Sodium in PDB 3egk: Knoble Inhibitor

All present enzymatic activity of Knoble Inhibitor:
3.4.21.5;

The structure of Knoble Inhibitor, PDB code: 3egk was solved by B.Baum, A.Heine, G.Klebe, M.Muenzel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 2.20
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	70.200, 71.430, 72.580, 90.00, 100.52, 90.00
R / Rfree (%)	20.5 / 31.2

The structure of Knoble Inhibitor also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Knoble Inhibitor (pdb code 3egk). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Knoble Inhibitor, PDB code: 3egk:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Knoble Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Knoble Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ H:Na602 b:0.0 occ:1.00 O H:HOH1115 2.5 20.9 1.0 O H:ARG221A 2.5 35.1 1.0 O H:HOH1092 2.6 33.1 1.0 O H:LYS224 2.6 10.2 1.0 O H:HOH1022 2.8 14.7 1.0 C H:ARG221A 3.4 23.2 1.0 C H:LYS224 3.7 20.9 1.0 O H:HOH1043 3.9 21.5 1.0 N H:ARG221A 3.9 14.9 1.0 C H:ASP221 4.0 10.7 1.0 N H:LYS224 4.0 12.0 1.0 O H:TYR184A 4.1 9.4 1.0 N H:ASP222 4.2 27.2 1.0 CA H:ASP221 4.2 7.2 1.0 CA H:ASP222 4.2 22.3 1.0 CA H:ARG221A 4.3 11.9 1.0 N H:GLY223 4.4 12.2 1.0 CA H:LYS224 4.4 13.5 1.0 O H:ASP221 4.5 20.4 1.0 C H:ASP222 4.5 11.6 1.0 OD1 H:ASP221 4.6 12.8 1.0 O H:HOH1023 4.7 25.1 1.0 N H:TYR225 4.7 14.2 1.0 CB H:LYS224 4.8 12.2 1.0 CA H:TYR225 4.9 19.3 1.0 N H:ASP221 4.9 14.4 1.0

Sodium binding site 2 out of 2 in the Knoble Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Knoble Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ H:Na603 b:7.5 occ:1.00 O H:THR172 2.5 6.3 1.0 O H:LYS169 2.5 15.7 1.0 O H:HOH1025 2.9 41.0 1.0 C H:LYS169 3.5 13.5 1.0 C H:THR172 3.7 5.2 1.0 CA H:ASP170 4.2 16.4 1.0 N H:ASP170 4.3 17.4 1.0 CA H:ARG173 4.4 12.9 1.0 N H:THR172 4.5 9.2 1.0 CA H:LYS169 4.5 15.1 1.0 N H:ARG173 4.5 4.2 1.0 C H:ASP170 4.6 13.9 1.0 CA H:THR172 4.7 0.0 1.0 CB H:LYS169 4.8 14.1 1.0 C H:ARG173 4.9 18.8 1.0 OD1 H:ASP170 4.9 9.6 1.0 N H:SER171 4.9 13.6 1.0 CG2 H:THR172 5.0 12.7 1.0

C.Gerlach, M.Munzel, B.Baum, H.-D.Gerber, T.Craan, W.E.Diederich, G.Klebe. Knoble: A Knowledge-Based Approach For the Design and Synthesis of Readily Accessible Small-Molecule Chemical Probes to Test Protein Binding Angew.Chem.Int.Ed.Engl. V. 46 9105 2007.
ISSN: ISSN 1433-7851
PubMed: 17955562
DOI: 10.1002/ANIE.200703323