Zinc in PDB 3tg4: Structure of SMYD2 in Complex with Sam

All present enzymatic activity of Structure of SMYD2 in Complex with Sam:
2.1.1.43;

The structure of Structure of SMYD2 in Complex with Sam, PDB code: 3tg4 was solved by K.Zhao, L.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.88 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	52.480, 67.480, 141.970, 90.00, 90.00, 90.00
R / Rfree (%)	19 / 22.4

The binding sites of Zinc atom in the Structure of SMYD2 in Complex with Sam (pdb code 3tg4). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Structure of SMYD2 in Complex with Sam, PDB code: 3tg4:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Structure of SMYD2 in Complex with Sam


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of SMYD2 in Complex with Sam within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn435 b:24.9 occ:1.00 SG A:CYS55 2.3 28.2 1.0 SG A:CYS78 2.3 31.8 1.0 SG A:CYS52 2.3 27.3 1.0 SG A:CYS74 2.4 32.6 1.0 CB A:CYS52 3.1 26.3 1.0 CB A:CYS74 3.2 30.0 1.0 CB A:CYS78 3.3 29.2 1.0 CB A:CYS55 3.5 26.9 1.0 N A:CYS74 3.8 28.2 1.0 N A:CYS55 3.9 25.1 1.0 CA A:CYS74 4.1 30.4 1.0 CA A:CYS55 4.3 25.4 1.0 CA A:CYS52 4.6 25.2 1.0 CB A:TYR54 4.7 25.8 1.0 CA A:CYS78 4.7 29.7 1.0 CB A:THR57 4.8 30.7 1.0 C A:CYS55 4.9 24.4 1.0 OG1 A:THR57 4.9 31.6 1.0 C A:TYR73 4.9 28.8 1.0 C A:TYR54 4.9 24.1 1.0 CD1 A:TYR54 5.0 27.6 1.0

Zinc binding site 2 out of 3 in the Structure of SMYD2 in Complex with Sam


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of SMYD2 in Complex with Sam within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn436 b:25.3 occ:1.00 NE2 A:HIS86 2.1 28.2 1.0 SG A:CYS68 2.3 32.5 1.0 SG A:CYS90 2.3 31.2 1.0 SG A:CYS65 2.3 31.7 1.0 CE1 A:HIS86 3.1 26.3 1.0 CD2 A:HIS86 3.2 27.4 1.0 CB A:CYS90 3.3 28.8 1.0 CB A:CYS68 3.3 35.2 1.0 CB A:CYS65 3.3 32.6 1.0 N A:CYS68 3.6 38.6 1.0 CA A:CYS90 3.9 28.0 1.0 CA A:CYS68 4.0 37.5 1.0 ND1 A:HIS86 4.2 22.7 1.0 CG A:HIS86 4.3 24.1 1.0 O A:HOH520 4.4 30.8 1.0 CB A:ARG67 4.5 42.1 1.0 CB A:ALA71 4.6 27.0 1.0 CA A:CYS65 4.7 34.5 1.0 C A:CYS90 4.7 29.6 1.0 C A:ARG67 4.7 41.4 1.0 N A:LYS69 4.8 38.4 1.0 O A:CYS90 4.8 30.4 1.0 C A:CYS68 4.9 38.2 1.0 N A:ARG67 4.9 41.6 1.0 CA A:ARG67 4.9 42.8 1.0 C A:CYS65 5.0 36.6 1.0 N A:CYS90 5.0 26.3 1.0

Zinc binding site 3 out of 3 in the Structure of SMYD2 in Complex with Sam


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of SMYD2 in Complex with Sam within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn437 b:32.1 occ:1.00 SG A:CYS262 2.3 47.6 1.0 SG A:CYS267 2.3 51.1 1.0 SG A:CYS264 2.3 47.8 1.0 SG A:CYS209 2.4 43.8 1.0 CB A:CYS209 3.2 41.7 1.0 CB A:CYS262 3.3 47.1 1.0 CB A:CYS264 3.4 48.6 1.0 CB A:CYS267 3.4 54.4 1.0 N A:CYS209 3.5 39.2 1.0 N A:CYS264 3.8 52.5 1.0 CA A:CYS209 4.0 39.3 1.0 N A:CYS267 4.1 53.2 1.0 CA A:CYS264 4.1 51.8 1.0 CE1 A:HIS207 4.2 38.0 1.0 CA A:CYS267 4.4 55.0 1.0 C A:CYS262 4.4 52.1 1.0 CA A:CYS262 4.5 49.4 1.0 C A:SER208 4.5 37.1 1.0 NH2 A:ARG250 4.6 42.4 1.0 O A:CYS262 4.7 52.9 1.0 C A:CYS264 4.7 53.6 1.0 N A:GLU263 4.7 53.4 1.0 NE A:ARG250 4.8 37.1 1.0 ND1 A:HIS207 4.8 38.5 1.0 CA A:SER208 4.8 38.1 1.0 O A:CYS264 4.8 55.0 1.0 CB A:GLU266 4.9 48.0 1.0

L.Wang, L.Li, H.Zhang, X.Luo, J.Dai, S.Zhou, J.Gu, J.Zhu, P.Atadja, C.Lu, E.Li, K.Zhao. Structure of Human SMYD2 Reveals the Basis of P53 Tumor Suppressor Methylation J.Biol.Chem. 2011.
ISSN: ESSN 1083-351X
PubMed: 21880715
DOI: 10.1074/JBC.M111.262410