Nickel in PDB 6il0: K3U Complex Structure of Peptide Deformylase From Xanthomonas Oryzae Pv. Oryzae

All present enzymatic activity of K3U Complex Structure of Peptide Deformylase From Xanthomonas Oryzae Pv. Oryzae:
3.5.1.88;

The structure of K3U Complex Structure of Peptide Deformylase From Xanthomonas Oryzae Pv. Oryzae, PDB code: 6il0 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)	49.91 / 1.93
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	58.682, 58.682, 265.531, 90.00, 90.00, 120.00
R / Rfree (%)	19.5 / 23.1

The structure of K3U Complex Structure of Peptide Deformylase From Xanthomonas Oryzae Pv. Oryzae also contains other interesting chemical elements:

Fluorine

(F)

3 atoms

The binding sites of Nickel atom in the K3U Complex Structure of Peptide Deformylase From Xanthomonas Oryzae Pv. Oryzae (pdb code 6il0). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 3 binding sites of Nickel where determined in the K3U Complex Structure of Peptide Deformylase From Xanthomonas Oryzae Pv. Oryzae, PDB code: 6il0:
Jump to Nickel binding site number: 1; 2; 3;

Nickel binding site 1 out of 3 in the K3U Complex Structure of Peptide Deformylase From Xanthomonas Oryzae Pv. Oryzae


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of K3U Complex Structure of Peptide Deformylase From Xanthomonas Oryzae Pv. Oryzae within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni202 b:23.8 occ:1.00 F A:K3U201 1.7 23.4 1.0 F1 A:K3U201 2.1 43.2 1.0 NE2 A:HIS141 2.2 22.9 1.0 NE2 A:HIS145 2.2 19.8 1.0 C12 A:K3U201 2.3 46.2 1.0 SG A:CSD99 2.3 32.7 1.0 OD1 A:CSD99 2.8 32.1 1.0 CE1 A:HIS141 3.1 26.5 1.0 CE1 A:HIS145 3.1 25.4 1.0 F2 A:K3U201 3.1 76.7 1.0 CD2 A:HIS145 3.2 18.6 1.0 CD2 A:HIS141 3.2 25.6 1.0 NE2 A:GLN51 3.4 22.2 1.0 CB A:CSD99 3.5 32.3 1.0 C11 A:K3U201 3.7 47.8 1.0 OD2 A:CSD99 3.8 35.6 1.0 CA A:CSD99 3.9 28.7 1.0 CD A:GLN51 3.9 23.3 1.0 O A:HOH321 3.9 24.6 1.0 OE1 A:GLN51 4.0 23.4 1.0 ND1 A:HIS145 4.3 21.1 1.0 ND1 A:HIS141 4.3 24.1 1.0 CG A:HIS145 4.3 18.7 1.0 CG A:HIS141 4.3 24.1 1.0 C3 A:K3U201 4.4 49.5 1.0 OE1 A:GLU142 4.5 27.9 1.0 N A:LEU100 4.5 29.5 1.0 OE2 A:GLU142 4.6 27.2 1.0 O A:GLY98 4.6 29.8 1.0 O A:HOH324 4.6 20.9 1.0 C A:CSD99 4.7 28.4 1.0 CD A:GLU142 4.9 24.9 1.0 C4 A:K3U201 5.0 44.5 1.0 CG A:GLN51 5.0 21.5 1.0

Nickel binding site 2 out of 3 in the K3U Complex Structure of Peptide Deformylase From Xanthomonas Oryzae Pv. Oryzae


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of K3U Complex Structure of Peptide Deformylase From Xanthomonas Oryzae Pv. Oryzae within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni203 b:30.0 occ:1.00 OE2 A:GLU132 2.3 35.9 1.0 OE1 A:GLU132 2.6 40.6 1.0 CD A:GLU132 2.8 35.2 1.0 CG A:GLU132 4.3 32.1 1.0 CE1 A:TYR114 5.0 35.0 1.0 CB A:GLU132 5.0 26.2 1.0

Nickel binding site 3 out of 3 in the K3U Complex Structure of Peptide Deformylase From Xanthomonas Oryzae Pv. Oryzae


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of K3U Complex Structure of Peptide Deformylase From Xanthomonas Oryzae Pv. Oryzae within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni204 b:16.9 occ:1.00 NE2 A:HIS43 2.0 31.8 1.0 CE1 A:HIS43 2.9 44.9 1.0 CD2 A:HIS43 3.1 31.8 1.0 ND1 A:HIS43 4.1 44.7 1.0 CG A:HIS43 4.2 35.8 1.0 O A:ALA41 4.5 26.6 1.0 O A:GLY40 4.8 23.6 1.0

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