Nickel in PDB 6jfa: Met-Ala-Ser Bound Crystal Structure of Class I Type B Peptide Deformylase From Pseudomonas Aeruginosa

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

The structure of Met-Ala-Ser Bound Crystal Structure of Class I Type B Peptide Deformylase From Pseudomonas Aeruginosa, PDB code: 6jfa 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)	31.67 / 1.93
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	44.815, 122.826, 143.978, 90.00, 90.00, 90.00
R / Rfree (%)	23.6 / 28.8

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

Nickel binding site 1 out of 3 in the Met-Ala-Ser 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 Met-Ala-Ser 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:45.7 occ:1.00 NE2 A:HIS149 2.1 27.7 1.0 NE2 A:HIS145 2.3 42.2 1.0 O C:HOH103 2.7 49.7 1.0 SG A:CYS103 2.8 47.6 1.0 CD2 A:HIS149 3.1 29.9 1.0 CE1 A:HIS149 3.1 34.8 1.0 CD2 A:HIS145 3.1 41.9 1.0 CE1 A:HIS145 3.3 41.4 1.0 N C:MET1 3.7 81.8 1.0 NE2 A:GLN55 3.8 37.0 1.0 O A:HOH342 3.8 31.7 1.0 OE1 A:GLN55 3.9 35.4 1.0 CB A:CYS103 3.9 45.5 1.0 CD A:GLN55 4.0 37.2 1.0 ND1 A:HIS149 4.2 33.5 1.0 CG A:HIS149 4.2 30.6 1.0 CG A:HIS145 4.3 40.6 1.0 CA A:CYS103 4.3 48.6 1.0 ND1 A:HIS145 4.3 42.7 1.0 OE2 A:GLU146 4.3 53.7 1.0 CA C:MET1 4.3 82.5 1.0 O A:HOH331 4.6 37.5 1.0 OE1 A:GLU146 4.7 69.7 1.0 CD A:GLU146 4.8 53.5 1.0 N A:LEU104 4.8 50.0 1.0 O A:GLY102 5.0 46.3 1.0

Nickel binding site 2 out of 3 in the Met-Ala-Ser 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 Met-Ala-Ser 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:51.2 occ:1.00 NE2 B:HIS149 2.0 40.1 1.0 NE2 B:HIS145 2.2 36.7 1.0 SG B:CYS103 2.8 46.6 1.0 CE1 B:HIS149 3.0 42.4 1.0 CD2 B:HIS145 3.0 39.8 1.0 CD2 B:HIS149 3.0 41.9 1.0 CE1 B:HIS145 3.3 42.0 1.0 OE2 B:GLU146 3.6 71.0 1.0 NE2 B:GLN55 3.6 34.9 1.0 O B:HOH340 3.6 37.2 1.0 CB B:CYS103 3.6 46.7 1.0 OE1 B:GLN55 3.9 35.7 1.0 CD B:GLN55 4.0 39.2 1.0 ND1 B:HIS149 4.1 40.7 1.0 CG B:HIS149 4.1 36.1 1.0 CG B:HIS145 4.2 40.6 1.0 CA B:CYS103 4.3 43.8 1.0 ND1 B:HIS145 4.3 39.7 1.0 CD B:GLU146 4.4 58.5 1.0 OE1 B:GLU146 4.6 64.5 1.0 O B:HOH330 4.6 42.0 1.0 O B:GLY102 5.0 48.2 1.0 N B:LEU104 5.0 43.1 1.0

Nickel binding site 3 out of 3 in the Met-Ala-Ser 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 Met-Ala-Ser 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:Ni202 b:89.0 occ:1.00 O B:HOH301 1.8 45.6 1.0 OE1 B:GLU25 2.4 63.6 1.0 OE2 B:GLU25 2.7 57.5 1.0 CD B:GLU25 2.9 58.0 1.0 OG B:SER24 3.6 56.6 1.0 N B:SER24 4.2 49.6 1.0 CG B:GLU25 4.4 56.3 1.0 CB B:PRO23 4.5 58.4 1.0 CA B:PRO23 4.7 57.3 1.0 N B:GLU25 4.7 47.7 1.0 C B:PRO23 4.8 50.0 1.0 CB B:SER24 4.8 53.0 1.0 CA B:SER24 5.0 50.7 1.0

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