Nickel in PDB 1g27: Crystal Structure of E.Coli Polypeptide Deformylase Complexed with the Inhibitor Bb-3497

All present enzymatic activity of Crystal Structure of E.Coli Polypeptide Deformylase Complexed with the Inhibitor Bb-3497:
3.5.1.31;

The structure of Crystal Structure of E.Coli Polypeptide Deformylase Complexed with the Inhibitor Bb-3497, PDB code: 1g27 was solved by J.M.Clements, P.Beckett, A.Brown, C.Catlin, M.Lobell, S.Palan, W.Thomas, M.Whittaker, P.J.Baker, H.F.Rodgers, V.Barynin, D.W.Rice, M.G.Hunter, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.10
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	143.140, 64.470, 85.290, 90.00, 123.11, 90.00
R / Rfree (%)	n/a / n/a

The binding sites of Nickel atom in the Crystal Structure of E.Coli Polypeptide Deformylase Complexed with the Inhibitor Bb-3497 (pdb code 1g27). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 3 binding sites of Nickel where determined in the Crystal Structure of E.Coli Polypeptide Deformylase Complexed with the Inhibitor Bb-3497, PDB code: 1g27:
Jump to Nickel binding site number: 1; 2; 3;

Nickel binding site 1 out of 3 in the Crystal Structure of E.Coli Polypeptide Deformylase Complexed with the Inhibitor Bb-3497


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of E.Coli Polypeptide Deformylase Complexed with the Inhibitor Bb-3497 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni9001 b:25.0 occ:1.00 O2 A:BB11001 1.9 34.4 1.0 O1 A:BB11001 2.2 21.4 1.0 NE2 A:HIS136 2.2 24.2 1.0 SG A:CYS90 2.2 25.2 1.0 NE2 A:HIS132 2.4 24.7 1.0 N1 A:BB11001 2.7 22.1 1.0 C1 A:BB11001 2.7 17.2 1.0 CD2 A:HIS132 3.0 24.4 1.0 CE1 A:HIS136 3.1 24.1 1.0 CD2 A:HIS136 3.2 24.3 1.0 NE2 A:GLN50 3.3 18.9 1.0 CB A:CYS90 3.5 21.7 1.0 CE1 A:HIS132 3.5 25.0 1.0 CA A:CYS90 3.8 23.3 1.0 CD A:GLN50 4.0 31.7 1.0 O A:HOH9027 4.0 30.8 1.0 C2 A:BB11001 4.0 26.4 1.0 N A:LEU91 4.2 22.3 1.0 ND1 A:HIS136 4.2 24.9 1.0 OE1 A:GLN50 4.2 21.4 1.0 CG A:HIS132 4.3 23.9 1.0 CG A:HIS136 4.3 23.4 1.0 C3 A:BB11001 4.4 28.1 1.0 C A:CYS90 4.5 26.3 1.0 ND1 A:HIS132 4.5 25.4 1.0 O A:HOH9026 4.5 23.8 1.0 OE1 A:GLU133 4.5 30.9 1.0 C7 A:BB11001 4.6 26.3 1.0 O A:GLY89 4.7 27.6 1.0

Nickel binding site 2 out of 3 in the Crystal Structure of E.Coli Polypeptide Deformylase Complexed with the Inhibitor Bb-3497


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of E.Coli Polypeptide Deformylase Complexed with the Inhibitor Bb-3497 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni9002 b:27.1 occ:1.00 NE2 B:HIS136 2.0 21.6 1.0 O2 B:BB12002 2.0 24.4 1.0 NE2 B:HIS132 2.2 24.0 1.0 SG B:CYS90 2.2 28.8 1.0 O1 B:BB12002 2.4 29.7 1.0 CE1 B:HIS136 2.9 20.1 1.0 N1 B:BB12002 2.9 19.7 1.0 C1 B:BB12002 2.9 24.3 1.0 CD2 B:HIS132 3.1 24.6 1.0 CD2 B:HIS136 3.1 22.9 1.0 CE1 B:HIS132 3.2 23.6 1.0 CB B:CYS90 3.3 26.1 1.0 NE2 B:GLN50 3.4 22.1 1.0 CA B:CYS90 3.7 27.0 1.0 O B:HOH9022 3.8 30.5 1.0 CD B:GLN50 3.9 29.9 1.0 ND1 B:HIS136 4.0 20.6 1.0 OE1 B:GLN50 4.1 23.5 1.0 N B:LEU91 4.1 27.8 1.0 CG B:HIS136 4.2 20.7 1.0 C2 B:BB12002 4.2 28.6 1.0 ND1 B:HIS132 4.3 25.1 1.0 CG B:HIS132 4.3 23.5 1.0 C B:CYS90 4.4 28.3 1.0 C3 B:BB12002 4.5 26.2 1.0 C7 B:BB12002 4.6 19.8 1.0 O B:HOH9004 4.6 26.7 1.0 OE1 B:GLU133 4.7 34.4 1.0 O B:GLY89 4.8 31.1 1.0 OE2 B:GLU133 4.9 27.3 1.0 N B:CYS90 5.0 29.2 1.0

Nickel binding site 3 out of 3 in the Crystal Structure of E.Coli Polypeptide Deformylase Complexed with the Inhibitor Bb-3497


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Crystal Structure of E.Coli Polypeptide Deformylase Complexed with the Inhibitor Bb-3497 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni9003 b:32.5 occ:1.00 NE2 C:HIS132 2.0 21.8 1.0 O2 C:BB13003 2.1 36.9 1.0 NE2 C:HIS136 2.2 26.0 1.0 SG C:CYS90 2.2 28.5 1.0 O1 C:BB13003 2.4 33.0 1.0 N1 C:BB13003 2.8 34.2 1.0 C1 C:BB13003 2.9 30.7 1.0 CE1 C:HIS132 3.0 21.6 1.0 CD2 C:HIS132 3.1 22.1 1.0 CE1 C:HIS136 3.1 24.3 1.0 CD2 C:HIS136 3.1 27.2 1.0 CB C:CYS90 3.2 27.5 1.0 NE2 C:GLN50 3.3 32.7 1.0 CA C:CYS90 3.6 29.9 1.0 O C:HOH9008 3.8 29.0 1.0 N C:LEU91 3.9 37.9 1.0 CD C:GLN50 4.0 46.7 1.0 C2 C:BB13003 4.1 37.3 1.0 ND1 C:HIS132 4.1 22.6 1.0 CG C:HIS132 4.2 21.8 1.0 C C:CYS90 4.2 38.6 1.0 ND1 C:HIS136 4.3 25.7 1.0 OE1 C:GLN50 4.3 43.9 1.0 CG C:HIS136 4.3 26.1 1.0 C3 C:BB13003 4.5 42.2 1.0 C7 C:BB13003 4.6 25.7 1.0 OE1 C:GLU133 4.7 31.7 1.0 O C:HOH9011 4.7 27.8 1.0 O C:GLY89 4.7 34.5 1.0 N C:CYS90 4.9 31.9 1.0 N C:SER92 4.9 33.3 1.0

J.M.Clements, R.P.Beckett, A.Brown, G.Catlin, M.Lobell, S.Palan, W.Thomas, M.Whittaker, S.Wood, S.Salama, P.J.Baker, H.F.Rodgers, V.Barynin, D.W.Rice, M.G.Hunter. Antibiotic Activity and Characterization of Bb-3497, A Novel Peptide Deformylase Inhibitor. Antimicrob.Agents Chemother. V. 45 563 2001.
ISSN: ISSN 0066-4804
PubMed: 11158755
DOI: 10.1128/AAC.45.2.563-570.2001