Sodium in PDB 8bk5: A Structure of the Truncated Lpmip with Bound Inhibitor JK095.

All present enzymatic activity of A Structure of the Truncated Lpmip with Bound Inhibitor JK095.:
5.2.1.8;

The structure of A Structure of the Truncated Lpmip with Bound Inhibitor JK095., PDB code: 8bk5 was solved by J.J.Whittaker, A.Guskov, B.Goretzki, U.A.Hellmich, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.37 / 1.44
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	53.54, 53.54, 77.36, 90, 90, 120
R / Rfree (%)	18.4 / 22.3

The structure of A Structure of the Truncated Lpmip with Bound Inhibitor JK095. also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Sodium atom in the A Structure of the Truncated Lpmip with Bound Inhibitor JK095. (pdb code 8bk5). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the A Structure of the Truncated Lpmip with Bound Inhibitor JK095., PDB code: 8bk5:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the A Structure of the Truncated Lpmip with Bound Inhibitor JK095.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of A Structure of the Truncated Lpmip with Bound Inhibitor JK095. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na202 b:33.3 occ:1.00 O A:HOH338 2.8 24.6 1.0 OD1 A:ASN7 2.8 22.5 1.0 O A:HOH387 2.9 31.2 1.0 O A:HOH315 3.0 33.0 1.0 O A:HOH317 3.6 24.8 1.0 CD A:LYS10 3.6 30.6 1.0 CA A:ASN7 3.8 21.2 1.0 NZ A:LYS10 3.8 39.2 1.0 CG A:ASN7 3.9 21.4 1.0 CB A:LYS10 3.9 22.9 1.0 O A:GLU6 3.9 23.2 1.0 O A:HOH371 4.0 25.8 1.0 N A:ASN7 4.0 23.8 1.0 C A:GLU6 4.1 24.7 1.0 CE A:LYS10 4.1 35.6 1.0 CG A:LYS10 4.3 26.1 1.0 CB A:ASN7 4.4 20.6 1.0 CB A:GLU6 4.6 27.4 1.0 O A:HOH351 4.6 25.3 1.0 OE1 A:GLU121 4.8 21.8 1.0 C A:ASN7 4.9 20.8 1.0 CA A:GLU6 5.0 26.5 1.0

Sodium binding site 2 out of 3 in the A Structure of the Truncated Lpmip with Bound Inhibitor JK095.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of A Structure of the Truncated Lpmip with Bound Inhibitor JK095. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na203 b:27.1 occ:1.00 O A:GLY95 2.7 21.4 1.0 O A:HOH384 2.8 39.0 1.0 OG1 A:THR97 2.8 18.9 1.0 ND2 A:ASN37 3.0 34.0 1.0 N A:THR97 3.4 15.2 1.0 C A:SER96 3.6 16.4 1.0 CB A:ASN37 3.6 25.8 1.0 CB A:THR97 3.6 16.6 1.0 CD2 A:HIS128 3.7 19.9 1.0 NE2 A:HIS128 3.8 20.6 1.0 C A:GLY95 3.8 18.2 1.0 CG A:ASN37 3.8 31.8 1.0 CA A:SER96 4.0 17.4 1.0 O A:HOH347 4.1 40.9 1.0 CA A:THR97 4.1 15.1 1.0 O A:SER96 4.1 16.6 1.0 O A:ASN37 4.1 21.9 1.0 O A:HOH336 4.3 30.3 1.0 N A:SER96 4.3 17.9 1.0 CG A:HIS128 4.4 19.0 1.0 CE1 A:HIS128 4.5 20.1 1.0 O A:HOH389 4.5 45.6 1.0 C A:ASN37 4.6 21.8 1.0 O A:HOH323 4.7 24.0 1.0 CA A:ASN37 4.7 21.8 1.0 ND1 A:HIS128 4.8 20.4 1.0 CA A:GLY95 4.9 18.1 1.0

Sodium binding site 3 out of 3 in the A Structure of the Truncated Lpmip with Bound Inhibitor JK095.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of A Structure of the Truncated Lpmip with Bound Inhibitor JK095. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na204 b:30.0 occ:1.00 O A:HOH355 3.7 32.8 1.0 N A:LYS69 3.7 21.9 1.0 N A:GLY71 3.8 24.9 1.0 CA A:LYS69 3.9 24.3 1.0 CA A:GLY71 4.2 26.4 1.0 N A:THR70 4.2 23.4 1.0 C A:LYS69 4.3 23.6 1.0 C A:GLU68 4.8 20.7 1.0 O A:THR67 4.9 17.4 1.0 C A:GLY71 4.9 27.4 1.0 C A:THR70 5.0 24.3 1.0

C.Wiedemann, J.J.Whittaker, V.H.P.Carrillo, B.Goretzki, M.Dajka, F.Tebbe, J.M.Harder, P.R.Krajczy, B.Joseph, F.Hausch, A.Guskov, U.A.Hellmich. Legionella Pneumophila Macrophage Infectivity Potentiator Protein Appendage Domains Modulate Protein Dynamics and Inhibitor Binding. Int.J.Biol.Macromol. 26366 2023.
ISSN: ISSN 0141-8130
PubMed: 37633566
DOI: 10.1016/J.IJBIOMAC.2023.126366