Iron in PDB 5kob: Crystal Structure of A Peptide Deformylase From Burkholderia Xenovorans

All present enzymatic activity of Crystal Structure of A Peptide Deformylase From Burkholderia Xenovorans:
3.5.1.88;

The structure of Crystal Structure of A Peptide Deformylase From Burkholderia Xenovorans, PDB code: 5kob was solved by Ssgcid, Seattle Structural Genomics Center For Infectious Disease(Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.07 / 1.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	63.550, 92.000, 142.110, 90.00, 90.00, 90.00
R / Rfree (%)	16.5 / 19.2

The binding sites of Iron atom in the Crystal Structure of A Peptide Deformylase From Burkholderia Xenovorans (pdb code 5kob). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Crystal Structure of A Peptide Deformylase From Burkholderia Xenovorans, PDB code: 5kob:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Crystal Structure of A Peptide Deformylase From Burkholderia Xenovorans


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 A Peptide Deformylase From Burkholderia Xenovorans within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:15.5 occ:0.83 NE2 A:HIS141 2.2 18.9 1.0 NE2 A:HIS145 2.2 17.9 1.0 O A:HOH306 2.2 21.5 1.0 SG A:CYS99 2.3 18.0 1.0 CD2 A:HIS141 3.0 18.7 1.0 CE1 A:HIS145 3.2 17.7 1.0 CD2 A:HIS145 3.2 17.0 1.0 CE1 A:HIS141 3.3 17.8 1.0 O A:HOH423 3.3 24.4 1.0 CB A:CYS99 3.4 15.5 1.0 O A:HOH387 3.6 15.8 1.0 NE2 A:GLN51 3.7 15.7 1.0 CA A:CYS99 4.0 16.0 1.0 OE1 A:GLN51 4.0 17.0 1.0 CD A:GLN51 4.0 17.0 1.0 OE2 A:GLU142 4.2 24.9 1.0 CG A:HIS141 4.2 16.3 1.0 ND1 A:HIS145 4.3 15.9 1.0 CG A:HIS145 4.3 15.7 1.0 ND1 A:HIS141 4.3 18.0 1.0 O A:HOH381 4.4 15.4 1.0 N A:LEU100 4.5 16.2 1.0 OE1 A:GLU142 4.6 23.6 1.0 C A:CYS99 4.7 16.5 1.0 CD A:GLU142 4.7 23.0 1.0 O A:GLY98 4.8 17.2 1.0

Iron binding site 2 out of 4 in the Crystal Structure of A Peptide Deformylase From Burkholderia Xenovorans


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 A Peptide Deformylase From Burkholderia Xenovorans within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe201 b:18.6 occ:0.88 NE2 B:HIS145 2.2 18.6 1.0 NE2 B:HIS141 2.2 21.8 1.0 O B:HOH324 2.3 27.7 1.0 SG B:CYS99 2.4 20.2 1.0 CD2 B:HIS141 3.0 22.9 1.0 O B:HOH402 3.0 30.8 1.0 CE1 B:HIS145 3.1 20.0 1.0 CD2 B:HIS145 3.1 20.1 1.0 CE1 B:HIS141 3.3 16.1 1.0 CB B:CYS99 3.4 15.1 1.0 O B:HOH384 3.6 17.8 1.0 NE2 B:GLN51 3.7 19.7 1.0 CA B:CYS99 4.0 20.1 1.0 OE1 B:GLN51 4.1 21.6 1.0 CD B:GLN51 4.1 19.8 1.0 CG B:HIS141 4.2 18.3 1.0 ND1 B:HIS145 4.2 17.0 1.0 CG B:HIS145 4.3 16.1 1.0 ND1 B:HIS141 4.3 18.5 1.0 O B:HOH367 4.4 16.3 1.0 OE2 B:GLU142 4.4 31.7 1.0 N B:LEU100 4.5 19.2 1.0 OE1 B:GLU142 4.6 31.7 1.0 C B:CYS99 4.7 19.2 1.0 O B:GLY98 4.8 22.3 1.0 CD B:GLU142 4.9 30.9 1.0

Iron binding site 3 out of 4 in the Crystal Structure of A Peptide Deformylase From Burkholderia Xenovorans


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of A Peptide Deformylase From Burkholderia Xenovorans within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe201 b:17.9 occ:0.86 NE2 C:HIS145 2.2 19.7 1.0 O C:HOH305 2.2 25.1 1.0 NE2 C:HIS141 2.2 21.1 1.0 SG C:CYS99 2.3 18.9 1.0 CD2 C:HIS141 3.0 18.9 1.0 CE1 C:HIS145 3.2 18.9 1.0 O C:HOH398 3.2 29.6 1.0 CD2 C:HIS145 3.2 21.1 1.0 CE1 C:HIS141 3.3 20.0 1.0 CB C:CYS99 3.4 15.3 1.0 O C:HOH370 3.5 18.1 1.0 NE2 C:GLN51 3.7 19.1 1.0 CA C:CYS99 3.9 17.0 1.0 OE1 C:GLN51 4.0 18.6 1.0 CD C:GLN51 4.1 17.9 1.0 OE2 C:GLU142 4.1 25.5 1.0 CG C:HIS141 4.3 16.0 1.0 ND1 C:HIS145 4.3 19.1 1.0 CG C:HIS145 4.3 17.9 1.0 ND1 C:HIS141 4.4 16.9 1.0 O C:HOH349 4.4 17.3 1.0 N C:LEU100 4.5 17.0 1.0 OE1 C:GLU142 4.6 28.4 1.0 C C:CYS99 4.7 17.0 1.0 O C:GLY98 4.7 18.7 1.0 CD C:GLU142 4.8 25.0 1.0

Iron binding site 4 out of 4 in the Crystal Structure of A Peptide Deformylase From Burkholderia Xenovorans


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of A Peptide Deformylase From Burkholderia Xenovorans within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe201 b:19.7 occ:0.83 NE2 D:HIS145 2.3 19.7 1.0 NE2 D:HIS141 2.3 21.8 1.0 O D:HOH341 2.3 28.8 1.0 SG D:CYS99 2.4 21.4 1.0 CD2 D:HIS141 3.1 22.1 1.0 CE1 D:HIS145 3.2 20.6 1.0 CD2 D:HIS145 3.3 19.2 1.0 CE1 D:HIS141 3.3 22.8 1.0 O D:HOH351 3.4 26.5 1.0 CB D:CYS99 3.4 19.0 1.0 O D:HOH379 3.4 19.3 1.0 NE2 D:GLN51 3.8 21.3 1.0 CA D:CYS99 4.0 19.1 1.0 OE1 D:GLN51 4.0 21.5 1.0 CD D:GLN51 4.1 19.1 1.0 CG D:HIS141 4.3 18.8 1.0 ND1 D:HIS145 4.4 19.1 1.0 ND1 D:HIS141 4.4 19.2 1.0 CG D:HIS145 4.4 18.4 1.0 O D:HOH370 4.4 18.2 1.0 OE1 D:GLU142 4.5 36.1 1.0 O D:HOH376 4.6 45.7 1.0 N D:LEU100 4.6 21.4 1.0 OE2 D:GLU142 4.6 38.3 1.0 O D:GLY98 4.7 22.4 1.0 C D:CYS99 4.8 20.4 1.0 CD D:GLU142 4.9 33.5 1.0

S.J.Mayclin, D.G.Conrady, T.E.Edwards, B.Staker, P.Myler, L.Stewart. Crystal Structure of A Peptide Deformylase From Burkholderia Xenovorans To Be Published.