Sodium in PDB 2xe4: Structure of Oligopeptidase B From Leishmania Major

All present enzymatic activity of Structure of Oligopeptidase B From Leishmania Major:
3.4.21.83;

The structure of Structure of Oligopeptidase B From Leishmania Major, PDB code: 2xe4 was solved by K.Mcluskey, N.G.Paterson, N.D.Bland, J.C.Mottram, N.W.Isaacs, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	117.85 / 1.65
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	95.478, 142.776, 208.919, 90.00, 90.00, 90.00
R / Rfree (%)	14 / 17.8

The structure of Structure of Oligopeptidase B From Leishmania Major also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Sodium atom in the Structure of Oligopeptidase B From Leishmania Major (pdb code 2xe4). 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 Oligopeptidase B From Leishmania Major, PDB code: 2xe4:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structure of Oligopeptidase B From Leishmania Major


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Oligopeptidase B From Leishmania Major within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1795 b:47.1 occ:1.00 O A:HOH2131 2.3 52.0 1.0 O A:ILE91 2.4 34.1 1.0 O A:HOH2132 2.5 43.7 1.0 O A:ILE94 2.5 35.6 1.0 O A:HOH2138 2.6 42.1 1.0 C A:ILE91 3.6 34.7 1.0 C A:ILE94 3.7 36.1 1.0 CA A:SER92 3.8 35.1 1.0 C A:SER92 4.0 35.1 1.0 O A:SER92 4.0 35.3 1.0 O A:HOH2061 4.2 53.5 1.0 N A:SER92 4.2 33.7 1.0 N A:GLU96 4.2 39.0 1.0 O A:HOH2135 4.2 52.6 1.0 CG2 A:ILE91 4.3 39.8 1.0 O A:HOH2065 4.4 58.8 1.0 CA A:ASN95 4.4 37.5 1.0 CG A:GLU96 4.4 45.1 1.0 N A:ASN95 4.5 35.7 1.0 N A:ILE94 4.5 33.6 1.0 O A:HOH2136 4.5 38.8 1.0 O A:HOH2139 4.6 51.6 1.0 CG1 A:ILE94 4.6 34.3 1.0 CA A:ILE94 4.6 35.0 1.0 CA A:ILE91 4.8 36.4 1.0 N A:HIS93 4.8 34.5 1.0 C A:ASN95 4.8 37.6 1.0

Sodium binding site 2 out of 2 in the Structure of Oligopeptidase B From Leishmania Major


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Oligopeptidase B From Leishmania Major within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1797 b:34.7 occ:1.00 OD1 A:ASP174 2.5 32.5 1.0 OD1 A:ASN178 2.6 35.3 1.0 O A:VAL180 2.6 34.5 1.0 O A:HOH2216 2.7 44.3 1.0 O A:HOH2226 3.0 62.4 1.0 OG A:SER176 3.1 39.1 1.0 CG A:ASP174 3.4 33.5 1.0 CG A:ASN178 3.6 36.7 1.0 C A:VAL180 3.7 34.4 1.0 O A:HOH2222 3.9 63.4 1.0 O A:HOH2099 4.0 65.3 1.0 N A:VAL180 4.1 33.2 1.0 CA A:ASP174 4.1 32.4 1.0 N A:SER176 4.1 35.7 1.0 ND2 A:ASN178 4.1 43.3 1.0 CB A:ASP174 4.1 34.0 1.0 CB A:SER176 4.1 36.8 1.0 N A:MET175 4.2 34.6 1.0 CB A:VAL180 4.2 34.1 1.0 OD2 A:ASP174 4.2 33.1 1.0 CA A:VAL180 4.3 32.1 1.0 C A:ASP174 4.5 34.7 1.0 N A:ASN178 4.6 34.2 1.0 CA A:SER176 4.6 36.0 1.0 N A:GLY177 4.7 33.0 1.0 CB A:ASN178 4.8 35.1 1.0 N A:GLU179 4.8 33.5 1.0 O A:HOH2220 4.8 71.1 1.0 O A:HOH2215 4.9 55.8 1.0 N A:TYR181 4.9 32.9 1.0 C A:MET175 5.0 37.3 1.0

K.Mcluskey, N.G.Paterson, N.D.Bland, N.W.Isaacs, J.C.Mottram. Crystal Structure of Leishmania Major Oligopeptidase B Gives Insight Into the Enzymatic Properties of A Trypanosomatid Virulence Factor. J.Biol.Chem. V. 285 39249 2010.
ISSN: ISSN 0021-9258
PubMed: 20926390
DOI: 10.1074/JBC.M110.156679