Sodium in PDB 4nt8: Formyl-Methionine-Alanine Complex Structure of Peptide Deformylase From Xanthomoonas Oryzae Pv. Oryzae

All present enzymatic activity of Formyl-Methionine-Alanine Complex Structure of Peptide Deformylase From Xanthomoonas Oryzae Pv. Oryzae:
3.5.1.88;

The structure of Formyl-Methionine-Alanine Complex Structure of Peptide Deformylase From Xanthomoonas Oryzae Pv. Oryzae, PDB code: 4nt8 was solved by H.P.T.Ngo, J.K.Kim, L.W.Kang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.35 / 2.20
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	58.584, 58.584, 266.188, 90.00, 90.00, 120.00
R / Rfree (%)	19 / 23.5

The structure of Formyl-Methionine-Alanine Complex Structure of Peptide Deformylase From Xanthomoonas Oryzae Pv. Oryzae also contains other interesting chemical elements:

Cadmium

(Cd)

3 atoms

The binding sites of Sodium atom in the Formyl-Methionine-Alanine Complex Structure of Peptide Deformylase From Xanthomoonas Oryzae Pv. Oryzae (pdb code 4nt8). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Formyl-Methionine-Alanine Complex Structure of Peptide Deformylase From Xanthomoonas Oryzae Pv. Oryzae, PDB code: 4nt8:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Formyl-Methionine-Alanine Complex Structure of Peptide Deformylase From Xanthomoonas Oryzae Pv. Oryzae


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Formyl-Methionine-Alanine Complex Structure of Peptide Deformylase From Xanthomoonas Oryzae Pv. Oryzae within 5.0Å range: probe atom residue distance (Å) B Occ A:Na205 b:37.7 occ:1.00 O A:HOH374 2.2 33.1 1.0 O A:HOH371 2.2 44.8 1.0 O A:HOH370 2.3 38.0 1.0 O A:GLY148 2.3 27.5 1.0 O A:LEU14 3.3 27.9 1.0 C A:GLY148 3.4 26.4 1.0 CB A:LEU14 3.8 28.5 1.0 CA A:LEU14 3.9 27.0 1.0 O A:HOH375 3.9 45.2 1.0 CA A:GLY148 3.9 26.9 1.0 C A:LEU14 4.0 27.9 1.0 CD2 A:LEU14 4.1 27.9 1.0 CH3 A:ACT204 4.2 28.1 1.0 CG A:LEU14 4.5 29.4 1.0 O A:ACT204 4.6 32.0 1.0 N A:ARG149 4.6 26.1 1.0 O A:VAL147 4.7 28.3 1.0 C A:ACT204 4.7 28.6 1.0 O A:HOH376 4.8 41.2 1.0

Sodium binding site 2 out of 2 in the Formyl-Methionine-Alanine Complex Structure of Peptide Deformylase From Xanthomoonas Oryzae Pv. Oryzae


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Formyl-Methionine-Alanine Complex Structure of Peptide Deformylase From Xanthomoonas Oryzae Pv. Oryzae within 5.0Å range: probe atom residue distance (Å) B Occ A:Na206 b:44.1 occ:1.00 O A:HOH337 2.3 45.7 1.0 O A:HOH359 2.3 41.4 1.0 OD2 A:ASP164 2.3 60.8 1.0 O A:LEU105 2.3 32.9 1.0 C A:LEU105 3.3 29.8 1.0 CG A:ASP164 3.5 55.4 1.0 N A:LEU105 3.8 32.0 1.0 C A:GLY104 4.1 33.4 1.0 CA A:GLY98 4.1 21.4 1.0 CA A:LEU105 4.1 30.5 1.0 CB A:ARG106 4.1 31.9 1.0 N A:ARG106 4.1 30.0 1.0 O A:HOH331 4.3 30.5 1.0 CG A:ARG106 4.3 35.0 1.0 O A:ALA208 4.4 53.9 1.0 CB A:ASP164 4.4 47.8 1.0 OD1 A:ASP164 4.4 59.9 1.0 O A:HOH334 4.5 49.9 1.0 O A:GLY104 4.5 38.0 1.0 N A:GLY104 4.5 31.4 1.0 CA A:ARG106 4.6 30.8 1.0 CA A:GLY104 4.6 33.0 1.0 CD A:ARG106 4.9 38.5 1.0 C A:GLY98 4.9 23.9 1.0 N A:CSD99 5.0 25.1 1.0

H.P.T.Ngo, J.K.Kim, L.W.Kang. Substrate Complex Structure of XOO1075, A Peptide Deformylase, From Xanthomonas Oryzae Pv. Oryzae To Be Published.