Nickel in PDB 3rdh: X-Ray Induced Covalent Inhibition of 14-3-3

The structure of X-Ray Induced Covalent Inhibition of 14-3-3, PDB code: 3rdh was solved by J.R.Horton, A.K.Upadhyay, H.Fu, X.Cheng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.77 / 2.39
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	94.745, 94.745, 237.862, 90.00, 90.00, 120.00
R / Rfree (%)	23.5 / 28.6

The binding sites of Nickel atom in the X-Ray Induced Covalent Inhibition of 14-3-3 (pdb code 3rdh). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the X-Ray Induced Covalent Inhibition of 14-3-3, PDB code: 3rdh:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in the X-Ray Induced Covalent Inhibition of 14-3-3


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of X-Ray Induced Covalent Inhibition of 14-3-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni247 b:45.4 occ:1.00 N A:SER-1 1.8 41.5 1.0 N A:GLY-2 1.9 36.4 1.0 ND1 A:HIS0 2.0 45.9 1.0 N A:HIS0 2.0 43.4 1.0 C A:GLY-2 2.6 41.7 1.0 CA A:GLY-2 2.7 41.1 1.0 C A:SER-1 2.8 43.3 1.0 CA A:SER-1 2.9 42.2 1.0 CE1 A:HIS0 3.0 43.1 1.0 CG A:HIS0 3.0 42.0 1.0 CA A:HIS0 3.1 44.8 1.0 CB A:HIS0 3.3 44.1 1.0 N A:MET1 3.4 47.3 1.0 C A:HIS0 3.8 45.7 1.0 O A:GLY-2 3.8 42.5 1.0 CB A:SER-1 3.9 43.8 1.0 CE1 C:TYR126 4.0 39.0 1.0 O A:SER-1 4.0 45.8 1.0 OH C:TYR126 4.0 43.5 1.0 NE2 A:HIS0 4.1 43.6 1.0 CD2 A:HIS0 4.1 42.4 1.0 CZ C:TYR126 4.5 42.6 1.0 CG C:GLN144 4.7 58.5 1.0 CA A:MET1 4.7 50.6 1.0 OG A:SER-1 4.8 45.9 1.0 CB A:MET1 4.9 53.5 1.0 O A:HIS0 5.0 47.2 1.0 CG A:MET1 5.0 54.4 1.0

Nickel binding site 2 out of 4 in the X-Ray Induced Covalent Inhibition of 14-3-3


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of X-Ray Induced Covalent Inhibition of 14-3-3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni247 b:50.3 occ:1.00 N B:SER-1 1.7 48.1 1.0 N B:GLY-2 1.9 42.2 1.0 N B:HIS0 1.9 45.8 1.0 ND1 B:HIS0 2.1 44.7 1.0 C B:GLY-2 2.5 47.1 1.0 CA B:GLY-2 2.6 45.1 1.0 C B:SER-1 2.7 48.9 1.0 CA B:SER-1 2.7 48.3 1.0 CG B:HIS0 3.0 42.7 1.0 CA B:HIS0 3.0 46.1 1.0 CE1 B:HIS0 3.1 41.0 1.0 CB B:HIS0 3.3 45.8 1.0 N B:MET1 3.5 48.3 1.0 O B:GLY-2 3.7 48.4 1.0 CB B:SER-1 3.7 48.4 1.0 C B:HIS0 3.8 46.5 1.0 O B:SER-1 3.9 49.7 1.0 OH D:TYR126 4.0 40.4 1.0 CE1 D:TYR126 4.0 38.7 1.0 NE2 B:HIS0 4.2 43.0 1.0 CD2 B:HIS0 4.2 42.6 1.0 OG B:SER-1 4.3 51.0 1.0 CZ D:TYR126 4.5 40.5 1.0 CA B:MET1 4.8 49.6 1.0 CG D:GLN144 4.9 61.1 1.0 CG B:MET1 5.0 51.1 1.0 O B:HIS0 5.0 47.0 1.0 CB B:MET1 5.0 50.2 1.0

Nickel binding site 3 out of 4 in the X-Ray Induced Covalent Inhibition of 14-3-3


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of X-Ray Induced Covalent Inhibition of 14-3-3 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni247 b:42.3 occ:1.00 N C:GLY-2 1.8 30.2 1.0 ND1 C:HIS0 1.9 45.3 1.0 N C:SER-1 1.9 41.6 1.0 N C:HIS0 2.0 43.7 1.0 C C:GLY-2 2.7 40.4 1.0 CA C:GLY-2 2.7 38.1 1.0 CG C:HIS0 2.8 42.4 1.0 CE1 C:HIS0 2.9 39.4 1.0 C C:SER-1 2.9 44.0 1.0 CA C:SER-1 3.0 42.5 1.0 CA C:HIS0 3.1 44.0 1.0 CB C:HIS0 3.2 44.4 1.0 N C:MET1 3.5 47.9 1.0 C C:HIS0 3.8 45.2 1.0 O C:GLY-2 3.9 41.5 1.0 CB C:SER-1 3.9 41.5 1.0 NE2 C:HIS0 4.0 42.1 1.0 CD2 C:HIS0 4.0 39.5 1.0 CE1 A:TYR126 4.0 35.4 1.0 OH A:TYR126 4.0 37.6 1.0 O C:SER-1 4.1 46.4 1.0 CZ A:TYR126 4.5 36.6 1.0 CG A:GLN144 4.7 45.2 1.0 CA C:MET1 4.7 52.5 1.0 O C:MET1 4.8 51.7 1.0 OG C:SER-1 4.9 43.4 1.0 O C:HIS0 4.9 44.2 1.0

Nickel binding site 4 out of 4 in the X-Ray Induced Covalent Inhibition of 14-3-3


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of X-Ray Induced Covalent Inhibition of 14-3-3 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ni247 b:48.6 occ:1.00 N D:SER-1 1.9 46.8 1.0 ND1 D:HIS0 1.9 46.2 1.0 N D:GLY-2 1.9 45.2 1.0 N D:HIS0 2.0 45.0 1.0 C D:GLY-2 2.8 47.3 1.0 C D:SER-1 2.8 45.9 1.0 CE1 D:HIS0 2.8 45.9 1.0 CA D:SER-1 2.9 45.9 1.0 CA D:GLY-2 2.9 47.9 1.0 CG D:HIS0 2.9 43.6 1.0 CA D:HIS0 3.0 46.5 1.0 CB D:HIS0 3.3 46.2 1.0 N D:MET1 3.6 51.0 1.0 C D:HIS0 3.8 46.9 1.0 OH B:TYR126 3.9 43.0 1.0 NE2 D:HIS0 3.9 47.5 1.0 CE1 B:TYR126 3.9 40.9 1.0 O D:GLY-2 4.0 45.9 1.0 CD2 D:HIS0 4.0 45.0 1.0 CB D:SER-1 4.0 47.0 1.0 O D:SER-1 4.0 47.3 1.0 CZ B:TYR126 4.4 43.2 1.0 OG D:SER-1 4.7 48.5 1.0 CG B:GLN144 4.8 55.4 1.0 CA D:MET1 4.9 56.5 1.0

J.Zhao, Y.Du, J.R.Horton, A.K.Upadhyay, B.Lou, Y.Bai, X.Zhang, L.Du, M.Li, B.Wang, L.Zhang, J.T.Barbieri, F.R.Khuri, X.Cheng, H.Fu. Discovery and Structural Characterization of A Small Molecule 14-3-3 Protein-Protein Interaction Inhibitor. Proc.Natl.Acad.Sci.Usa V. 108 16212 2011.
ISSN: ISSN 0027-8424
PubMed: 21908710
DOI: 10.1073/PNAS.1100012108