Sodium in PDB 4z9d: Ecplta

All present enzymatic activity of Ecplta:
2.2.2.30;

The structure of Ecplta, PDB code: 4z9d was solved by D.R.Littler, M.D.Johnson, R.J.Summers, M.A.Schembri, J.Rossjohn, T.Beddoe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.89 / 1.80
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	44.520, 55.660, 73.060, 90.06, 104.07, 96.17
R / Rfree (%)	18.1 / 22.7

The binding sites of Sodium atom in the Ecplta (pdb code 4z9d). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Ecplta, PDB code: 4z9d:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Ecplta


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Ecplta within 5.0Å range: probe atom residue distance (Å) B Occ A:Na201 b:22.4 occ:1.00 O A:HOH402 2.4 16.7 1.0 O D:HOH370 2.4 14.0 1.0 O A:HOH381 2.4 14.5 1.0 O D:HOH409 2.5 13.1 1.0 O D:HOH421 2.8 16.8 1.0 O A:HOH393 2.8 16.1 1.0 O B:HOH335 4.1 19.0 1.0 OD1 A:ASN164 4.1 11.2 1.0 OD1 D:ASN164 4.1 13.9 1.0 O B:HOH364 4.2 11.8 1.0 CA A:GLY166 4.3 10.7 1.0 O B:HOH304 4.3 19.6 1.0 CA D:GLY166 4.4 11.7 1.0 O D:VAL167 4.5 5.2 1.0 N D:VAL167 4.6 10.3 1.0 O A:HOH356 4.6 13.5 1.0 N A:VAL167 4.7 8.5 1.0 O A:VAL167 4.7 7.7 1.0 ND2 A:ASN164 4.8 16.2 1.0 ND2 D:ASN164 4.8 15.2 1.0 CG A:ASN164 4.9 9.5 1.0 CG D:ASN164 4.9 9.9 1.0 C A:GLY166 4.9 9.5 1.0 C D:GLY166 4.9 8.8 1.0 N A:GLY166 5.0 10.1 1.0

Sodium binding site 2 out of 2 in the Ecplta


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Ecplta within 5.0Å range: probe atom residue distance (Å) B Occ B:Na201 b:27.1 occ:1.00 O B:HOH370 2.4 15.6 1.0 O C:HOH375 2.5 16.4 1.0 O C:HOH355 2.6 17.5 1.0 O B:HOH400 2.6 16.1 1.0 O B:HOH343 2.8 24.7 1.0 O C:HOH392 3.2 18.6 1.0 OD1 B:ASN164 4.1 15.9 1.0 OD1 C:ASN164 4.2 14.2 1.0 CA B:GLY166 4.3 16.1 1.0 O B:HOH342 4.3 11.5 1.0 CA C:GLY166 4.4 14.9 1.0 O B:VAL167 4.5 7.7 1.0 N B:VAL167 4.6 11.6 1.0 O C:VAL167 4.7 10.3 1.0 N C:VAL167 4.8 10.3 1.0 ND2 C:ASN164 4.8 19.7 1.0 C B:GLY166 4.9 11.6 1.0 N B:GLY166 4.9 13.8 1.0 CG B:ASN164 4.9 11.0 1.0 ND2 B:ASN164 4.9 20.6 1.0 CG C:ASN164 4.9 11.7 1.0 N C:GLY166 5.0 13.2 1.0

D.R.Littler, S.Y.Ang, D.G.Moriel, M.Kocan, O.Kleifeld, M.D.Johnson, M.T.Tran, A.W.Paton, J.C.Paton, R.Summers, M.Schrembri, J.Rossjohn, T.T.Beddoe. Structure and Function Analyses of A Pertussis-Like Toxin From Pathogenic Escherichia Coli Reveal A Distinct Mechanism of Inhibition of Trimeric G Proteins. J. Biol. Chem. 2017.
ISSN: ESSN 1083-351X
PubMed: 28663369
DOI: 10.1074/JBC.M117.796094