Cadmium in PDB 5e5d: Native Structure of XOO1075, A Peptide Deformylase From Xanthomonas Oryzae Pv. Oryzae

All present enzymatic activity of Native Structure of XOO1075, A Peptide Deformylase From Xanthomonas Oryzae Pv. Oryzae:
3.5.1.88;

The structure of Native Structure of XOO1075, A Peptide Deformylase From Xanthomonas Oryzae Pv. Oryzae, PDB code: 5e5d 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 / 2.60
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	58.968, 58.968, 266.285, 90.00, 90.00, 120.00
R / Rfree (%)	18.7 / 24

The binding sites of Cadmium atom in the Native Structure of XOO1075, A Peptide Deformylase From Xanthomonas Oryzae Pv. Oryzae (pdb code 5e5d). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 3 binding sites of Cadmium where determined in the Native Structure of XOO1075, A Peptide Deformylase From Xanthomonas Oryzae Pv. Oryzae, PDB code: 5e5d:
Jump to Cadmium binding site number: 1; 2; 3;

Cadmium binding site 1 out of 3 in the Native Structure of XOO1075, A 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 Native Structure of XOO1075, A Peptide Deformylase From Xanthomonas Oryzae Pv. Oryzae within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd201 b:31.0 occ:1.00 O A:HOH302 2.0 19.3 1.0 OE2 A:GLU130 2.2 28.2 1.0 O A:HOH320 2.2 22.9 1.0 OE1 A:GLU128 2.2 29.0 1.0 OE1 A:GLU130 2.7 26.6 1.0 CD A:GLU130 2.8 27.1 1.0 OE2 A:GLU128 2.9 35.5 1.0 CD A:GLU128 2.9 33.2 1.0 CD A:ARG116 4.1 25.4 1.0 O A:GLU128 4.2 29.9 1.0 CG A:GLU130 4.3 26.3 1.0 O A:HOH352 4.3 28.2 1.0 CG A:GLU128 4.4 33.5 1.0 O A:HOH306 4.5 28.9 1.0 N A:GLU130 4.6 26.4 1.0 C A:GLU128 4.7 29.0 1.0 O A:HOH342 4.8 24.8 1.0 CA A:ARG129 4.8 27.7 1.0 C A:ARG129 4.8 27.8 1.0 NH1 A:ARG116 4.9 23.6 1.0 N A:ARG129 5.0 26.3 1.0

Cadmium binding site 2 out of 3 in the Native Structure of XOO1075, A 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 Native Structure of XOO1075, A Peptide Deformylase From Xanthomonas Oryzae Pv. Oryzae within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd202 b:38.0 occ:1.00 O A:HOH310 2.2 21.1 1.0 NE2 A:HIS141 2.3 27.0 1.0 NE2 A:HIS145 2.3 26.0 1.0 SG A:CYS99 2.4 35.5 1.0 O A:HOH402 3.1 37.4 1.0 CE1 A:HIS145 3.1 22.0 1.0 CD2 A:HIS141 3.2 28.3 1.0 CE1 A:HIS141 3.2 27.5 1.0 CD2 A:HIS145 3.4 24.4 1.0 CB A:CYS99 3.4 41.8 1.0 NE2 A:GLN51 3.6 22.1 1.0 CA A:CYS99 3.8 41.1 1.0 OE1 A:GLN51 3.8 24.2 1.0 CD A:GLN51 3.9 22.4 1.0 O A:HOH371 3.9 24.6 1.0 O A:HOH303 4.2 41.6 1.0 OE2 A:GLU142 4.3 38.4 1.0 O A:GLY98 4.3 41.1 1.0 ND1 A:HIS145 4.3 22.7 1.0 ND1 A:HIS141 4.4 26.4 1.0 CG A:HIS141 4.4 26.9 1.0 CG A:HIS145 4.4 24.4 1.0 OE1 A:GLU142 4.5 37.1 1.0 O A:HOH370 4.5 24.1 1.0 N A:LEU100 4.6 41.4 1.0 C A:CYS99 4.7 41.8 1.0 CD A:GLU142 4.8 36.0 1.0 N A:CYS99 4.9 38.3 1.0 CG A:GLN51 5.0 20.5 1.0

Cadmium binding site 3 out of 3 in the Native Structure of XOO1075, A 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 Native Structure of XOO1075, A Peptide Deformylase From Xanthomonas Oryzae Pv. Oryzae within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd203 b:99.8 occ:1.00 OE1 A:GLU132 2.2 71.0 1.0 O A:HOH338 2.6 35.2 1.0 CD A:GLU132 3.4 55.4 1.0 OE2 A:GLU132 4.1 57.6 1.0 CG A:GLU132 4.4 40.5 1.0 CE2 A:TYR114 4.5 33.7 1.0 OH A:TYR114 4.7 36.2 1.0

H.P.T.Ngo, L.W.Kang. Native Structure of XOO1075, A Peptide Deformylase From Xanthomonas Oryzae Pv. Oryzae To Be Published.