Iron in PDB 3cmd: Crystal Structure of Peptide Deformylase From Vre-E.Faecium

All present enzymatic activity of Crystal Structure of Peptide Deformylase From Vre-E.Faecium:
3.5.1.88;

The structure of Crystal Structure of Peptide Deformylase From Vre-E.Faecium, PDB code: 3cmd was solved by K.Y.Hwang, K.H.Nam, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.70
Space group	P 64 2 2
Cell size a, b, c (Å), α, β, γ (°)	149.470, 149.470, 143.329, 90.00, 90.00, 120.00
R / Rfree (%)	20 / 22.9

The structure of Crystal Structure of Peptide Deformylase From Vre-E.Faecium also contains other interesting chemical elements:

Sodium

(Na)

8 atoms

The binding sites of Iron atom in the Crystal Structure of Peptide Deformylase From Vre-E.Faecium (pdb code 3cmd). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Crystal Structure of Peptide Deformylase From Vre-E.Faecium, PDB code: 3cmd:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Crystal Structure of Peptide Deformylase From Vre-E.Faecium


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of Peptide Deformylase From Vre-E.Faecium within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe188 b:63.6 occ:1.00 SG A:CYS114 2.3 6.8 1.0 NE2 A:HIS161 2.4 7.5 1.0 NE2 A:HIS157 2.5 11.1 1.0 CB A:CYS114 2.9 11.1 1.0 O6 A:MLI191 2.9 22.5 1.0 C2 A:MLI191 2.9 27.2 1.0 CE1 A:HIS161 3.2 7.2 1.0 O7 A:MLI191 3.2 27.6 1.0 O A:HOH294 3.3 7.7 1.0 CA A:CYS114 3.4 20.8 1.0 CE1 A:HIS157 3.4 10.8 1.0 CD2 A:HIS161 3.5 8.8 1.0 CD2 A:HIS157 3.5 10.2 1.0 NE2 A:GLN65 3.6 1.0 1.0 C1 A:MLI191 3.7 28.3 1.0 O A:GLY113 4.1 22.5 1.0 C A:CYS114 4.2 22.1 1.0 CD A:GLN65 4.3 5.0 1.0 ND1 A:HIS161 4.4 8.7 1.0 N A:LEU115 4.4 16.2 1.0 OE1 A:GLN65 4.5 7.3 1.0 O A:HOH201 4.5 0.0 1.0 N A:CYS114 4.5 20.5 1.0 CG A:HIS161 4.6 9.2 1.0 ND1 A:HIS157 4.6 13.2 1.0 CG A:HIS157 4.7 12.2 1.0 C A:GLY113 4.7 22.1 1.0 O9 A:MLI191 4.7 30.2 1.0 OE2 A:GLU158 4.8 15.0 1.0 C3 A:MLI191 4.8 30.8 1.0 N A:SER116 5.0 19.8 1.0

Iron binding site 2 out of 2 in the Crystal Structure of Peptide Deformylase From Vre-E.Faecium


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of Peptide Deformylase From Vre-E.Faecium within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe188 b:81.0 occ:1.00 NE2 B:HIS161 2.4 11.4 1.0 SG B:CYS114 2.4 6.0 1.0 NE2 B:HIS157 2.5 6.6 1.0 O6 B:MLI195 3.1 51.1 1.0 O7 B:MLI195 3.1 49.8 1.0 CB B:CYS114 3.2 11.9 1.0 CD2 B:HIS157 3.2 5.1 1.0 CE1 B:HIS161 3.3 11.6 1.0 C2 B:MLI195 3.4 51.4 1.0 CD2 B:HIS161 3.4 12.7 1.0 NE2 B:GLN65 3.4 15.7 1.0 O B:HOH197 3.5 3.7 1.0 CA B:CYS114 3.5 14.0 1.0 CE1 B:HIS157 3.6 6.1 1.0 O B:GLY113 4.0 25.9 1.0 CD B:GLN65 4.2 15.0 1.0 C B:CYS114 4.4 15.2 1.0 ND1 B:HIS161 4.4 12.3 1.0 OE1 B:GLN65 4.4 15.6 1.0 CG B:HIS157 4.5 6.0 1.0 CG B:HIS161 4.5 12.5 1.0 N B:LEU115 4.5 15.3 1.0 OE2 B:GLU158 4.5 18.6 1.0 ND1 B:HIS157 4.6 6.9 1.0 N B:CYS114 4.7 15.5 1.0 C1 B:MLI195 4.7 50.0 1.0 C B:GLY113 4.8 25.6 1.0 O B:HOH203 4.8 2.9 1.0 OE1 B:GLU158 4.9 13.9 1.0

K.H.Nam, J.I.Ham, A.Priyadarshi, E.E.Kim, N.Chung, K.Y.Hwang. Insight Into the Antibacterial Drug Design and Architectural Mechanism of Peptide Recognition From the E. Faecium Peptide Deformylase Structure. Proteins V. 74 261 2009.
ISSN: ISSN 0887-3585
PubMed: 18831047
DOI: 10.1002/PROT.22257