Zinc in PDB 8owo: SMYD3 in Complex with Fragment FL01507

All present enzymatic activity of SMYD3 in Complex with Fragment FL01507:
2.1.1.354;

The structure of SMYD3 in Complex with Fragment FL01507, PDB code: 8owo 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)	53.08 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	61.08, 66.14, 107.28, 90, 90, 90
R / Rfree (%)	16.1 / 20

The binding sites of Zinc atom in the SMYD3 in Complex with Fragment FL01507 (pdb code 8owo). 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 FL01507, PDB code: 8owo:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the SMYD3 in Complex with Fragment FL01507


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 FL01507 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:22.4 occ:1.00 SG A:CYS266 2.3 18.3 1.0 SG A:CYS208 2.3 20.9 1.0 SG A:CYS261 2.3 24.3 1.0 SG A:CYS263 2.4 21.6 1.0 HB3 A:CYS261 3.1 24.2 1.0 HB2 A:CYS266 3.1 19.7 1.0 HB2 A:CYS208 3.2 23.1 1.0 CB A:CYS261 3.3 20.2 1.0 CB A:CYS266 3.4 16.4 1.0 HB3 A:CYS263 3.4 30.8 1.0 H A:CYS263 3.4 31.3 1.0 CB A:CYS208 3.4 19.3 1.0 H A:CYS266 3.4 20.3 1.0 CB A:CYS263 3.5 25.7 1.0 HH21 A:ARG249 3.7 18.7 1.0 H A:CYS208 3.7 20.7 1.0 HB2 A:CYS261 3.7 24.2 1.0 HE A:ARG249 3.8 20.4 1.0 HB3 A:CYS208 4.0 23.1 1.0 N A:CYS266 4.0 16.9 1.0 HB2 A:ARG265 4.0 22.6 1.0 HE2 A:HIS206 4.0 18.8 1.0 HB3 A:CYS266 4.1 19.7 1.0 N A:CYS263 4.1 26.1 1.0 HB2 A:CYS263 4.3 30.8 1.0 CA A:CYS266 4.3 16.2 1.0 CA A:CYS263 4.3 28.6 1.0 N A:CYS208 4.4 17.2 1.0 NH2 A:ARG249 4.5 15.6 1.0 CA A:CYS261 4.5 21.7 1.0 CA A:CYS208 4.5 17.1 1.0 NE A:ARG249 4.6 17.0 1.0 C A:CYS261 4.6 23.2 1.0 HA A:CYS266 4.6 19.5 1.0 O A:CYS261 4.7 20.6 1.0 NE2 A:HIS206 4.8 15.7 1.0 O A:HOH951 4.9 19.4 1.0 HD2 A:HIS206 4.9 21.4 1.0 C A:CYS263 4.9 23.1 1.0 H A:ARG265 4.9 20.9 1.0 HA A:CYS261 4.9 26.0 1.0 CB A:ARG265 4.9 18.8 1.0 N A:ASP262 5.0 25.4 1.0 C A:ARG265 5.0 19.5 1.0

Zinc binding site 2 out of 3 in the SMYD3 in Complex with Fragment FL01507


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 FL01507 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:25.1 occ:1.00 SG A:CYS75 2.3 24.7 1.0 SG A:CYS71 2.3 26.2 1.0 SG A:CYS52 2.3 25.5 1.0 SG A:CYS49 2.4 26.2 1.0 H A:CYS52 3.0 26.1 1.0 HB3 A:CYS52 3.1 30.1 1.0 HB3 A:CYS71 3.1 25.9 1.0 HB2 A:CYS75 3.1 33.6 1.0 CB A:CYS75 3.1 28.0 1.0 HB3 A:CYS75 3.1 33.6 1.0 H A:CYS71 3.2 32.2 1.0 HB3 A:CYS49 3.2 34.4 1.0 CB A:CYS49 3.2 28.7 1.0 HB2 A:CYS49 3.3 34.4 1.0 CB A:CYS52 3.3 25.1 1.0 CB A:CYS71 3.3 21.6 1.0 HG A:SER72 3.7 31.4 1.0 N A:CYS52 3.8 21.8 1.0 O A:HOH1082 3.8 30.0 1.0 HB3 A:ARG51 3.8 30.7 1.0 N A:CYS71 3.9 26.8 1.0 HB2 A:CYS52 4.1 30.1 1.0 HB2 A:CYS71 4.1 25.9 1.0 CA A:CYS52 4.1 22.7 1.0 CA A:CYS71 4.2 29.0 1.0 O A:HOH966 4.2 36.2 1.0 HG2 A:ARG51 4.3 31.6 1.0 OG A:SER72 4.4 26.1 1.0 H A:ARG51 4.5 24.4 1.0 CA A:CYS75 4.6 20.4 1.0 HH11 A:ARG51 4.7 51.0 1.0 H A:LEU54 4.7 35.0 1.0 CB A:ARG51 4.7 25.6 1.0 CA A:CYS49 4.7 23.9 1.0 HB2 A:LEU54 4.7 28.1 1.0 H A:LEU53 4.7 24.5 1.0 HA A:CYS75 4.8 24.5 1.0 H A:SER72 4.8 28.5 1.0 HA A:TYR70 4.8 32.1 1.0 HA A:CYS52 4.9 27.2 1.0 C A:CYS52 4.9 24.3 1.0 HB3 A:TYR70 4.9 29.6 1.0 C A:CYS71 4.9 29.8 1.0 C A:ARG51 4.9 26.9 1.0 H A:CYS75 4.9 27.3 1.0 N A:SER72 4.9 23.8 1.0 HA A:CYS71 5.0 34.9 1.0

Zinc binding site 3 out of 3 in the SMYD3 in Complex with Fragment FL01507


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 FL01507 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn504 b:30.0 occ:1.00 NE2 A:HIS83 2.0 27.0 1.0 SG A:CYS62 2.3 25.3 1.0 SG A:CYS87 2.3 28.7 1.0 SG A:CYS65 2.3 29.7 1.0 H A:CYS65 2.9 32.1 1.0 CE1 A:HIS83 2.9 25.6 1.0 HB3 A:CYS65 2.9 36.7 1.0 HE1 A:HIS83 3.0 30.8 1.0 HB3 A:CYS62 3.0 38.4 1.0 HB2 A:CYS87 3.1 35.4 1.0 CD2 A:HIS83 3.1 27.6 1.0 CB A:CYS65 3.2 30.6 1.0 CB A:CYS62 3.2 32.0 1.0 CB A:CYS87 3.2 29.5 1.0 HD2 A:HIS83 3.4 33.1 1.0 HB2 A:CYS62 3.4 38.4 1.0 HA A:CYS87 3.5 34.7 1.0 N A:CYS65 3.5 26.7 1.0 HZ3 A:TRP80 3.8 39.5 1.0 HB3 A:GLN64 3.8 38.7 1.0 CA A:CYS87 3.9 28.9 1.0 HB3 A:ALA68 3.9 33.7 1.0 CA A:CYS65 3.9 34.7 1.0 HB2 A:CYS65 4.0 36.7 1.0 HB3 A:CYS87 4.1 35.4 1.0 ND1 A:HIS83 4.1 24.6 1.0 HG2 A:GLN64 4.1 60.8 1.0 CG A:HIS83 4.2 26.6 1.0 H A:ARG66 4.2 39.0 1.0 H A:ALA68 4.4 34.9 1.0 H A:GLN64 4.4 37.7 1.0 HB2 A:ALA68 4.6 33.7 1.0 C A:GLN64 4.6 41.1 1.0 CB A:GLN64 4.6 32.2 1.0 CA A:CYS62 4.6 28.0 1.0 HA A:CYS65 4.7 41.7 1.0 H A:VAL67 4.7 38.1 1.0 CB A:ALA68 4.7 28.1 1.0 CZ3 A:TRP80 4.7 32.9 1.0 N A:ARG66 4.7 32.5 1.0 O A:HOH958 4.8 25.2 1.0 CG A:GLN64 4.8 50.6 1.0 C A:CYS65 4.8 35.9 1.0 C A:CYS87 4.8 31.4 1.0 HD1 A:HIS83 4.8 29.5 1.0 N A:GLN64 4.9 31.4 1.0 CA A:GLN64 4.9 33.8 1.0 OE1 A:GLN64 4.9 50.1 1.0 O A:CYS87 4.9 31.6 1.0 C A:CYS62 4.9 29.7 1.0 HH A:TYR70 5.0 30.4 1.0 N A:CYS87 5.0 28.1 1.0

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