Zinc in PDB 3n71: Crystal Structure of Cardiac Specific Histone Methyltransferase SMYD1

The structure of Crystal Structure of Cardiac Specific Histone Methyltransferase SMYD1, PDB code: 3n71 was solved by N.Sirinupong, Z.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.30
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	170.500, 170.500, 57.100, 90.00, 90.00, 120.00
R / Rfree (%)	20.9 / 25.6

The binding sites of Zinc atom in the Crystal Structure of Cardiac Specific Histone Methyltransferase SMYD1 (pdb code 3n71). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of Cardiac Specific Histone Methyltransferase SMYD1, PDB code: 3n71:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of Cardiac Specific Histone Methyltransferase SMYD1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Cardiac Specific Histone Methyltransferase SMYD1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn495 b:65.0 occ:1.00 SG A:CYS78 2.4 62.9 1.0 SG A:CYS52 2.5 52.8 1.0 SG A:CYS55 2.5 64.6 1.0 SG A:CYS74 2.7 59.6 1.0 CB A:CYS55 3.0 54.3 1.0 CB A:CYS52 3.3 43.3 1.0 CB A:CYS78 3.3 64.8 1.0 N A:CYS55 3.6 48.4 1.0 CB A:CYS74 3.6 60.2 1.0 CA A:CYS55 3.8 48.9 1.0 N A:CYS74 4.2 69.9 1.0 CB A:THR54 4.5 47.2 1.0 CA A:CYS74 4.5 67.9 1.0 C A:CYS55 4.6 44.1 1.0 C A:THR54 4.6 46.4 1.0 CA A:CYS52 4.7 49.5 1.0 CA A:CYS78 4.7 70.5 1.0 CG2 A:THR54 4.8 38.4 1.0 N A:PHE56 4.9 37.0 1.0 CA A:THR54 5.0 45.7 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of Cardiac Specific Histone Methyltransferase SMYD1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Cardiac Specific Histone Methyltransferase SMYD1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn496 b:75.2 occ:1.00 SG A:CYS68 2.3 62.0 1.0 NE2 A:HIS86 2.4 53.1 1.0 SG A:CYS90 2.5 72.3 1.0 SG A:CYS65 2.7 92.5 1.0 CB A:CYS68 3.0 72.3 1.0 CE1 A:HIS86 3.1 50.1 1.0 CB A:CYS90 3.3 67.7 1.0 CB A:CYS65 3.4 81.9 1.0 CD2 A:HIS86 3.5 49.3 1.0 N A:CYS68 3.6 78.1 1.0 CA A:CYS68 3.9 71.9 1.0 CA A:CYS90 4.0 63.4 1.0 ND1 A:HIS86 4.3 50.8 1.0 C A:GLN67 4.3 81.8 1.0 CB A:GLN67 4.4 89.0 1.0 CG A:HIS86 4.5 55.4 1.0 CB A:ALA71 4.6 53.5 1.0 O A:CYS65 4.7 77.1 1.0 CA A:GLN67 4.7 83.6 1.0 CA A:CYS65 4.8 80.2 1.0 C A:CYS68 4.9 71.5 1.0 N A:GLN67 4.9 82.5 1.0 C A:CYS90 4.9 65.0 1.0 C A:CYS65 5.0 77.1 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of Cardiac Specific Histone Methyltransferase SMYD1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Cardiac Specific Histone Methyltransferase SMYD1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn497 b:61.8 occ:1.00 SG A:CYS274 2.3 48.9 1.0 SG A:CYS279 2.4 53.0 1.0 SG A:CYS276 2.5 49.1 1.0 SG A:CYS208 2.6 48.4 1.0 CB A:CYS279 3.1 48.6 1.0 CB A:CYS274 3.4 53.8 1.0 CB A:CYS208 3.4 39.0 1.0 CB A:CYS276 3.6 54.2 1.0 NH1 A:ARG262 4.0 50.2 1.0 N A:CYS208 4.0 44.6 1.0 N A:CYS279 4.1 47.5 1.0 N A:CYS276 4.1 59.2 1.0 CA A:CYS279 4.2 54.6 1.0 CA A:CYS208 4.4 45.8 1.0 CA A:CYS276 4.4 48.0 1.0 NE2 A:HIS206 4.4 49.6 1.0 C A:CYS274 4.6 56.3 1.0 CA A:CYS274 4.6 60.6 1.0 CD1 A:LEU266 4.6 44.6 1.0 O A:CYS276 4.7 46.7 1.0 O A:CYS274 4.8 55.0 1.0 C A:CYS276 4.9 47.7 1.0 N A:SER275 4.9 53.8 1.0 CD2 A:HIS206 4.9 42.3 1.0

N.Sirinupong, J.Brunzelle, J.Ye, A.Pirzada, L.Nico, Z.Yang. Crystal Structure of Cardiac-Specific Histone Methyltransferase SMYD1 Reveals Unusual Active Site Architecture. J.Biol.Chem. V. 285 40635 2010.
ISSN: ISSN 0021-9258
PubMed: 20943667
DOI: 10.1074/JBC.M110.168187