Nickel in PDB 4wxk: Crystal Structure of A Peptide Deformylase From Haemophilus Influenzae

All present enzymatic activity of Crystal Structure of A Peptide Deformylase From Haemophilus Influenzae:
3.5.1.88;

The structure of Crystal Structure of A Peptide Deformylase From Haemophilus Influenzae, PDB code: 4wxk was solved by C.Kishor, A.Addlagatta, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.37 / 2.05
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	41.036, 80.961, 98.586, 90.00, 97.81, 90.00
R / Rfree (%)	16.1 / 22.2

The binding sites of Nickel atom in the Crystal Structure of A Peptide Deformylase From Haemophilus Influenzae (pdb code 4wxk). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the Crystal Structure of A Peptide Deformylase From Haemophilus Influenzae, PDB code: 4wxk:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in the Crystal Structure of A Peptide Deformylase From Haemophilus Influenzae


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of A Peptide Deformylase From Haemophilus Influenzae within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni201 b:13.5 occ:1.00 O A:HOH306 2.1 13.9 1.0 NE2 A:HIS133 2.1 18.4 1.0 NE2 A:HIS137 2.1 18.2 1.0 SG A:CYS91 2.2 17.8 1.0 CD2 A:HIS133 3.0 19.2 1.0 CE1 A:HIS137 3.0 17.0 1.0 CD2 A:HIS137 3.1 16.0 1.0 CE1 A:HIS133 3.1 19.4 1.0 CB A:CYS91 3.2 18.9 1.0 O A:HOH367 3.5 22.7 1.0 NE2 A:GLN51 3.7 19.9 1.0 O A:HOH363 3.7 22.4 1.0 OE1 A:GLN51 3.8 19.4 1.0 CA A:CYS91 3.9 19.1 1.0 OE2 A:GLU134 4.0 19.0 1.0 CD A:GLN51 4.0 20.0 1.0 CG A:HIS133 4.1 18.9 1.0 ND1 A:HIS137 4.2 17.6 1.0 ND1 A:HIS133 4.2 18.9 1.0 CG A:HIS137 4.2 16.9 1.0 O A:HOH343 4.3 14.2 1.0 OE1 A:GLU134 4.5 18.6 1.0 CD A:GLU134 4.5 18.1 1.0 O A:GLY90 4.6 18.6 1.0 N A:LEU92 4.7 18.6 1.0 C A:CYS91 4.7 19.3 1.0

Nickel binding site 2 out of 4 in the Crystal Structure of A Peptide Deformylase From Haemophilus Influenzae


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of A Peptide Deformylase From Haemophilus Influenzae within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni201 b:13.1 occ:1.00 O B:HOH303 2.0 16.3 1.0 NE2 B:HIS137 2.1 16.2 1.0 NE2 B:HIS133 2.1 21.4 1.0 SG B:CYS91 2.2 17.3 1.0 CD2 B:HIS133 2.9 19.7 1.0 CD2 B:HIS137 3.1 16.0 1.0 CE1 B:HIS137 3.1 15.7 1.0 CE1 B:HIS133 3.2 20.2 1.0 CB B:CYS91 3.3 16.6 1.0 O B:HOH372 3.5 16.9 1.0 NE2 B:GLN51 3.7 15.6 1.0 OE1 B:GLN51 3.8 17.4 1.0 O B:HOH359 3.8 13.9 1.0 CD B:GLN51 3.9 15.2 1.0 OE2 B:GLU134 3.9 18.2 1.0 CA B:CYS91 3.9 15.0 1.0 CG B:HIS133 4.2 19.2 1.0 ND1 B:HIS137 4.2 14.5 1.0 CG B:HIS137 4.2 13.9 1.0 ND1 B:HIS133 4.2 19.1 1.0 O B:HOH361 4.3 17.8 1.0 OE1 B:GLU134 4.4 16.8 1.0 CD B:GLU134 4.5 17.1 1.0 N B:LEU92 4.7 16.7 1.0 O B:GLY90 4.7 15.7 1.0 C B:CYS91 4.7 16.0 1.0 C2 B:GOL202 4.9 32.7 1.0 CG B:GLN51 5.0 15.6 1.0

Nickel binding site 3 out of 4 in the Crystal Structure of A Peptide Deformylase From Haemophilus Influenzae


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Crystal Structure of A Peptide Deformylase From Haemophilus Influenzae within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni201 b:16.2 occ:1.00 NE2 C:HIS133 2.0 18.6 1.0 O C:HOH304 2.1 21.0 1.0 NE2 C:HIS137 2.1 17.4 1.0 SG C:CYS91 2.2 20.8 1.0 CD2 C:HIS133 2.9 19.6 1.0 CE1 C:HIS137 3.0 17.4 1.0 CE1 C:HIS133 3.1 19.2 1.0 CD2 C:HIS137 3.1 16.1 1.0 CB C:CYS91 3.3 21.1 1.0 O C:HOH359 3.5 15.8 1.0 O C:HOH358 3.7 22.2 1.0 NE2 C:GLN51 3.8 21.7 1.0 OE1 C:GLN51 3.8 21.8 1.0 CA C:CYS91 3.9 19.0 1.0 OE2 C:GLU134 3.9 21.0 1.0 CD C:GLN51 4.0 21.6 1.0 CG C:HIS133 4.1 17.8 1.0 ND1 C:HIS133 4.1 18.9 1.0 ND1 C:HIS137 4.2 16.9 1.0 CG C:HIS137 4.2 16.9 1.0 O C:HOH324 4.4 19.8 1.0 OE1 C:GLU134 4.5 21.1 1.0 CD C:GLU134 4.5 22.1 1.0 O C:GLY90 4.6 18.8 1.0 N C:LEU92 4.7 22.4 1.0 C C:CYS91 4.7 19.2 1.0 C1 C:GOL202 4.9 40.4 1.0

Nickel binding site 4 out of 4 in the Crystal Structure of A Peptide Deformylase From Haemophilus Influenzae


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Crystal Structure of A Peptide Deformylase From Haemophilus Influenzae within 5.0Å range: probe atom residue distance (Å) B Occ D:Ni201 b:13.5 occ:1.00 NE2 D:HIS133 2.0 16.7 1.0 O D:HOH309 2.0 12.4 1.0 NE2 D:HIS137 2.1 17.5 1.0 SG D:CYS91 2.3 18.5 1.0 CD2 D:HIS133 2.9 17.6 1.0 CE1 D:HIS133 3.0 17.6 1.0 CE1 D:HIS137 3.0 17.6 1.0 CD2 D:HIS137 3.1 16.9 1.0 CB D:CYS91 3.2 16.7 1.0 O D:HOH352 3.7 15.3 1.0 NE2 D:GLN51 3.8 17.6 1.0 OE1 D:GLN51 3.8 18.0 1.0 O D:HOH350 3.8 19.2 1.0 CA D:CYS91 3.9 16.4 1.0 CD D:GLN51 4.0 18.9 1.0 OE2 D:GLU134 4.0 20.5 1.0 ND1 D:HIS133 4.1 17.1 1.0 CG D:HIS133 4.1 16.0 1.0 ND1 D:HIS137 4.1 18.1 1.0 CG D:HIS137 4.2 16.6 1.0 O D:HOH339 4.3 16.2 1.0 OE1 D:GLU134 4.4 18.7 1.0 CD D:GLU134 4.5 20.7 1.0 O D:GLY90 4.7 16.5 1.0 C D:CYS91 4.7 18.0 1.0 N D:LEU92 4.8 18.4 1.0 C1 D:GOL202 4.9 32.6 1.0 C3 D:GOL202 5.0 31.8 1.0

C.Kishor, A.Addlagatta. Crystal Structure of A Peptide Deformylase From Haemophilus Influenzae To Be Published.