3 with Diperodon R Enantiomer Bound to Allosteric Site, PDB code: 6yuh:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of SMYD3 with Diperodon R Enantiomer Bound to Allosteric Site


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of SMYD3 with Diperodon R Enantiomer Bound to Allosteric Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn504 b:22.0 occ:1.00 SG A:CYS208 2.3 21.7 1.0 SG A:CYS263 2.3 20.2 1.0 SG A:CYS261 2.4 21.5 1.0 SG A:CYS266 2.4 19.4 1.0 CB A:CYS263 3.3 22.1 1.0 CB A:CYS261 3.4 28.3 1.0 CB A:CYS208 3.4 17.5 1.0 CB A:CYS266 3.4 16.1 1.0 N A:CYS266 4.1 23.5 1.0 N A:CYS208 4.1 19.5 1.0 N A:CYS263 4.1 25.0 1.0 CA A:CYS263 4.2 25.5 1.0 CA A:CYS266 4.3 18.5 1.0 CA A:CYS208 4.4 18.6 1.0 NH2 A:ARG249 4.5 21.6 1.0 NE2 A:HIS206 4.5 16.1 1.0 O A:CYS263 4.6 18.8 1.0 C A:CYS263 4.6 22.6 1.0 NE A:ARG249 4.6 19.9 1.0 CA A:CYS261 4.6 24.7 1.0 O A:HOH793 4.7 26.9 1.0 C A:CYS261 4.8 26.8 1.0 O A:CYS261 4.9 24.5 1.0 CD2 A:HIS206 5.0 14.9 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of SMYD3 with Diperodon R Enantiomer Bound to Allosteric Site


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of SMYD3 with Diperodon R Enantiomer Bound to Allosteric Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn505 b:23.6 occ:1.00 SG A:CYS49 2.2 22.0 1.0 SG A:CYS75 2.3 24.9 1.0 SG A:CYS52 2.4 23.7 1.0 SG A:CYS71 2.4 27.2 1.0 CB A:CYS49 3.1 26.2 1.0 CB A:CYS75 3.2 25.4 1.0 CB A:CYS52 3.3 23.8 1.0 CB A:CYS71 3.6 23.1 1.0 N A:CYS52 3.7 23.3 1.0 O A:HOH839 3.9 27.5 1.0 N A:CYS71 4.1 23.3 1.0 CA A:CYS52 4.1 23.7 1.0 O A:HOH824 4.2 31.4 1.0 CA A:CYS71 4.4 29.8 1.0 OG A:SER72 4.5 22.6 1.0 CB A:ARG51 4.6 24.2 1.0 CA A:CYS49 4.6 24.7 1.0 CA A:CYS75 4.7 25.2 1.0 C A:ARG51 4.8 28.7 1.0 C A:CYS52 4.9 23.6 1.0 N A:ARG51 4.9 21.6 1.0 C A:CYS71 5.0 27.4 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of SMYD3 with Diperodon R Enantiomer Bound to Allosteric Site


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of SMYD3 with Diperodon R Enantiomer Bound to Allosteric Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn506 b:33.9 occ:1.00 NE2 A:HIS83 2.1 26.8 1.0 SG A:CYS65 2.2 32.9 1.0 SG A:CYS87 2.4 33.2 1.0 SG A:CYS62 2.5 40.7 1.0 CE1 A:HIS83 3.0 26.7 1.0 CD2 A:HIS83 3.1 22.4 1.0 CB A:CYS87 3.2 35.9 1.0 CB A:CYS65 3.4 45.1 1.0 CB A:CYS62 3.4 30.6 1.0 N A:CYS65 3.7 48.8 1.0 CA A:CYS87 3.9 29.0 1.0 CA A:CYS65 4.1 45.3 1.0 ND1 A:HIS83 4.2 25.4 1.0 CG A:HIS83 4.2 26.5 1.0 CB A:GLN64 4.5 50.1 1.0 CB A:ALA68 4.6 25.8 1.0 C A:CYS87 4.7 28.2 1.0 CA A:CYS62 4.7 36.3 1.0 C A:GLN64 4.8 49.8 1.0 O A:HOH690 4.8 31.5 1.0 CZ3 A:TRP80 4.8 49.8 1.0 N A:GLN64 4.8 48.5 1.0 O A:CYS87 4.8 32.8 1.0 N A:ARG66 4.9 43.9 1.0 C A:CYS65 4.9 47.6 1.0 C A:CYS62 4.9 36.4 1.0 CA A:GLN64 5.0 50.9 1.0

V.O.Talibov, E.Fabini, E.Fitzgerald, D.Tedesco, D.Eriksson, M.J.Talu, M.M.Rachman, F.Mihalic, E.Manoni, M.Naldi, P.Sanese, G.Forte, M.L.Signorile, X.Barril, C.Simone, M.Bartolini, D.Dobritzsch, A.Del Rio, U.H.Danielson. Discovery of An Allosteric Ligand Binding Site in SMYD3 Lysine Methyltransferase. Chembiochem 2021.
ISSN: ESSN 1439-7633
PubMed: 33400854
DOI: 10.1002/CBIC.202000736