Sodium in PDB 8ovr: Clostridium Perfringens Chitinase CP56_3454 Apo Form

The structure of Clostridium Perfringens Chitinase CP56_3454 Apo Form, PDB code: 8ovr was solved by Y.Bloch, S.N.Savvides, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.09 / 1.60
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	192.876, 59.803, 68.707, 90, 108.18, 90
R / Rfree (%)	15.3 / 17.2

The binding sites of Sodium atom in the Clostridium Perfringens Chitinase CP56_3454 Apo Form (pdb code 8ovr). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Clostridium Perfringens Chitinase CP56_3454 Apo Form, PDB code: 8ovr:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Clostridium Perfringens Chitinase CP56_3454 Apo Form


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Clostridium Perfringens Chitinase CP56_3454 Apo Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Na703 b:18.7 occ:1.00 OD2 A:ASP125 2.2 23.5 1.0 O A:PHE64 2.2 22.1 1.0 OE2 A:GLU177 2.3 26.2 1.0 OD1 A:ASP63 2.3 21.9 1.0 O A:HOH1203 2.3 30.7 1.0 O A:HOH1055 2.3 24.0 1.0 CD A:GLU177 3.0 21.4 1.0 OE1 A:GLU177 3.1 21.7 1.0 H A:PHE64 3.1 24.7 1.0 HB2 A:ASP125 3.3 26.4 1.0 CG A:ASP63 3.4 22.8 1.0 CG A:ASP125 3.4 23.5 1.0 C A:PHE64 3.4 19.9 1.0 HA A:ASN65 3.5 24.5 1.0 OD2 A:ASP63 3.7 23.5 1.0 CB A:ASP125 3.9 22.0 1.0 H A:ASP125 3.9 21.1 1.0 N A:PHE64 3.9 20.6 1.0 O A:HOH839 4.0 33.7 1.0 HD2 A:LYS122 4.1 29.4 1.0 O A:HOH1343 4.1 46.8 1.0 HB3 A:LYS122 4.1 21.7 1.0 N A:ASN65 4.3 22.3 1.0 CA A:ASN65 4.4 20.4 1.0 CA A:PHE64 4.4 17.0 1.0 O A:HOH1248 4.4 44.8 1.0 OD1 A:ASP125 4.4 23.2 1.0 N A:ASP125 4.5 17.6 1.0 O A:LYS122 4.5 19.4 1.0 HA A:LYS122 4.5 22.4 1.0 CG A:GLU177 4.5 23.8 1.0 HB3 A:ASP125 4.6 26.4 1.0 H A:GLY124 4.7 22.2 1.0 CB A:ASP63 4.7 18.1 1.0 HA A:ASP63 4.7 22.5 1.0 HG2 A:GLU177 4.8 28.5 1.0 CA A:ASP125 4.9 16.7 1.0 HG3 A:GLU177 4.9 28.5 1.0 CD2 A:PHE64 4.9 21.5 1.0 CD A:LYS122 4.9 24.5 1.0 C A:LYS122 4.9 17.0 1.0 HD3 A:LYS122 5.0 29.4 1.0 CB A:LYS122 5.0 18.1 1.0 CG A:PHE64 5.0 19.7 1.0

Sodium binding site 2 out of 2 in the Clostridium Perfringens Chitinase CP56_3454 Apo Form


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Clostridium Perfringens Chitinase CP56_3454 Apo Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Na704 b:16.2 occ:1.00 OD1 A:ASP232 2.1 17.4 1.0 OE2 A:GLU290 2.1 18.5 1.0 O A:HOH832 2.1 16.5 1.0 O A:GLY288 2.1 17.8 1.0 CD A:GLU290 3.1 23.6 1.0 C A:GLY288 3.2 18.2 1.0 CG A:ASP232 3.2 19.1 1.0 OE1 A:GLU290 3.4 22.9 1.0 HA3 A:GLY288 3.5 25.1 1.0 HA A:ASP232 3.5 18.8 1.0 HA2 A:GLY288 3.7 25.1 1.0 CA A:GLY288 3.7 20.9 1.0 HD21 A:ASN236 3.8 27.2 1.0 O A:HOH1264 3.9 35.9 1.0 OD2 A:ASP232 3.9 17.5 1.0 O A:HOH1143 4.0 18.9 1.0 CA A:ASP232 4.3 15.6 1.0 O A:ASP232 4.3 16.9 1.0 HA A:ALA289 4.3 18.7 1.0 CB A:ASP232 4.3 16.8 1.0 N A:ALA289 4.3 16.9 1.0 ND2 A:ASN236 4.3 22.7 1.0 O A:HOH924 4.4 33.7 1.0 CG A:GLU290 4.4 21.3 1.0 OD1 A:ASN236 4.4 29.4 1.0 HG3 A:GLU290 4.5 25.6 1.0 HB2 A:PHE235 4.6 19.5 1.0 H A:GLU290 4.6 20.8 1.0 CA A:ALA289 4.7 15.6 1.0 C A:ALA289 4.7 17.5 1.0 CG A:ASN236 4.7 22.3 1.0 N A:GLU290 4.7 17.4 1.0 C A:ASP232 4.7 16.8 1.0 HB2 A:ASP232 4.8 20.1 1.0 HD22 A:ASN236 4.9 27.2 1.0 HB3 A:PHE235 4.9 19.5 1.0 HG2 A:GLU290 5.0 25.6 1.0 HB3 A:ASP232 5.0 20.1 1.0

Y.Bloch, S.N.Savvides. Clostridium Perfringens Chitinase CP56_3454 Apo Form To Be Published.