Iron in PDB 4nub: Crystal Structure of Escherichia Coli Ribosomal Oxygenase Ycfd

The structure of Crystal Structure of Escherichia Coli Ribosomal Oxygenase Ycfd, PDB code: 4nub was solved by L.M.Van Staalduinen, Z.Jia, Montreal-Kingston Bacterial Structuralgenomics Initiative (Bsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.93 / 2.70
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	75.731, 75.731, 210.898, 90.00, 90.00, 90.00
R / Rfree (%)	17.8 / 22.8

The binding sites of Iron atom in the Crystal Structure of Escherichia Coli Ribosomal Oxygenase Ycfd (pdb code 4nub). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total only one binding site of Iron was determined in the Crystal Structure of Escherichia Coli Ribosomal Oxygenase Ycfd, PDB code: 4nub:

Iron binding site 1 out of 1 in the Crystal Structure of Escherichia Coli Ribosomal Oxygenase Ycfd


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 Escherichia Coli Ribosomal Oxygenase Ycfd within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:38.3 occ:1.00 NE2 A:HIS125 2.0 39.0 1.0 NE2 A:HIS187 2.2 36.7 1.0 OD2 A:ASP127 2.2 70.0 1.0 O A:HOH513 2.5 33.2 1.0 O A:HOH508 2.6 27.8 1.0 CE1 A:HIS125 3.0 41.5 1.0 CG A:ASP127 3.0 65.9 1.0 CD2 A:HIS125 3.0 29.2 1.0 CE1 A:HIS187 3.1 26.1 1.0 OD1 A:ASP127 3.1 70.8 1.0 CD2 A:HIS187 3.2 31.9 1.0 O A:HOH509 3.6 58.2 1.0 ND1 A:HIS125 4.1 36.7 1.0 CG A:HIS125 4.2 32.9 1.0 ND1 A:HIS187 4.2 22.5 1.0 CG A:HIS187 4.3 26.7 1.0 CB A:ASP127 4.5 45.2 1.0

L.M.Van Staalduinen, S.K.Novakowski, Z.Jia. Structure and Functional Analysis of Ycfd, A Novel 2-Oxoglutarate/Fe(2+)-Dependent Oxygenase Involved in Translational Regulation in Escherichia Coli. J.Mol.Biol. V. 426 1898 2014.
ISSN: ISSN 0022-2836
PubMed: 24530688
DOI: 10.1016/J.JMB.2014.02.008