Cadmium in PDB 5cvq: Structure of XOO1075, A Peptide Deformylase From Xanthomonas Oryzae Pv Oryzae, in Complex with Actinonin

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

The structure of Structure of XOO1075, A Peptide Deformylase From Xanthomonas Oryzae Pv Oryzae, in Complex with Actinonin, PDB code: 5cvq 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)	27.84 / 2.50
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	58.641, 58.641, 265.848, 90.00, 90.00, 120.00
R / Rfree (%)	17.2 / 21.8

The binding sites of Cadmium atom in the Structure of XOO1075, A Peptide Deformylase From Xanthomonas Oryzae Pv Oryzae, in Complex with Actinonin (pdb code 5cvq). 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 Actinonin, PDB code: 5cvq:
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 Actinonin


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 Actinonin within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd201 b:27.0 occ:1.00 OE1 A:GLU130 2.2 28.4 1.0 O A:HOH301 2.2 29.6 1.0 OE1 A:GLU128 2.2 28.8 1.0 OE2 A:GLU130 2.3 27.7 1.0 O A:HOH344 2.5 23.1 1.0 CD A:GLU130 2.6 26.6 1.0 OE2 A:GLU128 2.8 36.8 1.0 CD A:GLU128 2.9 30.9 1.0 NH1 A:ARG116 4.1 30.0 1.0 CG A:GLU130 4.2 25.8 1.0 O A:GLU128 4.3 27.4 1.0 CG A:GLU128 4.4 27.6 1.0 N A:GLU130 4.4 24.9 1.0 O A:HOH371 4.5 21.5 1.0 CD A:ARG116 4.5 22.3 1.0 CA A:ARG129 4.7 25.2 1.0 C A:GLU128 4.7 26.4 1.0 C A:ARG129 4.8 24.4 1.0 N A:ARG129 4.9 24.3 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 Actinonin


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 Actinonin within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd202 b:30.5 occ:1.00 NE2 A:HIS141 2.2 28.9 1.0 NE2 A:HIS145 2.3 23.9 1.0 O4 A:BB2205 2.4 22.6 1.0 O2 A:BB2205 2.5 25.8 1.0 SG A:CYS99 2.6 27.0 1.0 C3 A:BB2205 2.9 25.7 1.0 N1 A:BB2205 3.0 26.7 1.0 CD2 A:HIS141 3.2 28.0 1.0 CE1 A:HIS145 3.2 21.8 1.0 CE1 A:HIS141 3.2 26.5 1.0 CD2 A:HIS145 3.3 20.9 1.0 NE2 A:GLN51 3.3 16.5 1.0 CB A:CYS99 3.5 29.7 1.0 O A:HOH362 3.7 30.8 1.0 CD A:GLN51 3.8 18.4 1.0 CA A:CYS99 3.8 28.1 1.0 OE1 A:GLN51 4.1 20.9 1.0 C5 A:BB2205 4.3 24.6 1.0 ND1 A:HIS141 4.3 28.0 1.0 CG A:HIS141 4.4 28.1 1.0 ND1 A:HIS145 4.4 22.6 1.0 CG A:HIS145 4.4 21.2 1.0 N A:LEU100 4.4 27.4 1.0 O A:HOH337 4.5 15.7 1.0 C A:CYS99 4.6 28.9 1.0 C6 A:BB2205 4.6 23.4 1.0 OE1 A:GLU142 4.7 21.2 1.0 C7 A:BB2205 4.8 24.2 1.0 CG A:GLN51 4.9 18.1 1.0 O A:GLY98 4.9 29.2 1.0 OE2 A:GLU142 4.9 19.5 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 Actinonin


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 Actinonin within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd204 b:44.4 occ:1.00 OE1 A:GLU132 2.2 38.2 1.0 O A:HOH348 2.2 22.1 1.0 OE2 A:GLU132 2.8 40.2 1.0 CD A:GLU132 2.9 37.8 1.0 CG A:GLU132 4.3 30.5 1.0 CE2 A:TYR114 4.9 37.6 1.0

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