Nickel in PDB 6jf9: Apo Crystal Structure of Class I Type B Peptide Deformylase From Pseudomonas Aeruginosa

All present enzymatic activity of Apo Crystal Structure of Class I Type B Peptide Deformylase From Pseudomonas Aeruginosa:
3.5.1.88;

The structure of Apo Crystal Structure of Class I Type B Peptide Deformylase From Pseudomonas Aeruginosa, PDB code: 6jf9 was solved by I.H.Lee, T.H.Ho, L.W.Kang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.99 / 1.70
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	44.486, 122.045, 149.380, 90.00, 90.00, 90.00
R / Rfree (%)	24.3 / 28.1

The binding sites of Nickel atom in the Apo Crystal Structure of Class I Type B Peptide Deformylase From Pseudomonas Aeruginosa (pdb code 6jf9). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Apo Crystal Structure of Class I Type B Peptide Deformylase From Pseudomonas Aeruginosa, PDB code: 6jf9:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Apo Crystal Structure of Class I Type B Peptide Deformylase From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Apo Crystal Structure of Class I Type B Peptide Deformylase From Pseudomonas Aeruginosa within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni201 b:50.3 occ:1.00 SG A:CYS103 2.0 25.1 1.0 NE2 A:HIS145 2.4 23.2 1.0 NE2 A:HIS149 2.4 18.6 1.0 O A:HOH306 2.6 30.6 1.0 CE1 A:HIS149 3.1 17.9 1.0 CB A:CYS103 3.1 22.9 1.0 CD2 A:HIS145 3.3 24.4 1.0 CE1 A:HIS145 3.3 21.6 1.0 O A:HOH319 3.5 21.2 1.0 CD2 A:HIS149 3.6 18.4 1.0 O A:HOH330 3.7 28.6 1.0 NE2 A:GLN55 3.8 17.2 1.0 CA A:CYS103 3.8 24.2 1.0 CD A:GLN55 4.3 18.8 1.0 OE1 A:GLN55 4.3 17.3 1.0 ND1 A:HIS149 4.3 18.4 1.0 ND1 A:HIS145 4.4 21.6 1.0 CG A:HIS145 4.4 20.1 1.0 O A:GLY102 4.5 31.1 1.0 O A:HOH321 4.5 16.0 1.0 CG A:HIS149 4.6 16.0 1.0 OE2 A:GLU146 4.6 36.0 1.0 N A:LEU104 4.7 24.9 1.0 C A:CYS103 4.7 24.4 1.0 N A:CYS103 4.9 23.6 1.0

Nickel binding site 2 out of 2 in the Apo Crystal Structure of Class I Type B Peptide Deformylase From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Apo Crystal Structure of Class I Type B Peptide Deformylase From Pseudomonas Aeruginosa within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni201 b:49.0 occ:1.00 NE2 B:HIS149 2.1 20.8 1.0 SG B:CYS103 2.2 23.3 1.0 O B:HOH303 2.3 22.9 1.0 NE2 B:HIS145 2.4 22.4 1.0 CE1 B:HIS149 2.9 21.9 1.0 CB B:CYS103 3.2 21.5 1.0 CD2 B:HIS149 3.2 25.2 1.0 CD2 B:HIS145 3.3 20.9 1.0 CE1 B:HIS145 3.4 21.4 1.0 O B:HOH328 3.6 26.1 1.0 NE2 B:GLN55 3.6 18.0 1.0 O B:HOH318 3.6 19.3 1.0 CA B:CYS103 3.9 23.3 1.0 CD B:GLN55 4.1 18.2 1.0 OE1 B:GLN55 4.1 18.5 1.0 ND1 B:HIS149 4.1 24.6 1.0 OE2 B:GLU146 4.2 25.4 1.0 CG B:HIS149 4.3 21.1 1.0 O B:HOH323 4.4 18.9 1.0 CG B:HIS145 4.4 19.8 1.0 ND1 B:HIS145 4.5 22.5 1.0 N B:LEU104 4.7 22.9 1.0 C B:CYS103 4.8 22.7 1.0 O B:GLY102 4.8 27.2 1.0 CD2 B:LEU154 5.0 29.7 1.0

I.H.Lee, T.H.Ho, L.W.Kang. Apo Crystal Structure of Class I Type B Peptide Deformylase From Pseudomonas Aeruginosa To Be Published.