Zinc in PDB 5hi7: Co-Crystal Structure of Human SMYD3 with An Aza-Sah Compound

All present enzymatic activity of Co-Crystal Structure of Human SMYD3 with An Aza-Sah Compound:
2.1.1.43;

The structure of Co-Crystal Structure of Human SMYD3 with An Aza-Sah Compound, PDB code: 5hi7 was solved by P.A.Elkins, W.G.Bonnette, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.71 / 2.15
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.470, 66.401, 104.851, 90.00, 90.00, 90.00
R / Rfree (%)	19.8 / 22.6

The structure of Co-Crystal Structure of Human SMYD3 with An Aza-Sah Compound also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Zinc atom in the Co-Crystal Structure of Human SMYD3 with An Aza-Sah Compound (pdb code 5hi7). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Co-Crystal Structure of Human SMYD3 with An Aza-Sah Compound, PDB code: 5hi7:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Co-Crystal Structure of Human SMYD3 with An Aza-Sah Compound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Co-Crystal Structure of Human SMYD3 with An Aza-Sah Compound within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:27.8 occ:1.00 SG A:CYS261 2.2 25.6 1.0 SG A:CYS263 2.3 29.4 1.0 SG A:CYS266 2.3 24.6 1.0 SG A:CYS208 2.4 26.6 1.0 HB2 A:CYS208 3.1 32.3 1.0 HB3 A:CYS261 3.1 32.9 1.0 HB2 A:CYS266 3.2 30.6 1.0 HB3 A:CYS263 3.2 36.5 1.0 CB A:CYS261 3.3 27.4 1.0 CB A:CYS208 3.4 26.9 1.0 H A:CYS208 3.4 31.2 1.0 CB A:CYS266 3.4 25.5 1.0 CB A:CYS263 3.4 30.4 1.0 H A:CYS266 3.5 30.6 1.0 H A:CYS263 3.5 37.4 1.0 HE2 A:HIS206 3.5 22.6 1.0 HB2 A:CYS261 3.8 32.9 1.0 HE A:ARG249 3.8 24.6 1.0 HH21 A:ARG249 3.9 26.7 1.0 HB3 A:CYS208 4.0 32.3 1.0 N A:CYS266 4.1 25.5 1.0 HB3 A:CYS266 4.1 30.6 1.0 N A:CYS208 4.1 26.0 1.0 N A:CYS263 4.1 31.2 1.0 HB2 A:CYS263 4.1 36.5 1.0 HB2 A:ARG265 4.2 31.7 1.0 CA A:CYS263 4.2 31.2 1.0 NE2 A:HIS206 4.3 18.9 1.0 CA A:CYS266 4.3 26.5 1.0 CA A:CYS208 4.4 26.1 1.0 O A:CYS263 4.5 30.5 1.0 CA A:CYS261 4.5 28.6 1.0 HD2 A:HIS206 4.5 21.8 1.0 C A:CYS261 4.6 30.0 1.0 O A:CYS261 4.6 30.7 1.0 NE A:ARG249 4.6 20.5 1.0 C A:CYS263 4.6 31.0 1.0 HA A:CYS266 4.7 31.8 1.0 NH2 A:ARG249 4.7 22.2 1.0 HD11 A:LEU253 4.7 27.2 1.0 CD2 A:HIS206 4.8 18.1 1.0 HA A:CYS261 4.9 34.3 1.0 HA A:CYS208 4.9 31.3 1.0 HA A:SER207 4.9 29.3 1.0 HD12 A:LEU253 4.9 27.2 1.0

Zinc binding site 2 out of 3 in the Co-Crystal Structure of Human SMYD3 with An Aza-Sah Compound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Co-Crystal Structure of Human SMYD3 with An Aza-Sah Compound within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:36.8 occ:1.00 NE2 A:HIS83 2.0 32.4 1.0 SG A:CYS87 2.3 34.3 1.0 SG A:CYS65 2.4 36.4 1.0 SG A:CYS62 2.5 35.9 1.0 HB2 A:CYS87 2.8 41.0 1.0 H A:CYS65 2.9 52.0 1.0 HB3 A:CYS65 2.9 47.5 1.0 CE1 A:HIS83 2.9 31.8 1.0 CD2 A:HIS83 3.0 31.4 1.0 CB A:CYS87 3.1 34.2 1.0 HB3 A:CYS62 3.1 44.4 1.0 HE1 A:HIS83 3.1 38.2 1.0 CB A:CYS65 3.2 39.6 1.0 HD2 A:HIS83 3.3 37.6 1.0 CB A:CYS62 3.3 37.0 1.0 HA A:CYS87 3.4 41.1 1.0 HB2 A:CYS62 3.6 44.4 1.0 N A:CYS65 3.6 43.4 1.0 CA A:CYS87 3.8 34.3 1.0 HB3 A:CYS87 3.9 41.0 1.0 HB2 A:CYS65 4.0 47.5 1.0 CA A:CYS65 4.0 42.7 1.0 HB3 A:ALA68 4.0 38.8 1.0 ND1 A:HIS83 4.0 30.6 1.0 CG A:HIS83 4.1 30.5 1.0 H A:ARG66 4.4 52.2 1.0 H A:ALA68 4.4 42.1 1.0 H A:GLN64 4.5 55.1 1.0 H A:VAL67 4.6 49.6 1.0 CB A:GLN64 4.7 46.2 1.0 C A:CYS87 4.7 35.6 1.0 CA A:CYS62 4.7 38.8 1.0 O A:CYS87 4.7 36.0 1.0 HA A:CYS65 4.7 51.3 1.0 HB2 A:ALA68 4.7 38.8 1.0 C A:GLN64 4.8 45.3 1.0 HD1 A:HIS83 4.8 36.7 1.0 CB A:ALA68 4.8 32.4 1.0 N A:ARG66 4.9 43.5 1.0 N A:GLN64 4.9 45.9 1.0 C A:CYS65 4.9 43.3 1.0 N A:CYS87 4.9 33.2 1.0

Zinc binding site 3 out of 3 in the Co-Crystal Structure of Human SMYD3 with An Aza-Sah Compound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Co-Crystal Structure of Human SMYD3 with An Aza-Sah Compound within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:31.9 occ:1.00 SG A:CYS75 2.2 31.9 1.0 SG A:CYS71 2.3 34.9 1.0 SG A:CYS52 2.3 32.9 1.0 SG A:CYS49 2.3 30.0 1.0 H A:CYS52 3.0 38.5 1.0 HB3 A:CYS49 3.0 38.1 1.0 CB A:CYS49 3.1 31.8 1.0 HB2 A:CYS49 3.2 38.1 1.0 CB A:CYS75 3.2 32.2 1.0 HB3 A:CYS52 3.2 39.4 1.0 H A:CYS71 3.3 40.4 1.0 HB3 A:CYS75 3.3 38.6 1.0 HB2 A:CYS75 3.3 38.6 1.0 HB3 A:CYS71 3.4 43.0 1.0 CB A:CYS52 3.4 32.9 1.0 CB A:CYS71 3.5 35.8 1.0 HB3 A:ARG51 3.6 43.7 1.0 N A:CYS52 3.8 32.1 1.0 HG A:SER72 3.9 41.8 1.0 N A:CYS71 4.0 33.7 1.0 HB2 A:CYS52 4.2 39.4 1.0 CA A:CYS52 4.2 32.1 1.0 HB2 A:CYS71 4.2 43.0 1.0 CA A:CYS71 4.3 35.6 1.0 H A:ARG51 4.4 39.4 1.0 H A:SER72 4.5 42.0 1.0 CB A:ARG51 4.5 36.4 1.0 CA A:CYS49 4.6 32.0 1.0 CA A:CYS75 4.7 33.0 1.0 OG A:SER72 4.7 34.8 1.0 HA A:TYR70 4.8 38.4 1.0 H A:LEU53 4.8 37.8 1.0 H A:LEU54 4.8 43.2 1.0 N A:SER72 4.8 35.0 1.0 HA A:CYS75 4.8 39.5 1.0 HB2 A:LEU54 4.9 47.8 1.0 C A:ARG51 4.9 31.5 1.0 HD1 A:TYR70 4.9 37.3 1.0 C A:CYS71 4.9 35.6 1.0 HD3 A:LYS56 4.9 69.5 1.0 HA A:CYS52 5.0 38.5 1.0 HA A:CYS49 5.0 38.4 1.0 N A:ARG51 5.0 32.9 1.0 HG3 A:ARG51 5.0 47.6 1.0 C A:CYS52 5.0 32.2 1.0

G.S.Van Aller, A.P.Graves, P.A.Elkins, W.G.Bonnette, P.J.Mcdevitt, F.Zappacosta, R.S.Annan, T.W.Dean, D.S.Su, C.L.Carpenter, H.P.Mohammad, R.G.Kruger. Structure-Based Design of A Novel SMYD3 Inhibitor That Bridges the Sam-and MEKK2-Binding Pockets. Structure V. 24 774 2016.
ISSN: ISSN 0969-2126
PubMed: 27066749
DOI: 10.1016/J.STR.2016.03.010