Cadmium in PDB 5cx0: Structure of XOO1075, A Peptide Deformylase From Xanthomonas Oryzae Pv. Oryzae, in Complex with Fragment 322

All present enzymatic activity of Structure of XOO1075, A Peptide Deformylase From Xanthomonas Oryzae Pv. Oryzae, in Complex with Fragment 322:
3.5.1.88;

The structure of Structure of XOO1075, A Peptide Deformylase From Xanthomonas Oryzae Pv. Oryzae, in Complex with Fragment 322, PDB code: 5cx0 was solved by H.P.T.Ngo, L.W.Kang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.40 / 2.50
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	58.751, 58.751, 266.092, 90.00, 90.00, 120.00
R / Rfree (%)	19.2 / 23.8

The binding sites of Cadmium atom in the Structure of XOO1075, A Peptide Deformylase From Xanthomonas Oryzae Pv. Oryzae, in Complex with Fragment 322 (pdb code 5cx0). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 3 binding sites of Cadmium where determined in the Structure of XOO1075, A Peptide Deformylase From Xanthomonas Oryzae Pv. Oryzae, in Complex with Fragment 322, PDB code: 5cx0:
Jump to Cadmium binding site number: 1; 2; 3;

Cadmium binding site 1 out of 3 in the Structure of XOO1075, A Peptide Deformylase From Xanthomonas Oryzae Pv. Oryzae, in Complex with Fragment 322


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Structure of XOO1075, A Peptide Deformylase From Xanthomonas Oryzae Pv. Oryzae, in Complex with Fragment 322 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd201 b:42.9 occ:1.00 NE2 A:HIS141 2.3 32.1 1.0 NE2 A:HIS145 2.3 34.6 1.0 SG A:CYS99 2.4 43.6 1.0 S7 A:56L205 2.7 65.0 1.0 CE1 A:HIS141 3.2 34.2 1.0 CE1 A:HIS145 3.3 29.0 1.0 C5 A:56L205 3.3 77.5 1.0 CD2 A:HIS141 3.3 34.7 1.0 CB A:CYS99 3.3 63.4 1.0 CD2 A:HIS145 3.4 30.0 1.0 O A:HOH305 3.4 33.2 1.0 NE2 A:GLN51 3.7 29.2 1.0 N4 A:56L205 3.8 72.5 1.0 CA A:CYS99 3.8 52.2 1.0 O A:HOH322 3.8 25.1 1.0 CD A:GLN51 4.0 26.7 1.0 OE1 A:GLN51 4.0 26.3 1.0 N6 A:56L205 4.0 71.8 1.0 O A:GLY98 4.3 45.8 1.0 O A:HOH338 4.3 39.2 1.0 ND1 A:HIS141 4.4 36.4 1.0 ND1 A:HIS145 4.4 30.6 1.0 CG A:HIS141 4.4 34.3 1.0 N A:LEU100 4.5 60.5 1.0 CG A:HIS145 4.5 30.7 1.0 OE1 A:GLU142 4.6 35.0 1.0 C A:CYS99 4.7 53.5 1.0 C3 A:56L205 4.8 64.5 1.0 CG A:GLN51 5.0 26.6 1.0 N A:CYS99 5.0 52.1 1.0

Cadmium binding site 2 out of 3 in the Structure of XOO1075, A Peptide Deformylase From Xanthomonas Oryzae Pv. Oryzae, in Complex with Fragment 322


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Structure of XOO1075, A Peptide Deformylase From Xanthomonas Oryzae Pv. Oryzae, in Complex with Fragment 322 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd202 b:62.0 occ:1.00 OE2 A:GLU37 2.6 42.2 1.0 O A:HOH355 2.7 26.7 1.0 O A:HOH357 2.9 27.9 1.0 OE1 A:GLU37 3.0 37.5 1.0 CD A:GLU37 3.2 38.7 1.0 N A:MET1 3.6 47.2 1.0 CA A:MET1 4.0 47.0 1.0 CG A:GLU37 4.6 34.7 1.0 N A:ILE2 4.6 40.6 1.0 C A:MET1 4.7 44.8 1.0

Cadmium binding site 3 out of 3 in the Structure of XOO1075, A Peptide Deformylase From Xanthomonas Oryzae Pv. Oryzae, in Complex with Fragment 322


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Structure of XOO1075, A Peptide Deformylase From Xanthomonas Oryzae Pv. Oryzae, in Complex with Fragment 322 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd203 b:37.1 occ:1.00 O A:HOH345 2.3 27.8 1.0 O A:HOH320 2.3 26.2 1.0 OE1 A:GLU128 2.5 34.4 1.0 OE2 A:GLU130 2.6 30.7 1.0 OE1 A:GLU130 2.6 33.9 1.0 OE2 A:GLU128 2.7 42.8 1.0 CD A:GLU130 2.9 32.7 1.0 CD A:GLU128 3.0 42.7 1.0 O A:HOH315 3.8 47.5 1.0 CD A:ARG116 4.2 31.7 1.0 O A:GLU128 4.2 35.1 1.0 CG A:GLU130 4.5 29.5 1.0 CG A:GLU128 4.5 38.5 1.0 N A:GLU130 4.5 32.6 1.0 NH1 A:ARG116 4.6 31.3 1.0 O A:HOH350 4.7 31.3 1.0 C A:GLU128 4.7 35.9 1.0 CA A:ARG129 4.8 33.4 1.0 C A:ARG129 4.8 33.3 1.0

H.P.T.Ngo, L.W.Kang. Structure of XOO1075, A Peptide Deformylase From Xanthomonas Oryzae Pv. Oryzae, in Complex with Fragment 322 To Be Published.