Zinc in PDB 7qnu: SMYD3 in Complex with Fragment FL08619

All present enzymatic activity of SMYD3 in Complex with Fragment FL08619:
2.1.1.354;

The structure of SMYD3 in Complex with Fragment FL08619, PDB code: 7qnu 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)	41.08 / 1.64
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	59.931, 65.886, 105.085, 90, 90, 90
R / Rfree (%)	18.5 / 23

The binding sites of Zinc atom in the SMYD3 in Complex with Fragment FL08619 (pdb code 7qnu). 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 FL08619, PDB code: 7qnu:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the SMYD3 in Complex with Fragment FL08619


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 FL08619 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:16.3 occ:1.00 SG A:CYS263 2.2 17.4 1.0 SG A:CYS208 2.3 16.8 1.0 SG A:CYS261 2.3 15.8 1.0 SG A:CYS266 2.3 15.7 1.0 HB2 A:CYS208 3.1 20.5 1.0 HB3 A:CYS261 3.2 21.0 1.0 HB2 A:CYS266 3.3 15.8 1.0 HB3 A:CYS263 3.3 26.4 1.0 H A:CYS263 3.3 24.7 1.0 CB A:CYS208 3.4 17.0 1.0 CB A:CYS261 3.4 17.5 1.0 H A:CYS266 3.4 18.8 1.0 CB A:CYS263 3.4 22.0 1.0 H A:CYS208 3.4 16.8 1.0 CB A:CYS266 3.5 13.1 1.0 HE2 A:HIS206 3.7 14.6 1.0 HE A:ARG249 3.7 17.4 1.0 HH21 A:ARG249 3.8 18.9 1.0 HB2 A:CYS261 3.9 21.0 1.0 N A:CYS263 4.0 20.5 1.0 HB3 A:CYS208 4.0 20.5 1.0 N A:CYS266 4.0 15.6 1.0 HB2 A:ARG265 4.1 20.7 1.0 N A:CYS208 4.1 14.0 1.0 HB3 A:CYS266 4.2 15.8 1.0 HB2 A:CYS263 4.2 26.4 1.0 CA A:CYS263 4.2 21.9 1.0 CA A:CYS266 4.3 12.2 1.0 CA A:CYS208 4.4 18.6 1.0 NE2 A:HIS206 4.5 12.1 1.0 NE A:ARG249 4.6 14.5 1.0 CA A:CYS261 4.6 16.8 1.0 C A:CYS261 4.6 18.7 1.0 NH2 A:ARG249 4.6 15.7 1.0 O A:HOH921 4.6 23.5 1.0 HD11 A:LEU253 4.6 27.3 1.0 O A:CYS263 4.6 15.6 1.0 HD2 A:HIS206 4.6 12.4 1.0 C A:CYS263 4.7 22.0 1.0 HA A:CYS266 4.7 14.2 1.0 O A:CYS261 4.7 18.3 1.0 HD12 A:LEU253 4.8 27.3 1.0 H A:ARG265 4.9 17.2 1.0 HA A:SER207 4.9 16.8 1.0 HA A:CYS208 4.9 22.4 1.0 HA A:CYS261 4.9 20.3 1.0 CD2 A:HIS206 5.0 10.3 1.0

Zinc binding site 2 out of 3 in the SMYD3 in Complex with Fragment FL08619


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 FL08619 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:16.8 occ:1.00 SG A:CYS75 2.2 17.6 1.0 SG A:CYS71 2.3 18.5 1.0 SG A:CYS49 2.3 16.8 1.0 SG A:CYS52 2.3 18.4 1.0 H A:CYS52 3.0 20.5 1.0 HB3 A:CYS49 3.1 23.3 1.0 HB3 A:CYS52 3.1 25.0 1.0 CB A:CYS75 3.1 21.8 1.0 CB A:CYS49 3.1 19.3 1.0 HB2 A:CYS75 3.2 26.2 1.0 HB3 A:CYS75 3.2 26.2 1.0 H A:CYS71 3.2 24.6 1.0 HB2 A:CYS49 3.3 23.3 1.0 CB A:CYS52 3.3 20.8 1.0 HB3 A:CYS71 3.3 25.0 1.0 CB A:CYS71 3.4 20.8 1.0 HG A:SER72 3.7 19.2 1.0 N A:CYS52 3.7 17.1 1.0 HB3 A:ARG51 3.8 17.9 1.0 N A:CYS71 4.0 20.4 1.0 HB2 A:CYS52 4.1 25.0 1.0 CA A:CYS52 4.1 17.2 1.0 HD3 A:ARG51 4.1 46.8 1.0 HH21 A:ARG51 4.1 46.5 1.0 HB2 A:CYS71 4.2 25.0 1.0 O A:HOH1034 4.2 38.4 1.0 O A:HOH948 4.2 26.6 1.0 CA A:CYS71 4.3 25.8 1.0 H A:ARG51 4.4 20.9 1.0 OG A:SER72 4.4 15.9 1.0 CA A:CYS75 4.6 17.0 1.0 CA A:CYS49 4.6 18.9 1.0 H A:LEU54 4.7 23.5 1.0 H A:SER72 4.7 18.9 1.0 HA A:TYR70 4.7 24.1 1.0 HB2 A:LEU54 4.7 24.9 1.0 CB A:ARG51 4.7 14.9 1.0 H A:LEU53 4.7 22.0 1.0 HA A:CYS75 4.7 20.5 1.0 NH2 A:ARG51 4.9 38.7 1.0 C A:ARG51 4.9 17.4 1.0 HD1 A:TYR70 4.9 19.0 1.0 HA A:CYS52 4.9 20.7 1.0 C A:CYS71 4.9 16.1 1.0 N A:SER72 4.9 15.7 1.0 H A:CYS75 5.0 20.3 1.0 C A:CYS52 5.0 18.2 1.0 HB3 A:TYR70 5.0 19.4 1.0

Zinc binding site 3 out of 3 in the SMYD3 in Complex with Fragment FL08619


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 FL08619 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn504 b:20.4 occ:1.00 NE2 A:HIS83 2.0 16.7 1.0 SG A:CYS65 2.2 20.5 1.0 SG A:CYS87 2.2 23.4 1.0 SG A:CYS62 2.4 19.5 1.0 HB3 A:CYS62 2.9 25.0 1.0 CE1 A:HIS83 2.9 13.2 1.0 H A:CYS65 2.9 35.6 1.0 HB2 A:CYS87 2.9 18.9 1.0 HE1 A:HIS83 3.0 15.9 1.0 CD2 A:HIS83 3.1 17.7 1.0 CB A:CYS87 3.1 16.0 1.0 CB A:CYS62 3.1 20.8 1.0 HB3 A:CYS65 3.1 30.3 1.0 CB A:CYS65 3.3 25.2 1.0 HB2 A:CYS62 3.3 25.0 1.0 HD2 A:HIS83 3.3 21.2 1.0 HA A:CYS87 3.4 21.1 1.0 N A:CYS65 3.7 29.6 1.0 HB3 A:GLN64 3.7 37.6 1.0 HB3 A:ALA68 3.8 24.8 1.0 CA A:CYS87 3.8 17.6 1.0 HZ3 A:TRP80 3.9 41.8 1.0 HB3 A:CYS87 3.9 18.9 1.0 ND1 A:HIS83 4.0 16.4 1.0 HB2 A:CYS65 4.1 30.3 1.0 CA A:CYS65 4.1 31.4 1.0 HG2 A:GLN64 4.1 52.2 1.0 CG A:HIS83 4.2 13.3 1.0 H A:GLN64 4.2 30.9 1.0 H A:ALA68 4.3 22.3 1.0 H A:ARG66 4.4 32.4 1.0 O A:HOH917 4.5 31.9 1.0 CB A:GLN64 4.5 31.2 1.0 CA A:CYS62 4.5 21.9 1.0 HB2 A:ALA68 4.5 24.8 1.0 CB A:ALA68 4.6 20.6 1.0 C A:CYS87 4.7 24.2 1.0 H A:VAL67 4.7 23.4 1.0 C A:GLN64 4.7 32.3 1.0 CZ3 A:TRP80 4.7 34.8 1.0 HD1 A:HIS83 4.8 19.8 1.0 N A:GLN64 4.8 25.7 1.0 O A:CYS87 4.8 23.5 1.0 CG A:GLN64 4.8 43.5 1.0 HA A:CYS65 4.8 37.8 1.0 N A:ARG66 4.9 27.0 1.0 C A:CYS62 4.9 20.4 1.0 C A:CYS65 4.9 35.0 1.0 N A:CYS87 4.9 18.5 1.0 CA A:GLN64 4.9 30.4 1.0 HD12 A:LEU90 5.0 24.8 1.0 HA A:CYS62 5.0 26.4 1.0 H A:CYS87 5.0 22.2 1.0

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