Nickel in PDB 6jfn: K4U Bound Crystal Structure of Class I Type B Peptide Deformylase From Pseudomonas Aeruginosa

All present enzymatic activity of K4U Bound Crystal Structure of Class I Type B Peptide Deformylase From Pseudomonas Aeruginosa:
3.5.1.88;

The structure of K4U Bound Crystal Structure of Class I Type B Peptide Deformylase From Pseudomonas Aeruginosa, PDB code: 6jfn 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)	31.66 / 2.04
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	44.147, 122.026, 146.621, 90.00, 90.00, 90.00
R / Rfree (%)	24.7 / 29

The binding sites of Nickel atom in the K4U Bound Crystal Structure of Class I Type B Peptide Deformylase From Pseudomonas Aeruginosa (pdb code 6jfn). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 3 binding sites of Nickel where determined in the K4U Bound Crystal Structure of Class I Type B Peptide Deformylase From Pseudomonas Aeruginosa, PDB code: 6jfn:
Jump to Nickel binding site number: 1; 2; 3;

Nickel binding site 1 out of 3 in the K4U Bound 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 K4U Bound 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:82.9 occ:1.00 NE2 A:HIS149 2.0 43.5 1.0 NE2 A:HIS145 2.4 34.0 1.0 SG A:CYS103 2.6 45.0 1.0 CE1 A:HIS149 2.8 44.2 1.0 CD2 A:HIS145 3.1 37.1 1.0 CD2 A:HIS149 3.2 44.8 1.0 CE1 A:HIS145 3.5 40.1 1.0 CB A:CYS103 3.6 41.7 1.0 NE2 A:GLN55 3.6 40.5 1.0 O A:HOH308 3.7 37.9 1.0 OE1 A:GLN55 4.0 42.1 1.0 CD A:GLN55 4.0 42.0 1.0 ND1 A:HIS149 4.0 40.7 1.0 O A:HOH306 4.0 44.7 1.0 OE2 A:GLU146 4.1 52.4 1.0 CG A:HIS149 4.2 37.5 1.0 CG A:HIS145 4.3 38.0 1.0 CA A:CYS103 4.3 43.9 1.0 ND1 A:HIS145 4.5 39.9 1.0 CD A:GLU146 4.8 59.8 1.0 OE1 A:GLU146 4.8 62.1 1.0 O A:HIS145 4.9 41.2 1.0 O A:GLY102 4.9 45.4 1.0

Nickel binding site 2 out of 3 in the K4U Bound 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 K4U Bound Crystal Structure of Class I Type B Peptide Deformylase From Pseudomonas Aeruginosa within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni202 b:88.0 occ:1.00 OE2 A:GLU25 2.7 60.7 1.0 OE1 A:GLU25 2.8 57.2 1.0 CD A:GLU25 3.1 55.4 1.0 OG A:SER24 3.9 61.4 1.0 CG A:GLU25 4.6 52.5 1.0 CB A:PRO23 4.8 55.7 1.0 N A:SER24 4.9 47.7 1.0

Nickel binding site 3 out of 3 in the K4U Bound 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 3 of K4U Bound 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:67.3 occ:1.00 SG B:CYS103 2.1 49.2 1.0 O1 B:LHY202 2.1 0.1 1.0 NE2 B:HIS149 2.3 29.5 1.0 O2 B:LHY202 2.4 57.9 1.0 NE2 B:HIS145 2.5 44.0 1.0 CE1 B:HIS149 2.9 33.4 1.0 C1 B:LHY202 3.0 85.3 1.0 N2 B:LHY202 3.1 78.2 1.0 CB B:CYS103 3.2 44.6 1.0 CE1 B:HIS145 3.4 44.3 1.0 O B:HOH307 3.4 38.3 1.0 CD2 B:HIS145 3.4 42.0 1.0 CD2 B:HIS149 3.5 32.5 1.0 NE2 B:GLN55 3.6 32.0 1.0 CA B:CYS103 3.9 43.4 1.0 ND1 B:HIS149 4.1 36.0 1.0 CD B:GLN55 4.1 32.7 1.0 N B:LHY202 4.2 87.7 1.0 OE1 B:GLN55 4.2 32.8 1.0 CG B:HIS149 4.5 32.9 1.0 ND1 B:HIS145 4.5 45.3 1.0 CG B:HIS145 4.5 41.5 1.0 N B:LEU104 4.6 45.9 1.0 C B:CYS103 4.7 46.2 1.0 O B:HOH303 4.7 32.8 1.0 CA B:LHY202 4.8 88.7 1.0 O B:GLY102 4.8 50.8 1.0 OE2 B:GLU146 4.8 53.6 1.0 CB B:LHY202 5.0 85.1 1.0

I.H.Lee, T.H.Ho, L.W.Kang. K4U Bound Crystal Structure of Class I Type B Peptide Deformylase From Pseudomonas Aeruginosa To Be Published.