Cadmium in PDB 6il2: K4U Complex Structure of Peptide Deformylase From Xanthomonas Oryzae Pv. Oryzae

All present enzymatic activity of K4U Complex Structure of Peptide Deformylase From Xanthomonas Oryzae Pv. Oryzae:
3.5.1.88;

The structure of K4U Complex Structure of Peptide Deformylase From Xanthomonas Oryzae Pv. Oryzae, PDB code: 6il2 was solved by I.H.Lee, L.W.Kang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.90 / 2.41
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	58.531, 58.531, 266.212, 90.00, 90.00, 120.00
R / Rfree (%)	19.2 / 23.2

The binding sites of Cadmium atom in the K4U Complex Structure of Peptide Deformylase From Xanthomonas Oryzae Pv. Oryzae (pdb code 6il2). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 3 binding sites of Cadmium where determined in the K4U Complex Structure of Peptide Deformylase From Xanthomonas Oryzae Pv. Oryzae, PDB code: 6il2:
Jump to Cadmium binding site number: 1; 2; 3;

Cadmium binding site 1 out of 3 in the K4U Complex Structure of Peptide Deformylase From Xanthomonas Oryzae Pv. Oryzae


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of K4U Complex Structure of Peptide Deformylase From Xanthomonas Oryzae Pv. Oryzae within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd201 b:48.1 occ:1.00 O2 A:LHY204 1.9 30.7 1.0 NE2 A:HIS145 2.3 34.2 1.0 NE2 A:HIS141 2.4 29.4 1.0 N2 A:LHY204 2.5 41.7 1.0 SG A:CSD99 2.6 36.3 1.0 O1 A:LHY204 2.8 48.4 1.0 C1 A:LHY204 2.9 48.4 1.0 OD1 A:CSD99 2.9 41.9 1.0 CD2 A:HIS141 3.2 30.6 1.0 CD2 A:HIS145 3.3 29.7 1.0 CE1 A:HIS145 3.3 29.7 1.0 CE1 A:HIS141 3.4 30.6 1.0 NE2 A:GLN51 3.5 23.4 1.0 OE1 A:GLN51 3.7 28.2 1.0 CD A:GLN51 3.7 24.5 1.0 CB A:CSD99 3.8 35.9 1.0 O A:HOH313 3.9 30.7 1.0 N A:LHY204 3.9 48.0 1.0 CA A:CSD99 3.9 34.8 1.0 OD2 A:CSD99 4.0 46.6 1.0 OE1 A:GLU142 4.3 29.1 1.0 O A:GLY98 4.4 34.4 1.0 ND1 A:HIS145 4.4 31.1 1.0 CG A:HIS141 4.4 30.1 1.0 CG A:HIS145 4.4 28.2 1.0 ND1 A:HIS141 4.5 34.5 1.0 O A:HOH314 4.5 27.5 1.0 OE2 A:GLU142 4.5 30.6 1.0 N A:LEU100 4.5 33.0 1.0 CA A:LHY204 4.6 48.0 1.0 C A:CSD99 4.8 35.6 1.0 CD A:GLU142 4.8 31.3 1.0 CG A:GLN51 4.9 24.5 1.0

Cadmium binding site 2 out of 3 in the K4U Complex Structure of Peptide Deformylase From Xanthomonas Oryzae Pv. Oryzae


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of K4U Complex Structure of Peptide Deformylase From Xanthomonas Oryzae Pv. Oryzae within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd202 b:37.2 occ:1.00 OE1 A:GLU128 2.0 34.3 1.0 OE1 A:GLU130 2.4 31.9 1.0 OE2 A:GLU130 2.6 26.5 1.0 CD A:GLU130 2.8 29.1 1.0 CD A:GLU128 2.9 38.4 1.0 OE2 A:GLU128 3.0 40.1 1.0 O A:HOH311 3.8 41.5 1.0 CG A:GLU128 4.3 37.5 1.0 CG A:GLU130 4.3 28.8 1.0 NE A:ARG116 4.5 29.2 1.0 O A:GLU128 4.5 33.9 1.0 N A:GLU130 4.5 28.5 1.0 CA A:ARG129 4.7 33.9 1.0 C A:GLU128 4.8 32.4 1.0 C A:ARG129 4.8 27.4 1.0 NH2 A:ARG116 4.9 33.6 1.0 N A:ARG129 5.0 32.8 1.0

Cadmium binding site 3 out of 3 in the K4U Complex Structure of Peptide Deformylase From Xanthomonas Oryzae Pv. Oryzae


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of K4U Complex Structure of Peptide Deformylase From Xanthomonas Oryzae Pv. Oryzae within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd203 b:50.0 occ:1.00 OE2 A:GLU132 2.6 41.3 1.0 OE1 A:GLU132 2.6 46.6 1.0 CD A:GLU132 2.9 39.6 1.0 CG A:GLU132 4.4 31.9 1.0 CE1 A:TYR114 4.9 40.7 1.0

I.H.Lee, L.W.Kang. Fbis Complex Structure of Peptide Deformylase From Xanthomonas Oryzae Pv. Oryzae To Be Published.