Zinc in PDB 7o2b: X-Ray Structure of SMYD3 in Complex with Benzodiazepine-Type Inhibitor 6

All present enzymatic activity of X-Ray Structure of SMYD3 in Complex with Benzodiazepine-Type Inhibitor 6:
2.1.1.354;

The structure of X-Ray Structure of SMYD3 in Complex with Benzodiazepine-Type Inhibitor 6, PDB code: 7o2b was solved by H.Steuber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.40 / 2.03
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	62.024, 66.171, 107.471, 90, 90, 90
R / Rfree (%)	20.4 / 25.8

The structure of X-Ray Structure of SMYD3 in Complex with Benzodiazepine-Type Inhibitor 6 also contains other interesting chemical elements:

Fluorine

(F)

1 atom

The binding sites of Zinc atom in the X-Ray Structure of SMYD3 in Complex with Benzodiazepine-Type Inhibitor 6 (pdb code 7o2b). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the X-Ray Structure of SMYD3 in Complex with Benzodiazepine-Type Inhibitor 6, PDB code: 7o2b:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the X-Ray Structure of SMYD3 in Complex with Benzodiazepine-Type Inhibitor 6


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of X-Ray Structure of SMYD3 in Complex with Benzodiazepine-Type Inhibitor 6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1002 b:28.2 occ:1.00 SG A:CYS49 2.2 20.6 1.0 SG A:CYS75 2.4 26.0 1.0 SG A:CYS52 2.4 27.8 1.0 SG A:CYS71 2.5 31.6 1.0 CB A:CYS75 3.1 25.9 1.0 CB A:CYS49 3.2 27.6 1.0 CB A:CYS71 3.3 31.0 1.0 CB A:CYS52 3.4 26.0 1.0 N A:CYS52 3.7 24.7 1.0 O A:HOH1303 3.7 34.0 1.0 N A:CYS71 4.0 34.4 1.0 O A:HOH1272 4.1 31.7 1.0 CA A:CYS52 4.1 26.0 1.0 CA A:CYS71 4.2 33.8 1.0 OG A:SER72 4.4 31.3 1.0 CA A:CYS49 4.6 26.1 1.0 CA A:CYS75 4.6 23.7 1.0 N A:SER72 4.8 34.2 1.0 C A:CYS71 4.8 36.6 1.0 C A:ARG51 4.9 26.2 1.0 CB A:ARG51 4.9 31.3 1.0 C A:CYS52 5.0 24.4 1.0

Zinc binding site 2 out of 3 in the X-Ray Structure of SMYD3 in Complex with Benzodiazepine-Type Inhibitor 6


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of X-Ray Structure of SMYD3 in Complex with Benzodiazepine-Type Inhibitor 6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1003 b:56.8 occ:1.00 SG A:CYS65 2.0 54.3 1.0 NE2 A:HIS83 2.4 54.1 1.0 SG A:CYS87 2.5 50.8 1.0 SG A:CYS62 2.8 57.2 1.0 CE1 A:HIS83 2.8 48.3 1.0 CB A:CYS65 3.0 57.6 1.0 CD2 A:HIS83 3.4 49.2 1.0 N A:CYS65 3.6 67.8 1.0 CB A:CYS87 3.6 49.6 1.0 CA A:CYS87 3.9 54.2 1.0 CA A:CYS65 3.9 63.6 1.0 CB A:CYS62 3.9 52.1 1.0 ND1 A:HIS83 3.9 46.0 1.0 CG A:HIS83 4.2 44.2 1.0 CB A:GLN64 4.3 81.4 1.0 CZ3 A:TRP80 4.4 43.0 1.0 O A:CYS87 4.4 49.2 1.0 O A:HIS83 4.4 49.0 1.0 C A:CYS87 4.6 56.5 1.0 C A:GLN64 4.7 71.3 1.0 N A:ARG66 4.9 64.9 1.0 C A:CYS65 4.9 62.9 1.0 CB A:ALA68 4.9 63.6 1.0

Zinc binding site 3 out of 3 in the X-Ray Structure of SMYD3 in Complex with Benzodiazepine-Type Inhibitor 6


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of X-Ray Structure of SMYD3 in Complex with Benzodiazepine-Type Inhibitor 6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1004 b:20.1 occ:1.00 SG A:CYS208 2.1 17.8 1.0 SG A:CYS261 2.4 22.2 1.0 SG A:CYS266 2.4 17.4 1.0 SG A:CYS263 2.5 20.9 1.0 CB A:CYS261 3.3 20.4 1.0 CB A:CYS266 3.4 15.5 1.0 CB A:CYS208 3.4 17.7 1.0 CB A:CYS263 3.5 20.2 1.0 N A:CYS266 4.0 16.1 1.0 N A:CYS263 4.2 21.7 1.0 CA A:CYS266 4.3 16.6 1.0 CA A:CYS263 4.4 21.5 1.0 N A:CYS208 4.5 16.2 1.0 NH2 A:ARG249 4.5 13.9 1.0 CA A:CYS208 4.6 16.4 1.0 CA A:CYS261 4.6 18.4 1.0 NE A:ARG249 4.6 13.2 1.0 C A:CYS261 4.7 19.5 1.0 NE2 A:HIS206 4.7 15.0 1.0 O A:CYS261 4.8 18.3 1.0 C A:CYS263 4.8 21.6 1.0 O A:HOH1271 4.8 18.0 1.0 O A:CYS263 4.9 21.7 1.0

S.Gradl, H.Steuber, J.Weiske, M.M.Szewczyk, N.Schmees, S.Siegel, D.Stoeckigt, C.D.Christ, F.Li, S.Organ, M.Abbey, S.Kennedy, I.Chau, V.Trush, D.Barsyte-Lovejoy, P.J.Brown, M.Vedadi, C.Arrowsmith, M.Husemann, V.Badock, M.Bauser, A.Haegebarth, I.V.Hartung, C.Stresemann. Discovery of the SMYD3 Inhibitor Bay-6035 Using Thermal Shift Assay (Tsa)-Based High-Throughput Screening. Slas Discov 19409 2021.
ISSN: ISSN 2472-5560
PubMed: 34154424
DOI: 10.1177/24725552211019409