Zinc in PDB 7qnr: SMYD3 in Complex with Fragment FL01791

All present enzymatic activity of SMYD3 in Complex with Fragment FL01791:
2.1.1.354;

The structure of SMYD3 in Complex with Fragment FL01791, PDB code: 7qnr was solved by B.A.Lund, D.Cederfelt, D.Dobritzsch, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.56 / 1.57
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.236, 66.218, 105.302, 90, 90, 90
R / Rfree (%)	20.4 / 23.5

The binding sites of Zinc atom in the SMYD3 in Complex with Fragment FL01791 (pdb code 7qnr). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the SMYD3 in Complex with Fragment FL01791, PDB code: 7qnr:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the SMYD3 in Complex with Fragment FL01791


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of SMYD3 in Complex with Fragment FL01791 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:22.6 occ:1.00 SG A:CYS261 2.3 22.6 1.0 SG A:CYS263 2.3 25.0 1.0 SG A:CYS266 2.3 20.3 1.0 SG A:CYS208 2.4 20.9 1.0 HB2 A:CYS208 3.1 27.5 1.0 HB3 A:CYS261 3.2 31.6 1.0 HB2 A:CYS266 3.2 29.8 1.0 CB A:CYS261 3.4 26.1 1.0 H A:CYS263 3.4 39.6 1.0 HB3 A:CYS263 3.4 35.2 1.0 CB A:CYS208 3.4 22.6 1.0 CB A:CYS266 3.4 24.6 1.0 CB A:CYS263 3.5 29.1 1.0 H A:CYS208 3.5 25.1 1.0 H A:CYS266 3.5 27.6 1.0 HE A:ARG249 3.8 30.6 1.0 HH21 A:ARG249 3.8 30.6 1.0 HB2 A:CYS261 3.8 31.6 1.0 HE2 A:HIS206 3.8 22.6 1.0 N A:CYS263 4.0 32.8 1.0 HB3 A:CYS208 4.1 27.5 1.0 N A:CYS266 4.1 22.8 1.0 HB3 A:CYS266 4.1 29.8 1.0 N A:CYS208 4.2 20.6 1.0 HB2 A:CYS263 4.2 35.2 1.0 HB2 A:ARG265 4.2 31.5 1.0 CA A:CYS263 4.3 28.9 1.0 CA A:CYS266 4.4 23.1 1.0 CA A:CYS208 4.5 20.3 1.0 CA A:CYS261 4.5 24.6 1.0 NE2 A:HIS206 4.6 18.6 1.0 C A:CYS261 4.6 27.5 1.0 NE A:ARG249 4.6 25.2 1.0 NH2 A:ARG249 4.6 25.3 1.0 HD2 A:HIS206 4.6 22.8 1.0 HD11 A:LEU253 4.6 24.2 1.0 HA A:CYS266 4.7 28.1 1.0 HD12 A:LEU253 4.7 24.2 1.0 O A:CYS263 4.7 24.8 1.0 C A:CYS263 4.7 28.0 1.0 O A:CYS261 4.8 29.0 1.0 O A:HOH790 4.9 31.3 1.0 HA A:CYS261 4.9 29.8 1.0 N A:ASP262 5.0 31.7 1.0 CD2 A:HIS206 5.0 18.7 1.0 HA A:SER207 5.0 25.0 1.0 HD13 A:LEU253 5.0 24.2 1.0 CD1 A:LEU253 5.0 19.9 1.0

Zinc binding site 2 out of 3 in the SMYD3 in Complex with Fragment FL01791


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of SMYD3 in Complex with Fragment FL01791 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:22.1 occ:1.00 SG A:CYS75 2.2 29.4 1.0 SG A:CYS52 2.3 24.6 1.0 SG A:CYS49 2.4 22.4 1.0 SG A:CYS71 2.4 25.8 1.0 H A:CYS52 3.0 30.1 1.0 HB3 A:CYS49 3.0 29.9 1.0 HB3 A:CYS52 3.1 28.1 1.0 CB A:CYS49 3.1 24.7 1.0 CB A:CYS75 3.2 30.5 1.0 HB2 A:CYS75 3.2 36.9 1.0 HB2 A:CYS49 3.2 29.9 1.0 H A:CYS71 3.2 31.2 1.0 HB3 A:CYS75 3.2 36.9 1.0 HB3 A:CYS71 3.3 33.9 1.0 CB A:CYS52 3.3 24.4 1.0 CB A:CYS71 3.4 28.0 1.0 HB3 A:ARG51 3.7 31.4 1.0 N A:CYS52 3.7 24.8 1.0 HG A:SER72 3.8 32.8 1.0 N A:CYS71 4.0 25.8 1.0 HB2 A:CYS52 4.1 28.1 1.0 CA A:CYS52 4.1 24.2 1.0 HB2 A:CYS71 4.2 33.9 1.0 CA A:CYS71 4.3 29.4 1.0 HD2 A:ARG51 4.3 52.6 1.0 O A:HOH859 4.3 37.1 1.0 H A:ARG51 4.4 28.7 1.0 OG A:SER72 4.6 27.4 1.0 CA A:CYS75 4.6 27.5 1.0 CA A:CYS49 4.6 24.9 1.0 CB A:ARG51 4.6 25.9 1.0 H A:SER72 4.6 31.1 1.0 H A:LEU53 4.7 25.5 1.0 H A:LEU54 4.7 31.0 1.0 HA A:TYR70 4.7 30.9 1.0 HH21 A:ARG51 4.8 58.0 1.0 HA A:CYS75 4.8 33.3 1.0 HB2 A:LEU54 4.8 33.8 1.0 C A:ARG51 4.9 24.6 1.0 H A:CYS75 4.9 34.0 1.0 HA A:CYS52 4.9 29.3 1.0 N A:SER72 4.9 26.6 1.0 HD3 A:ARG51 4.9 52.6 1.0 C A:CYS71 4.9 27.1 1.0 C A:CYS52 4.9 23.4 1.0 HD1 A:TYR70 4.9 29.8 1.0 HA A:CYS49 5.0 30.2 1.0

Zinc binding site 3 out of 3 in the SMYD3 in Complex with Fragment FL01791


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of SMYD3 in Complex with Fragment FL01791 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn504 b:27.6 occ:1.00 NE2 A:HIS83 2.1 25.7 1.0 SG A:CYS65 2.2 29.7 1.0 SG A:CYS87 2.3 29.2 1.0 SG A:CYS62 2.3 29.9 1.0 O A:HOH604 2.7 42.9 1.0 H A:CYS65 2.8 47.8 1.0 HB3 A:CYS62 2.9 40.4 1.0 HB2 A:CYS87 3.0 32.2 1.0 CE1 A:HIS83 3.1 23.5 1.0 CD2 A:HIS83 3.1 24.4 1.0 HB3 A:CYS65 3.2 39.4 1.0 CB A:CYS87 3.2 26.6 1.0 CB A:CYS62 3.2 33.4 1.0 HE1 A:HIS83 3.2 28.5 1.0 CB A:CYS65 3.3 32.8 1.0 HD2 A:HIS83 3.3 29.6 1.0 HB2 A:CYS62 3.5 40.4 1.0 HA A:CYS87 3.5 32.1 1.0 N A:CYS65 3.6 39.6 1.0 HB3 A:GLN64 3.7 58.9 1.0 CA A:CYS87 3.9 26.5 1.0 HB3 A:ALA68 4.0 33.2 1.0 HB3 A:CYS87 4.0 32.2 1.0 CA A:CYS65 4.1 41.5 1.0 HB2 A:CYS65 4.1 39.4 1.0 H A:ARG66 4.1 49.5 1.0 ND1 A:HIS83 4.2 26.5 1.0 HE21 A:GLN64 4.2 75.4 1.0 HZ3 A:TRP80 4.2 56.8 1.0 H A:GLN64 4.2 50.0 1.0 CG A:HIS83 4.2 24.0 1.0 H A:ALA68 4.3 36.0 1.0 O A:HOH818 4.5 33.2 1.0 CA A:CYS62 4.6 33.4 1.0 H A:VAL67 4.6 39.2 1.0 CB A:GLN64 4.6 48.9 1.0 N A:ARG66 4.7 41.0 1.0 HB2 A:ALA68 4.7 33.2 1.0 C A:GLN64 4.7 45.0 1.0 CB A:ALA68 4.8 27.4 1.0 C A:CYS87 4.8 32.5 1.0 HD12 A:LEU90 4.8 38.2 1.0 HA A:CYS65 4.8 50.1 1.0 N A:GLN64 4.8 41.4 1.0 C A:CYS65 4.8 44.6 1.0 C A:CYS62 4.9 33.2 1.0 O A:CYS87 4.9 33.1 1.0 HD1 A:HIS83 5.0 32.1 1.0 CA A:GLN64 5.0 43.8 1.0

B.A.Lund, D.Cederfelt, D.Dobritzsch. SMYD3 in Complex with Fragments To Be Published.