Zinc in PDB 9ckc: Crystal Structure of SMYD2 in Complex with Two PARP1 Peptides

All present enzymatic activity of Crystal Structure of SMYD2 in Complex with Two PARP1 Peptides:
2.1.1.43;

The structure of Crystal Structure of SMYD2 in Complex with Two PARP1 Peptides, PDB code: 9ckc was solved by Y.Zhang, E.Alshammari, N.Spellmon, J.Brunzelle, Z.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	66.58 / 2.10
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	142.792, 52.185, 144.916, 90, 113.24, 90
R / Rfree (%)	18.4 / 20.8

The binding sites of Zinc atom in the Crystal Structure of SMYD2 in Complex with Two PARP1 Peptides (pdb code 9ckc). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of SMYD2 in Complex with Two PARP1 Peptides, PDB code: 9ckc:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Crystal Structure of SMYD2 in Complex with Two PARP1 Peptides


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 SMYD2 in Complex with Two PARP1 Peptides within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:38.6 occ:1.00 NE2 A:HIS86 2.1 43.7 1.0 SG A:CYS68 2.3 42.2 1.0 SG A:CYS90 2.3 41.5 1.0 SG A:CYS65 2.4 53.8 1.0 CD2 A:HIS86 3.0 39.0 1.0 CE1 A:HIS86 3.0 33.0 1.0 CB A:CYS90 3.3 44.3 1.0 CB A:CYS68 3.4 51.1 1.0 CB A:CYS65 3.4 54.3 1.0 N A:CYS68 3.8 53.4 1.0 CA A:CYS90 3.9 36.9 1.0 ND1 A:HIS86 4.1 31.5 1.0 CG A:HIS86 4.2 37.2 1.0 CA A:CYS68 4.2 45.2 1.0 CB A:ARG67 4.4 61.6 1.0 C A:CYS90 4.8 38.2 1.0 CB A:ALA71 4.8 41.1 1.0 CA A:CYS65 4.8 56.2 1.0 C A:ARG67 4.8 57.0 1.0 O A:HOH661 4.9 47.9 1.0 C A:CYS68 5.0 49.2 1.0 O A:CYS90 5.0 40.2 1.0 N A:LYS69 5.0 46.6 1.0

Zinc binding site 2 out of 6 in the Crystal Structure of SMYD2 in Complex with Two PARP1 Peptides


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 SMYD2 in Complex with Two PARP1 Peptides within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:26.2 occ:1.00 SG A:CYS267 2.3 26.8 1.0 SG A:CYS209 2.3 24.3 1.0 SG A:CYS262 2.3 25.2 1.0 SG A:CYS264 2.4 28.8 1.0 CB A:CYS209 3.2 31.0 1.0 CB A:CYS262 3.2 26.1 1.0 CB A:CYS267 3.4 25.7 1.0 CB A:CYS264 3.5 31.3 1.0 N A:CYS209 3.6 24.7 1.0 N A:CYS264 4.0 28.0 1.0 CA A:CYS209 4.0 24.1 1.0 N A:CYS267 4.0 29.8 1.0 CA A:CYS264 4.3 31.2 1.0 CA A:CYS267 4.3 33.1 1.0 NE2 A:HIS207 4.4 21.6 1.0 CA A:CYS262 4.5 29.0 1.0 C A:CYS262 4.5 28.1 1.0 NH2 A:ARG250 4.5 23.5 1.0 NE A:ARG250 4.7 20.4 1.0 C A:SER208 4.7 32.3 1.0 N A:GLU263 4.7 35.1 1.0 CD2 A:HIS207 4.7 22.6 1.0 C A:CYS264 4.8 30.4 1.0 O A:CYS262 4.8 37.3 1.0 O A:CYS264 4.8 30.1 1.0

Zinc binding site 3 out of 6 in the Crystal Structure of SMYD2 in Complex with Two PARP1 Peptides


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 SMYD2 in Complex with Two PARP1 Peptides within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn504 b:45.2 occ:1.00 SG A:CYS55 2.4 49.3 1.0 SG A:CYS74 2.4 52.8 1.0 SG A:CYS78 2.4 50.7 1.0 SG A:CYS52 2.5 38.1 1.0 CB A:CYS74 3.2 48.0 1.0 CB A:CYS52 3.2 30.8 1.0 CB A:CYS78 3.4 47.3 1.0 CB A:CYS55 3.5 48.2 1.0 N A:CYS74 3.9 45.4 1.0 N A:CYS55 4.0 34.4 1.0 CA A:CYS74 4.2 46.8 1.0 CA A:CYS55 4.3 40.4 1.0 CB A:TYR54 4.7 33.2 1.0 CA A:CYS52 4.7 34.4 1.0 OG1 A:THR57 4.7 53.3 1.0 CA A:CYS78 4.8 53.2 1.0 CB A:THR57 4.9 54.9 1.0 C A:CYS55 4.9 31.7 1.0

Zinc binding site 4 out of 6 in the Crystal Structure of SMYD2 in Complex with Two PARP1 Peptides


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of SMYD2 in Complex with Two PARP1 Peptides within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn502 b:64.2 occ:1.00 SG B:CYS65 2.3 72.8 1.0 NE2 B:HIS86 2.3 78.8 1.0 SG B:CYS68 2.4 73.2 1.0 SG B:CYS90 2.7 96.6 1.0 CE1 B:HIS86 3.1 65.2 1.0 CB B:CYS68 3.2 77.5 1.0 CD2 B:HIS86 3.4 72.2 1.0 CB B:CYS65 3.4 72.1 1.0 CB B:CYS90 3.6 91.9 1.0 N B:CYS68 3.6 79.2 1.0 CA B:CYS90 3.9 81.1 1.0 CA B:CYS68 4.0 74.4 1.0 CB B:ARG67 4.3 76.8 1.0 ND1 B:HIS86 4.3 74.7 1.0 CG B:HIS86 4.4 69.7 1.0 C B:ARG67 4.6 70.9 1.0 C B:CYS90 4.7 85.8 1.0 O B:CYS90 4.7 82.1 1.0 CB B:ALA71 4.7 63.9 1.0 CA B:CYS65 4.8 73.4 1.0 NZ B:LYS87 4.8 116.6 1.0 CA B:ARG67 4.8 76.2 1.0 C B:CYS68 4.8 75.2 1.0 N B:ARG67 4.9 79.9 1.0 N B:LYS69 4.9 77.1 1.0 O B:CYS65 4.9 72.4 1.0 C B:CYS65 5.0 77.1 1.0

Zinc binding site 5 out of 6 in the Crystal Structure of SMYD2 in Complex with Two PARP1 Peptides


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of SMYD2 in Complex with Two PARP1 Peptides within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn503 b:30.7 occ:1.00 SG B:CYS267 2.3 38.4 1.0 SG B:CYS262 2.3 36.4 1.0 SG B:CYS209 2.4 32.0 1.0 SG B:CYS264 2.4 33.7 1.0 CB B:CYS209 3.2 25.6 1.0 CB B:CYS262 3.2 39.2 1.0 CB B:CYS267 3.4 40.2 1.0 CB B:CYS264 3.6 31.8 1.0 N B:CYS209 3.6 26.1 1.0 N B:CYS264 4.0 32.6 1.0 CA B:CYS209 4.0 28.9 1.0 N B:CYS267 4.0 35.7 1.0 CA B:CYS264 4.3 33.3 1.0 CA B:CYS267 4.3 38.6 1.0 NH2 B:ARG250 4.4 26.8 1.0 CA B:CYS262 4.4 36.6 1.0 C B:CYS262 4.5 36.2 1.0 NE2 B:HIS207 4.5 29.1 1.0 C B:SER208 4.7 27.3 1.0 N B:GLU263 4.7 30.4 1.0 NE B:ARG250 4.7 26.2 1.0 C B:CYS264 4.8 33.7 1.0 CD2 B:HIS207 4.8 31.3 1.0 O B:CYS262 4.8 38.7 1.0 O B:CYS264 4.8 33.8 1.0

Zinc binding site 6 out of 6 in the Crystal Structure of SMYD2 in Complex with Two PARP1 Peptides


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of SMYD2 in Complex with Two PARP1 Peptides within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn504 b:60.8 occ:1.00 SG B:CYS74 2.3 54.3 1.0 SG B:CYS78 2.3 76.6 1.0 SG B:CYS52 2.4 53.7 1.0 SG B:CYS55 2.6 53.9 1.0 CB B:CYS74 3.2 71.8 1.0 CB B:CYS52 3.2 52.7 1.0 CB B:CYS78 3.3 74.1 1.0 CB B:CYS55 3.6 62.5 1.0 N B:CYS74 3.8 74.1 1.0 N B:CYS55 4.0 50.0 1.0 CA B:CYS74 4.1 71.0 1.0 CA B:CYS55 4.4 49.2 1.0 CB B:TYR54 4.6 57.5 1.0 CA B:CYS52 4.7 48.2 1.0 CA B:CYS78 4.7 77.2 1.0 OG1 B:THR57 4.8 60.1 1.0 C B:TYR73 4.9 58.8 1.0 CB B:THR57 5.0 54.1 1.0

Y.Zhang, E.Alshammari, J.Sobota, N.Spellmon, E.Perry, T.Cao, T.Mugunamalwaththa, S.Smith, J.Brunzelle, G.Wu, T.Stemmler, J.Jin, C.Li, Z.Yang. Structure of the SMYD2-PARP1 Complex Reveals Both Productive and Allosteric Modes of Peptide Binding. Biorxiv 2024.
ISSN: ISSN 2692-8205
PubMed: 39677743
DOI: 10.1101/2024.12.03.626679