Sodium in PDB 5cvp: Structure of XOO1075, A Peptide Deformylase From Xanthomonas Oryzae Pv Oryze, in Complex with Fragment 571

All present enzymatic activity of Structure of XOO1075, A Peptide Deformylase From Xanthomonas Oryzae Pv Oryze, in Complex with Fragment 571:
3.5.1.88;

The structure of Structure of XOO1075, A Peptide Deformylase From Xanthomonas Oryzae Pv Oryze, in Complex with Fragment 571, PDB code: 5cvp 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 / 2.00
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	58.871, 58.871, 264.106, 90.00, 90.00, 120.00
R / Rfree (%)	17.4 / 21.6

The structure of Structure of XOO1075, A Peptide Deformylase From Xanthomonas Oryzae Pv Oryze, in Complex with Fragment 571 also contains other interesting chemical elements:

Cadmium	(Cd)	5 atoms
Chlorine	(Cl)	1 atom

The binding sites of Sodium atom in the Structure of XOO1075, A Peptide Deformylase From Xanthomonas Oryzae Pv Oryze, in Complex with Fragment 571 (pdb code 5cvp). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure of XOO1075, A Peptide Deformylase From Xanthomonas Oryzae Pv Oryze, in Complex with Fragment 571, PDB code: 5cvp:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structure of XOO1075, A Peptide Deformylase From Xanthomonas Oryzae Pv Oryze, in Complex with Fragment 571


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of XOO1075, A Peptide Deformylase From Xanthomonas Oryzae Pv Oryze, in Complex with Fragment 571 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na206 b:46.7 occ:1.00 O A:HOH311 2.4 39.6 1.0 OE1 A:GLU86 2.5 51.4 1.0 O A:HOH435 2.9 38.4 1.0 NH2 A:ARG116 3.0 24.4 1.0 CD A:GLU86 3.3 46.7 1.0 CD A:ARG116 3.5 24.8 1.0 CB A:GLU86 3.6 31.4 1.0 NE A:ARG118 3.7 49.5 1.0 CG A:GLU86 4.0 46.0 1.0 CG A:ARG116 4.0 24.5 1.0 CB A:ARG116 4.0 20.8 1.0 OE2 A:GLU86 4.1 48.3 1.0 CZ A:ARG116 4.1 28.9 1.0 NH2 A:ARG118 4.1 54.1 1.0 NE A:ARG116 4.2 23.5 1.0 CZ A:ARG118 4.3 53.5 1.0 CD A:ARG118 4.6 37.0 1.0 CG A:ARG118 4.9 30.2 1.0 CA A:GLU86 5.0 27.4 1.0

Sodium binding site 2 out of 2 in the Structure of XOO1075, A Peptide Deformylase From Xanthomonas Oryzae Pv Oryze, in Complex with Fragment 571


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of XOO1075, A Peptide Deformylase From Xanthomonas Oryzae Pv Oryze, in Complex with Fragment 571 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na207 b:33.8 occ:1.00 O A:LEU14 2.2 22.1 1.0 O A:HOH395 2.3 37.8 1.0 O A:HOH380 2.4 22.2 1.0 O A:HOH433 2.5 33.8 1.0 O A:HOH462 3.4 41.2 1.0 C A:LEU14 3.4 23.3 1.0 CB A:LEU14 3.9 20.4 1.0 CA A:LEU14 4.1 19.7 1.0 O A:HOH441 4.1 44.2 1.0 O A:GLY148 4.3 22.7 1.0 N A:ARG15 4.5 22.9 1.0 CA A:GLY148 4.7 19.1 1.0 CA A:ARG15 4.8 23.8 1.0 O A:VAL147 4.8 24.0 1.0 C A:GLY148 4.9 21.1 1.0

H.P.T.Ngo, L.W.Kang. Structure of XOO1075, A Peptide Deformylase From Xanthomonas Oryzae Pv Oryze, in Complex with Fragment 571 To Be Published.