Nickel in PDB 1s17: Identification of Novel Potent Bicyclic Peptide Deformylase Inhibitors

All present enzymatic activity of Identification of Novel Potent Bicyclic Peptide Deformylase Inhibitors:
3.5.1.88;

The structure of Identification of Novel Potent Bicyclic Peptide Deformylase Inhibitors, PDB code: 1s17 was solved by V.Molteni, X.He, J.Nabakka, K.Yang, A.Kreusch, P.Gordon, B.Bursulaya, N.S.Ryder, R.Goldberg, Y.He, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.68 / 1.95
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	69.009, 73.994, 76.864, 90.00, 90.00, 90.00
R / Rfree (%)	19.6 / 23.3

The binding sites of Nickel atom in the Identification of Novel Potent Bicyclic Peptide Deformylase Inhibitors (pdb code 1s17). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Identification of Novel Potent Bicyclic Peptide Deformylase Inhibitors, PDB code: 1s17:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Identification of Novel Potent Bicyclic Peptide Deformylase Inhibitors


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Identification of Novel Potent Bicyclic Peptide Deformylase Inhibitors within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni301 b:18.9 occ:1.00 NE2 A:HIS134 2.0 17.4 1.0 NE2 A:HIS138 2.0 15.5 1.0 OAP A:GNR501 2.1 23.4 1.0 SG A:CYS92 2.3 19.8 1.0 OAN A:GNR501 2.6 36.3 1.0 NAO A:GNR501 2.8 33.3 1.0 CD2 A:HIS134 3.0 18.1 1.0 CE1 A:HIS138 3.0 17.6 1.0 CAL A:GNR501 3.0 36.3 1.0 CE1 A:HIS134 3.0 19.1 1.0 CD2 A:HIS138 3.0 17.1 1.0 CB A:CYS92 3.4 16.5 1.0 O A:HOH508 3.4 21.2 1.0 NE2 A:GLN51 3.4 14.3 1.0 CA A:CYS92 3.9 18.9 1.0 CD A:GLN51 3.9 17.9 1.0 OE1 A:GLN51 4.0 18.6 1.0 ND1 A:HIS138 4.1 17.7 1.0 ND1 A:HIS134 4.1 16.9 1.0 CG A:HIS134 4.1 16.7 1.0 CG A:HIS138 4.2 16.6 1.0 N A:LEU93 4.4 18.4 1.0 CAK A:GNR501 4.4 38.5 1.0 O A:HOH507 4.5 20.0 1.0 OE1 A:GLU135 4.5 20.6 1.0 OE2 A:GLU135 4.5 24.4 1.0 C A:CYS92 4.6 18.4 1.0 CAI A:GNR501 4.7 40.7 1.0 SAJ A:GNR501 4.7 42.2 1.0 O A:GLY91 4.7 22.5 1.0 CD A:GLU135 4.9 21.6 1.0 CG A:GLN51 4.9 16.8 1.0

Nickel binding site 2 out of 2 in the Identification of Novel Potent Bicyclic Peptide Deformylase Inhibitors


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Identification of Novel Potent Bicyclic Peptide Deformylase Inhibitors within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni302 b:21.4 occ:1.00 NE2 B:HIS134 2.0 21.7 1.0 NE2 B:HIS138 2.0 17.6 1.0 OAP B:GNR601 2.1 28.4 1.0 SG B:CYS92 2.4 21.6 1.0 NAO B:GNR601 2.7 38.6 1.0 OAN B:GNR601 2.9 43.0 1.0 CD2 B:HIS138 3.0 15.7 1.0 CD2 B:HIS134 3.0 18.9 1.0 CE1 B:HIS134 3.0 17.4 1.0 CAL B:GNR601 3.1 42.3 1.0 CE1 B:HIS138 3.1 17.7 1.0 CB B:CYS92 3.3 20.2 1.0 O B:HOH609 3.5 20.1 1.0 NE2 B:GLN51 3.5 16.1 1.0 CA B:CYS92 3.8 20.4 1.0 CD B:GLN51 3.8 18.1 1.0 OE1 B:GLN51 3.9 16.9 1.0 ND1 B:HIS134 4.1 17.2 1.0 CG B:HIS134 4.1 19.4 1.0 CG B:HIS138 4.1 16.2 1.0 ND1 B:HIS138 4.2 17.3 1.0 N B:LEU93 4.4 20.0 1.0 CAK B:GNR601 4.4 43.6 1.0 OE1 B:GLU135 4.5 20.4 1.0 OE2 B:GLU135 4.5 22.9 1.0 O B:HOH603 4.5 16.9 1.0 C B:CYS92 4.5 20.8 1.0 CAI B:GNR601 4.6 44.1 1.0 SAJ B:GNR601 4.7 44.0 1.0 O B:GLY91 4.7 24.3 1.0 CD B:GLU135 4.8 21.6 1.0 CG B:GLN51 4.9 17.5 1.0 N B:SER94 4.9 20.2 1.0

V.Molteni, X.He, J.Nabakka, K.Yang, A.Kreusch, P.Gordon, B.Bursulaya, I.Warner, T.Shin, T.Biorac, N.S.Ryder, R.Goldberg, J.Doughty, Y.He. Identification of Novel Potent Bicyclic Peptide Deformylase Inhibitors Bioorg.Med.Chem.Lett. V. 14 1477 2004.
ISSN: ISSN 0960-894X
PubMed: 15006385
DOI: 10.1016/J.BMCL.2004.01.014