Sodium in PDB 8bbu: Crystal Structure of Medical Leech Destabilase (High Salt)

All present enzymatic activity of Crystal Structure of Medical Leech Destabilase (High Salt):
3.2.1.17;

The structure of Crystal Structure of Medical Leech Destabilase (High Salt), PDB code: 8bbu was solved by E.Marin, S.Bukhdruker, V.Manuvera, D.Kornilov, E.Zinovev, P.Bobrovsky, V.Lazarev, V.Borshchevskiy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.43 / 1.10
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	27.44, 36.17, 61.39, 106.81, 92.58, 95.49
R / Rfree (%)	12.5 / 15.5

The binding sites of Sodium atom in the Crystal Structure of Medical Leech Destabilase (High Salt) (pdb code 8bbu). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of Medical Leech Destabilase (High Salt), PDB code: 8bbu:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of Medical Leech Destabilase (High Salt)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Medical Leech Destabilase (High Salt) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na501 b:12.9 occ:0.50 O A:HOH747 2.3 23.6 1.0 O A:HOH655 2.4 14.1 1.0 O A:HOH675 2.4 11.9 0.5 O A:HOH694 2.5 18.9 1.0 O A:HOH657 2.5 17.1 1.0 O A:HOH719 2.5 21.1 1.0 O A:HOH675 2.6 28.0 0.5 O A:HOH632 3.6 22.0 0.5 O A:HOH699 3.8 15.1 1.0 O A:GLN56 4.0 9.0 1.0 O A:HOH722 4.0 20.4 0.5 OE2 A:GLU34 4.2 12.5 1.0 O A:HOH632 4.2 22.5 0.5 O A:HOH709 4.2 29.3 1.0 OE1 A:GLU34 4.3 11.9 1.0 OD2 A:ASP46 4.3 17.8 0.5 ND2 A:ASN113 4.5 12.8 1.0 O A:HOH772 4.5 32.0 1.0 O A:ASN113 4.6 9.6 1.0 CD A:GLU34 4.6 10.7 1.0 O A:HOH716 4.8 9.2 1.0 CB A:GLN56 4.8 9.3 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of Medical Leech Destabilase (High Salt)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Medical Leech Destabilase (High Salt) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na502 b:39.2 occ:1.00 O A:HOH732 2.3 25.2 1.0 O A:GLY35 2.3 16.7 1.0 O A:HOH614 2.3 37.1 1.0 O A:HOH762 2.4 38.5 1.0 O A:HOH799 2.5 46.5 1.0 O A:HOH627 2.5 33.4 1.0 C A:GLY35 3.2 12.7 1.0 OG A:SER38 3.6 18.2 1.0 CA A:GLY35 3.8 13.0 1.0 CB A:SER38 4.1 16.8 1.0 N A:CYS36 4.3 12.8 1.0 N A:SER38 4.4 13.3 1.0 CB A:CYS36 4.4 10.9 1.0 O A:HOH737 4.6 21.1 1.0 N A:ASP37 4.6 11.7 1.0 CA A:CYS36 4.6 10.5 1.0 C A:CYS36 4.7 10.9 1.0 N A:GLY35 4.9 13.3 1.0 O A:LYS32 4.9 11.9 0.5 O A:LYS32 4.9 12.5 0.5 CA A:SER38 4.9 13.3 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of Medical Leech Destabilase (High Salt)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Medical Leech Destabilase (High Salt) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na501 b:19.5 occ:0.50 O B:HOH603 1.9 24.8 0.5 O B:HOH675 2.1 16.4 0.2 O B:HOH616 2.2 23.4 0.5 O B:HOH616 2.3 20.3 0.5 O B:HOH707 2.4 34.3 0.5 O B:HOH707 2.4 34.8 0.5 O B:HOH675 2.4 20.4 0.5 O B:HOH607 2.5 14.9 0.5 O B:HOH603 2.5 23.7 0.5 O B:HOH684 2.5 36.6 0.5 O B:HOH675 2.8 25.6 0.2 OD2 B:ASP46 2.8 32.6 0.5 O B:HOH684 2.8 37.6 0.5 O B:HOH711 3.4 24.2 0.5 OD2 B:ASP46 3.4 32.8 0.5 CG B:ASP46 3.8 30.9 0.5 CG B:ASP46 3.9 31.0 0.5 OD1 B:ASP46 4.0 32.5 0.5 ND2 B:ASN113 4.1 18.4 1.0 OD1 B:ASP46 4.1 32.2 0.5 O B:HOH711 4.2 25.9 0.5 OE1 B:GLU34 4.2 14.8 1.0 OE2 B:GLU34 4.2 14.5 1.0 O B:GLN56 4.2 10.4 1.0 O B:HOH627 4.6 30.6 1.0 CE B:LYS58 4.6 16.7 1.0 CD B:GLU34 4.6 13.7 1.0 CB B:GLN56 4.7 11.1 1.0 OG B:SER51 4.7 12.9 0.6 O B:ASN113 4.9 11.9 1.0 CB B:ASP46 5.0 27.2 0.5

E.Marin, D.Kornilov, S.Bukhdruker, V.Manuvera, E.Zinovev, K.Kovalev, M.Shevtsov, A.Talyzina, P.Bobrovsky, P.Kuzmichev, A.Mishin, I.Gushchin, V.Gordeliy, V.Lazarev, V.Borshchevskiy. Structural Basis For Inhibition of Thrombolytic Destabilase From Medical Leech By Physiological Sodium Concentrations To Be Published.