Sodium in PDB 5cpd: Methionine-Alanine Complex Structure of Peptide Deformylase From Xanthomonas Oryzae Pv. Oryzae

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

The structure of Methionine-Alanine Complex Structure of Peptide Deformylase From Xanthomonas Oryzae Pv. Oryzae, PDB code: 5cpd was solved by H.P.T.Ngo, L.W.Kang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.40 / 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 (%)	19.1 / 24.7

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

Cadmium

(Cd)

3 atoms

The binding sites of Sodium atom in the Methionine-Alanine Complex Structure of Peptide Deformylase From Xanthomonas Oryzae Pv. Oryzae (pdb code 5cpd). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Methionine-Alanine Complex Structure of Peptide Deformylase From Xanthomonas Oryzae Pv. Oryzae, PDB code: 5cpd:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Methionine-Alanine Complex Structure of Peptide Deformylase From Xanthomonas 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 Methionine-Alanine Complex Structure of Peptide Deformylase From Xanthomonas Oryzae Pv. Oryzae within 5.0Å range: probe atom residue distance (Å) B Occ A:Na205 b:32.8 occ:1.00 O A:HOH308 2.3 33.1 1.0 O A:HOH362 2.3 45.1 1.0 O A:GLY148 2.4 28.5 1.0 O A:LEU14 3.5 28.9 1.0 C A:GLY148 3.6 26.8 1.0 CB A:LEU14 3.7 26.0 1.0 CD2 A:LEU14 3.9 23.4 1.0 CA A:LEU14 3.9 26.0 1.0 O A:HOH307 3.9 30.1 1.0 CH3 A:ACT204 3.9 25.6 1.0 O A:HOH399 4.2 52.8 1.0 C A:LEU14 4.2 28.9 1.0 CA A:GLY148 4.2 27.7 1.0 CG A:LEU14 4.3 28.2 1.0 OXT A:ACT204 4.5 30.2 1.0 C A:ACT204 4.6 27.6 1.0 N A:ARG149 4.7 27.3 1.0 CD1 A:LEU14 4.9 24.0 1.0

Sodium binding site 2 out of 2 in the Methionine-Alanine Complex Structure of Peptide Deformylase From Xanthomonas 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 Methionine-Alanine Complex Structure of Peptide Deformylase From Xanthomonas Oryzae Pv. Oryzae within 5.0Å range: probe atom residue distance (Å) B Occ A:Na206 b:41.2 occ:1.00 OD2 A:ASP164 2.3 61.6 1.0 O A:HOH366 2.3 40.8 1.0 O A:LEU105 2.3 33.5 1.0 O A:HOH381 2.6 40.7 1.0 C A:LEU105 3.3 30.8 1.0 CG A:ASP164 3.5 58.1 1.0 N A:LEU105 3.8 33.2 1.0 CA A:GLY98 4.0 19.7 1.0 CB A:ARG106 4.1 31.5 1.0 N A:ARG106 4.1 29.5 1.0 CA A:LEU105 4.1 30.9 1.0 C A:GLY104 4.2 36.1 1.0 O A:ALA209 4.2 52.8 1.0 CG A:ARG106 4.3 33.1 1.0 O A:HOH317 4.3 31.1 1.0 OD1 A:ASP164 4.4 63.2 1.0 CB A:ASP164 4.4 46.5 1.0 O A:GLY104 4.5 39.3 1.0 O A:HOH392 4.5 57.5 1.0 CA A:ARG106 4.5 32.9 1.0 N A:GLY104 4.6 33.8 1.0 CA A:GLY104 4.7 35.7 1.0 CD A:ARG106 4.8 35.8 1.0 C A:GLY98 4.9 23.7 1.0 N A:CSD99 4.9 23.1 1.0 N A:GLY98 4.9 21.2 1.0

H.P.T.Ngo, L.W.Kang. Methionine-Alanine Complex Structure of Peptide Deformylase From Xanthomonas Oryzae Pv. Oryzae To Be Published.