Zinc in PDB 5wcg: Set and Mynd Domain Containing Protein 2

All present enzymatic activity of Set and Mynd Domain Containing Protein 2:
2.1.1.43;

The structure of Set and Mynd Domain Containing Protein 2, PDB code: 5wcg was solved by A.Dong, H.Zeng, J.R.Walker, A.Hutch, A.Seitova, J.Tatlock, R.Kumpf, A.Owen, A.Taylor, A.Casimiro-Garcia, C.Bountra, C.H.Arrowsmith, A.M.Edwards, P.J.Brown, H.Wu, Structural Genomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.02
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	92.343, 98.312, 58.833, 90.00, 101.95, 90.00
R / Rfree (%)	17 / 21.3

The binding sites of Zinc atom in the Set and Mynd Domain Containing Protein 2 (pdb code 5wcg). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Set and Mynd Domain Containing Protein 2, PDB code: 5wcg:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Set and Mynd Domain Containing Protein 2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Set and Mynd Domain Containing Protein 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:26.7 occ:1.00 SG A:CYS78 2.3 28.0 1.0 SG A:CYS55 2.3 25.4 1.0 SG A:CYS52 2.4 23.7 1.0 SG A:CYS74 2.4 26.6 1.0 CB A:CYS52 3.1 23.3 1.0 CB A:CYS74 3.3 26.8 1.0 CB A:CYS78 3.3 27.8 1.0 CB A:CYS55 3.5 24.0 1.0 N A:CYS74 3.8 24.9 1.0 N A:CYS55 4.0 23.2 1.0 CA A:CYS74 4.1 27.3 1.0 CA A:CYS55 4.3 22.9 1.0 CA A:CYS52 4.6 23.5 1.0 OG1 A:THR57 4.6 27.4 1.0 CA A:CYS78 4.8 26.9 1.0 CB A:TYR54 4.8 25.0 1.0 CB A:THR57 4.8 25.6 1.0 C A:TYR73 4.9 24.9 1.0 C A:CYS55 5.0 21.7 1.0

Zinc binding site 2 out of 3 in the Set and Mynd Domain Containing Protein 2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Set and Mynd Domain Containing Protein 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:22.5 occ:1.00 SG A:CYS267 2.2 22.2 1.0 SG A:CYS264 2.4 22.2 1.0 SG A:CYS209 2.4 20.1 1.0 SG A:CYS262 2.4 21.4 1.0 CB A:CYS209 3.2 21.0 1.0 CB A:CYS262 3.2 21.0 1.0 CB A:CYS264 3.4 23.6 1.0 CB A:CYS267 3.5 25.0 1.0 N A:CYS209 3.6 18.0 1.0 N A:CYS264 3.8 24.5 1.0 CA A:CYS209 4.0 20.1 1.0 N A:CYS267 4.0 25.4 1.0 CA A:CYS264 4.1 24.6 1.0 NE2 A:HIS207 4.2 15.0 1.0 CA A:CYS267 4.3 26.0 1.0 C A:CYS262 4.4 25.2 1.0 CA A:CYS262 4.4 22.4 1.0 NH2 A:ARG250 4.6 22.1 1.0 O A:CYS262 4.6 24.1 1.0 C A:CYS264 4.7 23.6 1.0 N A:GLU263 4.7 27.2 1.0 CD2 A:HIS207 4.7 14.9 1.0 C A:SER208 4.7 17.3 1.0 NE A:ARG250 4.7 19.2 1.0 O A:CYS264 4.8 23.2 1.0 C A:GLU263 5.0 27.8 1.0 CB A:GLU266 5.0 33.6 1.0

Zinc binding site 3 out of 3 in the Set and Mynd Domain Containing Protein 2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Set and Mynd Domain Containing Protein 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:23.7 occ:1.00 NE2 A:HIS86 2.1 20.4 1.0 SG A:CYS68 2.2 23.4 1.0 SG A:CYS90 2.4 22.2 1.0 SG A:CYS65 2.4 27.0 1.0 CE1 A:HIS86 2.9 19.4 1.0 CB A:CYS68 3.2 26.0 1.0 CD2 A:HIS86 3.2 20.4 1.0 CB A:CYS90 3.2 21.1 1.0 CB A:CYS65 3.3 27.3 1.0 N A:CYS68 3.6 26.9 1.0 CA A:CYS90 3.9 20.6 1.0 CA A:CYS68 3.9 26.0 1.0 ND1 A:HIS86 4.1 19.2 1.0 CG A:HIS86 4.2 19.0 1.0 CB A:ARG67 4.3 30.7 1.0 C A:ARG67 4.6 29.3 1.0 O A:HOH726 4.6 25.3 1.0 CA A:CYS65 4.8 29.3 1.0 C A:CYS90 4.8 21.1 1.0 C A:CYS68 4.8 25.6 1.0 CB A:ALA71 4.8 25.5 1.0 N A:LYS69 4.8 25.6 1.0 CA A:ARG67 4.8 28.8 1.0 CZ3 A:TRP83 4.9 25.2 1.0 N A:ARG67 4.9 28.5 1.0 O A:CYS90 5.0 21.6 1.0 O A:CYS65 5.0 25.1 1.0

H.Zeng, A.Dong, J.R.Walker, A.Hutch, A.Seitova, J.Tatlock, R.Kumpf, A.Owen, A.Taylor, A.Casimiro-Garcia, C.Bountra, C.H.Arrowsmith, A.M.Edwards, P.J.Brown, H.Wu. The Crystal Structure of SMYD2 in Complex with Compound MTF003 To Be Published.