Zinc in PDB 1lru: Crystal Structure of E.Coli Peptide Deformylase Complexed with Antibiotic Actinonin

All present enzymatic activity of Crystal Structure of E.Coli Peptide Deformylase Complexed with Antibiotic Actinonin:
3.5.1.88;

The structure of Crystal Structure of E.Coli Peptide Deformylase Complexed with Antibiotic Actinonin, PDB code: 1lru was solved by J.-P.Guilloteau, M.Mathieu, C.Giglione, V.Blanc, A.Dupuy, M.Chevrier, P.Gil, A.Famechon, T.Meinnel, V.Mikol, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.00 / 2.10
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	141.040, 63.608, 83.494, 90.00, 123.35, 90.00
R / Rfree (%)	24 / n/a

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

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


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 E.Coli Peptide Deformylase Complexed with Antibiotic Actinonin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:23.9 occ:1.00 O2 A:BB2501 2.4 15.6 1.0 NE2 A:HIS132 2.4 16.8 1.0 O4 A:BB2501 2.4 22.2 1.0 SG A:CYS90 2.5 15.0 1.0 NE2 A:HIS136 2.6 26.2 1.0 CE1 A:HIS132 3.0 14.9 1.0 C3 A:BB2501 3.1 22.6 1.0 N1 A:BB2501 3.1 16.9 1.0 CD2 A:HIS136 3.3 27.5 1.0 CB A:CYS90 3.3 25.9 1.0 CD2 A:HIS132 3.5 14.7 1.0 CE1 A:HIS136 3.7 30.1 1.0 NE2 A:GLN50 3.8 27.7 1.0 CA A:CYS90 3.8 23.5 1.0 O A:HOH610 4.0 21.9 1.0 OE1 A:GLN50 4.1 25.0 1.0 CD A:GLN50 4.1 24.1 1.0 ND1 A:HIS132 4.2 11.7 1.0 N A:LEU91 4.2 22.7 1.0 CG A:HIS132 4.5 13.9 1.0 C A:CYS90 4.5 23.6 1.0 C5 A:BB2501 4.5 24.1 1.0 CG A:HIS136 4.5 27.2 1.0 ND1 A:HIS136 4.7 31.7 1.0 OE1 A:GLU133 4.7 16.2 1.0 O A:HOH611 4.8 18.2 1.0 C6 A:BB2501 4.8 24.8 1.0 O A:GLY89 4.9 18.6 1.0 N A:SER92 5.0 27.5 1.0

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


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 E.Coli Peptide Deformylase Complexed with Antibiotic Actinonin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn602 b:20.1 occ:1.00 O2 B:BB2502 2.3 11.8 1.0 NE2 B:HIS136 2.3 7.8 1.0 O4 B:BB2502 2.4 17.9 1.0 SG B:CYS90 2.5 11.6 1.0 NE2 B:HIS132 2.6 15.9 1.0 N1 B:BB2502 3.0 13.0 1.0 C3 B:BB2502 3.0 12.9 1.0 CD2 B:HIS132 3.2 11.5 1.0 NE2 B:GLN50 3.2 11.1 1.0 CE1 B:HIS136 3.2 3.9 1.0 CD2 B:HIS136 3.4 9.2 1.0 CB B:CYS90 3.5 6.7 1.0 CE1 B:HIS132 3.8 17.9 1.0 CA B:CYS90 3.8 11.7 1.0 CD B:GLN50 3.9 10.0 1.0 O B:HOH713 3.9 20.8 1.0 OE1 B:GLN50 4.1 10.0 1.0 N B:LEU91 4.2 13.7 1.0 ND1 B:HIS136 4.4 8.7 1.0 C5 B:BB2502 4.4 14.7 1.0 CG B:HIS136 4.5 3.1 1.0 CG B:HIS132 4.5 19.0 1.0 C B:CYS90 4.5 12.6 1.0 O B:HOH714 4.6 13.7 1.0 C6 B:BB2502 4.6 11.6 1.0 ND1 B:HIS132 4.7 19.1 1.0 O B:GLY89 4.8 15.7 1.0 OE1 B:GLU133 4.8 24.0 1.0 C7 B:BB2502 4.9 14.0 1.0 CG B:GLN50 5.0 12.2 1.0 N B:SER92 5.0 15.5 1.0

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


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 E.Coli Peptide Deformylase Complexed with Antibiotic Actinonin within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn603 b:17.8 occ:1.00 O4 C:BB2503 2.3 17.4 1.0 SG C:CYS90 2.4 20.2 1.0 O2 C:BB2503 2.4 17.4 1.0 NE2 C:HIS136 2.5 4.2 1.0 NE2 C:HIS132 2.6 5.5 1.0 C3 C:BB2503 2.9 18.1 1.0 N1 C:BB2503 3.0 21.4 1.0 CD2 C:HIS136 3.1 4.2 1.0 CD2 C:HIS132 3.3 10.5 1.0 NE2 C:GLN50 3.4 2.0 1.0 CB C:CYS90 3.5 17.1 1.0 CE1 C:HIS132 3.5 7.7 1.0 CE1 C:HIS136 3.6 3.5 1.0 CD C:GLN50 3.9 10.9 1.0 O C:HOH624 3.9 11.7 1.0 OE1 C:GLN50 3.9 7.5 1.0 CA C:CYS90 4.0 18.2 1.0 N C:LEU91 4.3 17.8 1.0 C5 C:BB2503 4.4 17.8 1.0 CG C:HIS136 4.4 2.0 1.0 CG C:HIS132 4.4 5.5 1.0 ND1 C:HIS132 4.5 10.9 1.0 C6 C:BB2503 4.6 20.4 1.0 ND1 C:HIS136 4.6 2.3 1.0 C C:CYS90 4.6 18.1 1.0 OE1 C:GLU133 4.6 16.9 1.0 O C:HOH626 4.7 15.2 1.0 OE2 C:GLU133 4.8 15.8 1.0 O C:GLY89 5.0 11.9 1.0 C7 C:BB2503 5.0 18.9 1.0

J.P.Guilloteau, M.Mathieu, C.Giglione, V.Blanc, A.Dupuy, M.Chevrier, P.Gil, A.Famechon, T.Meinnel, V.Mikol. The Crystal Structures of Four Peptide Deformylases Bound to the Antibiotic Actinonin Reveal Two Distinct Types: A Platform For the Structure-Based Design of Antibacterial Agents. J.Mol.Biol. V. 320 951 2002.
ISSN: ISSN 0022-2836
PubMed: 12126617
DOI: 10.1016/S0022-2836(02)00549-1