Sodium in PDB 8by5: C. Elegans Tofu-6 Etudor Tofu-1 Peptide Complex

The structure of C. Elegans Tofu-6 Etudor Tofu-1 Peptide Complex, PDB code: 8by5 was solved by R.Ketting, S.Falk, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.06 / 1.73
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	59.115, 68.128, 55.171, 90, 103.03, 90
R / Rfree (%)	16.2 / 20.7

The structure of C. Elegans Tofu-6 Etudor Tofu-1 Peptide Complex also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Sodium atom in the C. Elegans Tofu-6 Etudor Tofu-1 Peptide Complex (pdb code 8by5). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the C. Elegans Tofu-6 Etudor Tofu-1 Peptide Complex, PDB code: 8by5:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the C. Elegans Tofu-6 Etudor Tofu-1 Peptide Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of C. Elegans Tofu-6 Etudor Tofu-1 Peptide Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na404 b:27.0 occ:1.00 H A:ARG203 2.0 25.6 1.0 HE2 A:HIS170 2.0 33.1 1.0 OD2 A:ASP216 2.6 23.7 1.0 HB2 A:ASP216 2.8 21.3 1.0 O A:HOH541 2.8 18.6 1.0 N A:ARG203 2.8 21.4 1.0 NE2 A:HIS170 2.8 27.6 1.0 HG3 A:ARG203 2.9 24.8 1.0 HA A:ARG202 3.0 28.8 1.0 HB3 A:ARG202 3.1 26.9 1.0 HB2 A:ARG203 3.2 24.3 1.0 HE2 A:PHE217 3.2 26.7 1.0 HE1 A:MET173 3.3 39.4 1.0 CG A:ASP216 3.5 21.2 1.0 CB A:ASP216 3.5 17.8 1.0 CA A:ARG202 3.6 24.1 1.0 CB A:ARG203 3.6 20.3 1.0 CG A:ARG203 3.6 20.7 1.0 CD2 A:HIS170 3.7 29.5 1.0 C A:ARG202 3.7 21.9 1.0 HD2 A:HIS170 3.7 35.3 1.0 HE1 A:MET169 3.7 30.2 1.0 HG2 A:ARG202 3.7 32.7 1.0 HE A:ARG203 3.7 25.9 1.0 CB A:ARG202 3.8 22.5 1.0 CA A:ARG203 3.8 19.2 1.0 CE1 A:HIS170 3.8 28.1 1.0 H A:ASP216 3.9 20.3 1.0 HE1 A:HIS170 4.0 33.7 1.0 CE2 A:PHE217 4.0 22.3 1.0 HB3 A:ASP216 4.1 21.3 1.0 HE2 A:MET173 4.1 39.4 1.0 O A:ARG203 4.1 19.2 1.0 CE A:MET173 4.1 32.9 1.0 HE3 A:MET169 4.2 30.2 1.0 HD2 A:PHE217 4.2 22.5 1.0 CG A:ARG202 4.3 27.3 1.0 HG2 A:ARG203 4.3 24.8 1.0 CE A:MET169 4.4 25.2 1.0 NE A:ARG203 4.4 21.7 1.0 C A:ARG203 4.4 18.9 1.0 N A:ASP216 4.5 16.9 1.0 CD2 A:PHE217 4.5 18.8 1.0 HA A:ARG203 4.6 22.9 1.0 HB3 A:ARG203 4.6 24.3 1.0 CD A:ARG203 4.6 20.8 1.0 HB2 A:ARG202 4.6 26.9 1.0 CA A:ASP216 4.6 17.9 1.0 HE3 A:MET173 4.7 39.4 1.0 OD1 A:ASP216 4.7 20.0 1.0 HG23 A:VAL215 4.8 23.2 1.0 HG22 A:VAL215 4.8 23.2 1.0 O A:ARG202 4.8 23.4 1.0 CG A:HIS170 4.8 26.9 1.0 ND1 A:HIS170 4.9 25.4 1.0 HG3 A:ARG202 4.9 32.7 1.0 HE2 A:MET169 4.9 30.2 1.0 HD3 A:ARG203 5.0 24.9 1.0 N A:ARG202 5.0 23.8 1.0 HD2 A:ARG202 5.0 31.3 1.0

Sodium binding site 2 out of 2 in the C. Elegans Tofu-6 Etudor Tofu-1 Peptide Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of C. Elegans Tofu-6 Etudor Tofu-1 Peptide Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na405 b:38.6 occ:1.00 HE2 A:LYS268 2.6 53.7 1.0 HE2 A:LYS219 2.7 47.2 1.0 HD3 A:LYS219 2.7 40.2 1.0 HA A:VAL137 2.7 20.6 1.0 H A:ASP138 3.0 20.5 1.0 OD1 A:ASP138 3.3 25.9 1.0 HE3 A:LYS268 3.3 53.7 1.0 CE A:LYS219 3.3 39.4 1.0 CE A:LYS268 3.3 44.8 1.0 CD A:LYS219 3.4 33.5 1.0 O A:GLY218 3.4 19.4 1.0 HZ3 A:LYS219 3.4 82.4 1.0 HB A:VAL137 3.5 21.9 1.0 N A:ASP138 3.5 17.1 1.0 CA A:VAL137 3.5 17.2 1.0 HG12 A:VAL137 3.6 23.9 1.0 HD2 A:LYS219 3.7 40.2 1.0 C A:VAL137 3.8 17.6 1.0 NZ A:LYS219 3.9 68.7 1.0 HZ1 A:LYS268 3.9 80.4 1.0 CB A:VAL137 3.9 18.3 1.0 CG A:ASP138 3.9 25.4 1.0 NZ A:LYS268 4.1 67.0 1.0 HE3 A:LYS219 4.2 47.2 1.0 HZ1 A:LYS219 4.2 82.4 1.0 CG1 A:VAL137 4.2 20.0 1.0 O A:VAL136 4.3 20.3 1.0 HD2 A:LYS268 4.3 40.1 1.0 CD A:LYS268 4.4 33.5 1.0 HA A:LYS219 4.4 17.1 1.0 HZ3 A:LYS268 4.5 80.4 1.0 CA A:ASP138 4.5 16.5 1.0 C A:GLY218 4.5 18.5 1.0 HA A:ASP138 4.5 19.7 1.0 OD2 A:ASP138 4.6 19.5 1.0 O A:HOH536 4.6 44.9 1.0 HG2 A:LYS219 4.6 29.6 1.0 HZ2 A:LYS219 4.6 82.4 1.0 CB A:ASP138 4.6 18.3 1.0 CG A:LYS219 4.6 24.7 1.0 HB2 A:ASP138 4.7 21.9 1.0 HG2 A:LYS268 4.7 39.6 1.0 N A:VAL137 4.7 14.7 1.0 HG11 A:VAL137 4.8 23.9 1.0 O A:VAL137 4.8 17.0 1.0 HZ2 A:LYS268 4.9 80.4 1.0 HG13 A:VAL137 4.9 23.9 1.0 HG3 A:LYS268 5.0 39.6 1.0 OE2 A:GLU135 5.0 71.8 1.0 C A:VAL136 5.0 18.3 1.0 HA3 A:GLY218 5.0 21.2 1.0 CG A:LYS268 5.0 33.1 1.0

N.Podvalnaya, A.W.Bronkhorst, R.Lichtenberger, S.Hellmann, E.Nischwitz, T.Falk, E.Karaulanov, F.Butter, S.Falk, R.Ketting. Pirna Processing By A Trimeric Schlafen-Domain-Containing Nuclease. To Be Published.