Nickel in PDB 2ai9: S.Aureus Polypeptide Deformylase

All present enzymatic activity of S.Aureus Polypeptide Deformylase:
3.5.1.88;

The structure of S.Aureus Polypeptide Deformylase, PDB code: 2ai9 was solved by K.J.Smith, C.M.Petit, K.Aubart, M.Smyth, E.Mcmanus, J.Jones, A.Fosberry, C.Lewis, M.Lonetto, S.B.Christensen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.50
Space group	I 4
Cell size a, b, c (Å), α, β, γ (°)	167.300, 167.300, 42.250, 90.00, 90.00, 90.00
R / Rfree (%)	22.1 / 27.2

The binding sites of Nickel atom in the S.Aureus Polypeptide Deformylase (pdb code 2ai9). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the S.Aureus Polypeptide Deformylase, PDB code: 2ai9:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the S.Aureus Polypeptide Deformylase


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of S.Aureus Polypeptide Deformylase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni302 b:59.6 occ:0.85 SG A:CYS110 2.2 29.1 1.0 NE2 A:HIS153 2.4 23.9 1.0 NE2 A:HIS157 2.5 19.2 1.0 O A:HOH322 3.0 24.2 1.0 CB A:CYS110 3.0 39.4 1.0 CE1 A:HIS157 3.2 20.1 1.0 CE1 A:HIS153 3.2 21.4 1.0 O A:HOH327 3.2 36.3 1.0 CD2 A:HIS153 3.4 20.9 1.0 CA A:CYS110 3.6 40.2 1.0 O A:HOH412 3.7 29.3 1.0 NE2 A:GLN64 3.7 22.6 1.0 CD2 A:HIS157 3.7 18.3 1.0 O A:GLY109 4.2 46.3 1.0 ND1 A:HIS153 4.4 25.6 1.0 ND1 A:HIS157 4.4 18.7 1.0 CD A:GLN64 4.4 25.3 1.0 CG A:HIS153 4.5 20.6 1.0 C A:CYS110 4.5 41.6 1.0 N A:LEU111 4.6 41.9 1.0 CG A:HIS157 4.7 16.3 1.0 OE2 A:GLU154 4.7 17.1 1.0 N A:CYS110 4.8 44.0 1.0 OE1 A:GLN64 4.8 24.1 1.0 C A:GLY109 4.9 44.2 1.0 O A:HOH392 4.9 30.6 1.0

Nickel binding site 2 out of 2 in the S.Aureus Polypeptide Deformylase


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of S.Aureus Polypeptide Deformylase within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni301 b:57.7 occ:0.86 SG B:CYS110 2.2 20.3 1.0 NE2 B:HIS157 2.4 14.7 1.0 O B:HOH3010 2.5 25.2 1.0 NE2 B:HIS153 2.5 25.8 1.0 CE1 B:HIS157 3.1 10.6 1.0 CB B:CYS110 3.2 22.5 1.0 CE1 B:HIS153 3.2 25.7 1.0 O B:HOH3035 3.2 11.9 1.0 CD2 B:HIS153 3.5 27.5 1.0 CD2 B:HIS157 3.6 8.7 1.0 NE2 B:GLN64 3.8 8.1 1.0 CA B:CYS110 3.8 24.8 1.0 O B:HOH3050 4.0 35.5 1.0 ND1 B:HIS157 4.3 8.1 1.0 ND1 B:HIS153 4.3 28.4 1.0 CD B:GLN64 4.4 14.5 1.0 O B:GLY109 4.5 31.0 1.0 CG B:HIS153 4.5 23.6 1.0 OE1 B:GLN64 4.5 16.7 1.0 N B:LEU111 4.5 24.9 1.0 O B:HOH3013 4.6 12.6 1.0 CG B:HIS157 4.6 11.3 1.0 C B:CYS110 4.6 26.0 1.0 OE2 B:GLU154 4.7 18.7 1.0 N B:CYS110 4.9 26.0 1.0

K.J.Smith, C.M.Petit, K.Aubart, M.Smyth, E.Mcmanus, J.Jones, A.Fosberry, C.Lewis, M.Lonetto, S.B.Christensen. Structural Variation and Inhibitor Binding in Polypeptide Deformylase From Four Different Bacterial Species. Protein Sci. V. 12 349 2003.
ISSN: ISSN 0961-8368
PubMed: 12538898
DOI: 10.1110/PS.0229303