Sodium in PDB 3ssb: Structure of Insect Metalloproteinase Inhibitor in Complex with Thermolysin

All present enzymatic activity of Structure of Insect Metalloproteinase Inhibitor in Complex with Thermolysin:
3.4.24.27;

The structure of Structure of Insect Metalloproteinase Inhibitor in Complex with Thermolysin, PDB code: 3ssb was solved by J.L.Arolas, T.O.Botelho, A.Vilcinskas, F.X.Gomis-Ruth, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	45.640, 78.370, 92.290, 90.00, 90.08, 90.00
R / Rfree (%)	15.9 / 19.3

The structure of Structure of Insect Metalloproteinase Inhibitor in Complex with Thermolysin also contains other interesting chemical elements:

Calcium	(Ca)	6 atoms
Zinc	(Zn)	2 atoms

The binding sites of Sodium atom in the Structure of Insect Metalloproteinase Inhibitor in Complex with Thermolysin (pdb code 3ssb). 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 Insect Metalloproteinase Inhibitor in Complex with Thermolysin, PDB code: 3ssb:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structure of Insect Metalloproteinase Inhibitor in Complex with Thermolysin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Insect Metalloproteinase Inhibitor in Complex with Thermolysin within 5.0Å range: probe atom residue distance (Å) B Occ A:Na995 b:21.2 occ:1.00 O A:ASN183 2.3 19.5 1.0 O A:HOH533 2.4 19.8 1.0 OE2 A:GLU190 2.4 19.4 1.0 O A:HOH525 2.4 19.4 1.0 OD1 A:ASP185 2.5 20.1 1.0 OE1 A:GLU177 2.8 18.6 1.0 CG A:ASP185 3.3 21.5 1.0 CD A:GLU190 3.3 19.6 1.0 CD A:GLU177 3.4 18.7 1.0 C A:ASN183 3.5 20.9 1.0 OD2 A:ASP185 3.7 20.2 1.0 O A:HOH974 3.7 37.7 1.0 CG A:GLU190 3.7 19.6 1.0 CA A:CA997 3.8 16.9 1.0 OE2 A:GLU177 3.8 17.8 1.0 CA A:PRO184 4.1 20.0 1.0 N A:ASP185 4.1 19.2 1.0 CB A:ASN183 4.2 21.5 1.0 O A:HOH526 4.2 19.7 1.0 OD1 A:ASP191 4.2 19.0 1.0 C A:PRO184 4.2 20.5 1.0 OD2 A:ASP191 4.3 20.3 1.0 OE1 A:GLU190 4.3 21.5 1.0 N A:PRO184 4.3 20.4 1.0 CB A:ASP185 4.3 19.9 1.0 CG A:GLU177 4.4 19.6 1.0 CA A:ASN183 4.5 21.4 1.0 CG A:ASP191 4.5 19.2 1.0 O A:HOH521 4.8 19.0 1.0 CA A:ASP185 4.9 19.8 1.0 O A:PRO184 5.0 20.2 1.0

Sodium binding site 2 out of 2 in the Structure of Insect Metalloproteinase Inhibitor in Complex with Thermolysin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Insect Metalloproteinase Inhibitor in Complex with Thermolysin within 5.0Å range: probe atom residue distance (Å) B Occ B:Na995 b:29.0 occ:1.00 O B:ASN183 2.3 29.2 1.0 O B:HOH797 2.4 29.4 1.0 OE2 B:GLU190 2.4 25.8 1.0 O B:HOH795 2.4 23.6 1.0 OD1 B:ASP185 2.4 26.9 1.0 OE1 B:GLU177 2.9 24.6 1.0 CG B:ASP185 3.2 27.4 1.0 CD B:GLU190 3.3 24.8 1.0 CD B:GLU177 3.4 26.0 1.0 C B:ASN183 3.5 30.4 1.0 OD2 B:ASP185 3.6 26.0 1.0 CA B:CA997 3.7 23.8 1.0 OE2 B:GLU177 3.7 23.7 1.0 CG B:GLU190 3.7 25.5 1.0 O B:HOH801 3.8 39.5 1.0 CB B:ASN183 4.1 32.0 1.0 N B:ASP185 4.1 26.8 1.0 CA B:PRO184 4.2 28.5 1.0 OD1 B:ASP191 4.2 27.1 1.0 OD2 B:ASP191 4.2 27.0 1.0 C B:PRO184 4.3 28.2 1.0 O B:HOH793 4.3 27.6 1.0 CB B:ASP185 4.3 26.7 1.0 OE1 B:GLU190 4.4 25.5 1.0 CG B:GLU177 4.4 23.9 1.0 N B:PRO184 4.4 29.6 1.0 CA B:ASN183 4.5 31.5 1.0 CG B:ASP191 4.5 27.6 1.0 O B:HOH796 4.7 23.8 1.0 CA B:ASP185 4.9 27.1 1.0 O B:PRO184 5.0 27.9 1.0

J.L.Arolas, T.O.Botelho, A.Vilcinskas, F.X.Gomis-Ruth. Structural Evidence For Standard-Mechanism Inhibition in Metallopeptidases From A Complex Poised to Resynthesize A Peptide Bond. Angew.Chem.Int.Ed.Engl. V. 50 10357 2011.
ISSN: ISSN 1433-7851
PubMed: 21915964
DOI: 10.1002/ANIE.201103262