Zinc in PDB 3s7d: Structural Basis of Substrate Methylation and Inhibition of SMYD2

All present enzymatic activity of Structural Basis of Substrate Methylation and Inhibition of SMYD2:
2.1.1.43;

The structure of Structural Basis of Substrate Methylation and Inhibition of SMYD2, PDB code: 3s7d was solved by A.D.Ferguson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.07 / 2.30
Space group	I 4
Cell size a, b, c (Å), α, β, γ (°)	153.835, 153.835, 52.727, 90.00, 90.00, 90.00
R / Rfree (%)	18.4 / 21.1

The binding sites of Zinc atom in the Structural Basis of Substrate Methylation and Inhibition of SMYD2 (pdb code 3s7d). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Structural Basis of Substrate Methylation and Inhibition of SMYD2, PDB code: 3s7d:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Structural Basis of Substrate Methylation and Inhibition of SMYD2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structural Basis of Substrate Methylation and Inhibition of SMYD2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn437 b:50.0 occ:1.00 SG A:CYS78 2.2 47.6 1.0 SG A:CYS52 2.4 43.2 1.0 SG A:CYS55 2.4 44.8 1.0 SG A:CYS74 2.4 48.9 1.0 CB A:CYS52 3.1 39.9 1.0 CB A:CYS74 3.2 46.9 1.0 CB A:CYS78 3.3 44.1 1.0 CB A:CYS55 3.5 39.9 1.0 N A:CYS74 3.8 48.3 1.0 N A:CYS55 3.9 39.2 1.0 CA A:CYS74 4.1 48.2 1.0 CA A:CYS55 4.3 38.8 1.0 CA A:CYS52 4.6 40.5 1.0 OG1 A:THR57 4.6 49.0 1.0 CA A:CYS78 4.7 44.3 1.0 CB A:THR57 4.7 49.5 1.0 CB A:TYR54 4.7 40.6 1.0 C A:TYR54 4.9 42.9 1.0 C A:CYS55 4.9 41.4 1.0 C A:TYR73 5.0 52.6 1.0 CD1 A:TYR54 5.0 41.2 1.0

Zinc binding site 2 out of 3 in the Structural Basis of Substrate Methylation and Inhibition of SMYD2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structural Basis of Substrate Methylation and Inhibition of SMYD2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn438 b:45.2 occ:1.00 NE2 A:HIS86 2.2 42.2 1.0 SG A:CYS68 2.2 44.2 1.0 SG A:CYS90 2.3 43.4 1.0 SG A:CYS65 2.4 52.1 1.0 CD2 A:HIS86 3.1 42.1 1.0 CE1 A:HIS86 3.2 40.0 1.0 CB A:CYS68 3.2 43.3 1.0 CB A:CYS65 3.3 48.4 1.0 CB A:CYS90 3.3 38.7 1.0 N A:CYS68 3.7 49.1 1.0 CA A:CYS90 3.9 37.6 1.0 CA A:CYS68 4.0 46.9 1.0 CG A:HIS86 4.2 40.3 1.0 ND1 A:HIS86 4.3 40.3 1.0 O A:HOH493 4.4 38.2 1.0 CB A:ALA71 4.6 46.6 1.0 CB A:ARG67 4.6 60.4 1.0 CA A:CYS65 4.7 51.0 1.0 C A:CYS90 4.7 42.4 1.0 C A:ARG67 4.7 60.1 1.0 N A:LYS69 4.9 54.4 1.0 O A:CYS90 4.9 42.7 1.0 C A:CYS68 4.9 56.3 1.0 NH1 A:ARG67 4.9 81.7 1.0 CZ3 A:TRP83 4.9 45.8 1.0 N A:ARG67 4.9 58.5 1.0 C A:CYS65 4.9 54.6 1.0 N A:CYS90 5.0 37.6 1.0 CA A:ARG67 5.0 58.6 1.0

Zinc binding site 3 out of 3 in the Structural Basis of Substrate Methylation and Inhibition of SMYD2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structural Basis of Substrate Methylation and Inhibition of SMYD2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn439 b:39.6 occ:1.00 SG A:CYS267 2.2 40.2 1.0 SG A:CYS262 2.4 39.9 1.0 SG A:CYS264 2.4 43.6 1.0 SG A:CYS209 2.5 42.7 1.0 CB A:CYS209 3.1 38.7 1.0 CB A:CYS262 3.2 36.7 1.0 CB A:CYS267 3.3 38.4 1.0 CB A:CYS264 3.5 39.5 1.0 N A:CYS209 3.7 38.8 1.0 N A:CYS264 3.9 38.1 1.0 CA A:CYS209 4.0 38.0 1.0 N A:CYS267 4.0 40.9 1.0 CA A:CYS264 4.2 39.8 1.0 CA A:CYS267 4.2 40.6 1.0 CE1 A:HIS207 4.3 38.8 1.0 CA A:CYS262 4.4 38.3 1.0 NH2 A:ARG250 4.4 36.1 1.0 C A:CYS262 4.5 44.8 1.0 NE A:ARG250 4.7 43.1 1.0 C A:SER208 4.7 40.8 1.0 N A:GLU263 4.7 41.9 1.0 C A:CYS264 4.7 45.8 1.0 O A:CYS262 4.7 45.5 1.0 ND1 A:HIS207 4.7 40.8 1.0 O A:CYS264 4.7 45.5 1.0 CB A:GLU266 4.8 38.3 1.0

A.D.Ferguson, N.A.Larsen, T.Howard, H.Pollard, I.Green, C.Grande, T.Cheung, R.Garcia-Arenas, S.Cowen, J.Wu, R.Godin, H.Chen, N.Keen. Structural Basis of Substrate Methylation and Inhibition of SMYD2. Structure V. 19 1262 2011.
ISSN: ISSN 0969-2126
PubMed: 21782458
DOI: 10.1016/J.STR.2011.06.011