Nickel in PDB 1g2a: The Crystal Structure of E.Coli Peptide Deformylase Complexed with Actinonin

All present enzymatic activity of The Crystal Structure of E.Coli Peptide Deformylase Complexed with Actinonin:
3.5.1.31;

The structure of The Crystal Structure of E.Coli Peptide Deformylase Complexed with Actinonin, PDB code: 1g2a 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)	14.00 / 1.75
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	138.700, 63.100, 85.600, 90.00, 121.40, 90.00
R / Rfree (%)	19 / 25

The binding sites of Nickel atom in the The Crystal Structure of E.Coli Peptide Deformylase Complexed with Actinonin (pdb code 1g2a). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 3 binding sites of Nickel where determined in the The Crystal Structure of E.Coli Peptide Deformylase Complexed with Actinonin, PDB code: 1g2a:
Jump to Nickel binding site number: 1; 2; 3;

Nickel binding site 1 out of 3 in the The Crystal Structure of E.Coli Peptide Deformylase Complexed with Actinonin


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of The Crystal Structure of E.Coli Peptide Deformylase Complexed with Actinonin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni1169 b:18.8 occ:1.00 NE2 A:HIS136 2.0 13.2 1.0 NE2 A:HIS132 2.2 13.2 1.0 O4 A:BB21001 2.2 16.3 1.0 O2 A:BB21001 2.3 21.6 1.0 SG A:CYS90 2.3 15.1 1.0 C3 A:BB21001 2.7 19.4 1.0 N1 A:BB21001 2.8 15.9 1.0 CE1 A:HIS136 3.0 14.4 1.0 CD2 A:HIS132 3.1 18.1 1.0 CD2 A:HIS136 3.1 9.8 1.0 CE1 A:HIS132 3.2 16.8 1.0 NE2 A:GLN50 3.3 17.5 1.0 CB A:CYS90 3.4 12.9 1.0 O A:HOH1171 3.6 14.8 1.0 CA A:CYS90 3.7 13.1 1.0 CD A:GLN50 3.9 19.8 1.0 OE1 A:GLN50 4.1 15.8 1.0 C5 A:BB21001 4.1 15.4 1.0 ND1 A:HIS136 4.1 14.9 1.0 N A:LEU91 4.2 15.7 1.0 CG A:HIS136 4.2 14.0 1.0 CG A:HIS132 4.3 10.7 1.0 ND1 A:HIS132 4.3 13.4 1.0 C A:CYS90 4.4 14.9 1.0 C6 A:BB21001 4.4 18.0 1.0 O A:HOH1172 4.6 15.7 1.0 C7 A:BB21001 4.7 19.2 1.0 O A:GLY89 4.7 17.6 1.0 OE1 A:GLU133 4.9 16.8 1.0 OE2 A:GLU133 4.9 18.5 1.0 N A:CYS90 4.9 14.0 1.0

Nickel binding site 2 out of 3 in the The Crystal Structure of E.Coli Peptide Deformylase Complexed with Actinonin


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of The Crystal Structure of E.Coli Peptide Deformylase Complexed with Actinonin within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni2169 b:21.7 occ:1.00 O4 B:BB22002 2.1 21.9 1.0 NE2 B:HIS136 2.2 13.3 1.0 O2 B:BB22002 2.2 20.1 1.0 NE2 B:HIS132 2.3 15.2 1.0 SG B:CYS90 2.3 16.2 1.0 C3 B:BB22002 2.8 18.7 1.0 N1 B:BB22002 2.8 19.1 1.0 CD2 B:HIS132 3.0 13.4 1.0 CE1 B:HIS136 3.1 19.3 1.0 CD2 B:HIS136 3.2 14.0 1.0 CB B:CYS90 3.3 20.2 1.0 CE1 B:HIS132 3.4 22.5 1.0 NE2 B:GLN50 3.5 16.0 1.0 O B:HOH2190 3.6 21.1 1.0 CA B:CYS90 3.7 17.0 1.0 CD B:GLN50 4.0 12.5 1.0 OE1 B:GLN50 4.2 16.2 1.0 ND1 B:HIS136 4.2 13.9 1.0 N B:LEU91 4.2 17.6 1.0 C5 B:BB22002 4.2 19.9 1.0 CG B:HIS132 4.2 14.1 1.0 CG B:HIS136 4.3 13.2 1.0 ND1 B:HIS132 4.4 13.6 1.0 C B:CYS90 4.4 15.2 1.0 C6 B:BB22002 4.5 18.1 1.0 C7 B:BB22002 4.6 12.8 1.0 O B:HOH2174 4.7 18.3 1.0 OE1 B:GLU133 4.7 20.4 1.0 O B:GLY89 4.7 14.3 1.0 OE2 B:GLU133 4.9 16.2 1.0 N B:SER92 5.0 19.5 1.0

Nickel binding site 3 out of 3 in the The Crystal Structure of E.Coli Peptide Deformylase Complexed with Actinonin


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of The Crystal Structure of E.Coli Peptide Deformylase Complexed with Actinonin within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni3169 b:19.1 occ:1.00 O4 C:BB23003 2.0 19.0 1.0 NE2 C:HIS132 2.1 18.5 1.0 NE2 C:HIS136 2.1 15.3 1.0 SG C:CYS90 2.3 16.8 1.0 O2 C:BB23003 2.3 12.4 1.0 C3 C:BB23003 2.8 18.0 1.0 N1 C:BB23003 3.0 21.7 1.0 CD2 C:HIS132 3.1 13.9 1.0 CD2 C:HIS136 3.1 22.1 1.0 CE1 C:HIS136 3.1 17.3 1.0 CE1 C:HIS132 3.2 13.6 1.0 CB C:CYS90 3.3 15.4 1.0 NE2 C:GLN50 3.4 15.8 1.0 O C:HOH3175 3.7 17.6 1.0 CA C:CYS90 3.8 18.4 1.0 CD C:GLN50 3.9 16.0 1.0 OE1 C:GLN50 4.0 19.0 1.0 N C:LEU91 4.2 12.8 1.0 ND1 C:HIS136 4.2 16.4 1.0 CG C:HIS136 4.2 19.8 1.0 CG C:HIS132 4.3 13.4 1.0 C5 C:BB23003 4.3 18.3 1.0 ND1 C:HIS132 4.3 16.0 1.0 C C:CYS90 4.4 17.6 1.0 OE1 C:GLU133 4.5 18.0 1.0 C6 C:BB23003 4.6 18.8 1.0 O C:HOH3170 4.7 15.5 1.0 C7 C:BB23003 4.8 23.9 1.0 O C:GLY89 4.8 15.1 1.0 CG C:GLN50 4.9 15.4 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