Sodium in PDB 8a5b: Crystal Structure of Human Cathepsin L in Complex with Covalently Bound Mg-101

The structure of Crystal Structure of Human Cathepsin L in Complex with Covalently Bound Mg-101, PDB code: 8a5b was solved by S.Falke, J.Lieske, S.Guenther, P.Y.A.Reinke, W.Ewert, J.Loboda, K.Karnicar, A.Usenik, N.Lindic, A.Sekirnik, H.N.Chapman, W.Hinrichs, D.Turk, A.Meents, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.25 / 1.80
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	57.24, 62.2, 67.24, 105.35, 93.25, 115.81
R / Rfree (%)	17.8 / 22.5

The binding sites of Sodium atom in the Crystal Structure of Human Cathepsin L in Complex with Covalently Bound Mg-101 (pdb code 8a5b). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of Human Cathepsin L in Complex with Covalently Bound Mg-101, PDB code: 8a5b:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of Human Cathepsin L in Complex with Covalently Bound Mg-101


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 Human Cathepsin L in Complex with Covalently Bound Mg-101 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na302 b:39.0 occ:1.00 HB2 A:GLU192 2.4 41.6 1.0 OE1 A:GLU192 2.5 49.3 1.0 H A:GLU192 2.6 30.6 1.0 O A:TRP189 2.7 24.3 1.0 HA3 A:GLY190 2.7 22.3 1.0 H A:TRP193 3.1 31.4 1.0 N A:GLU192 3.3 25.5 1.0 CB A:GLU192 3.3 34.7 1.0 CA A:GLY190 3.5 18.6 1.0 C A:GLY190 3.5 19.3 1.0 CD A:GLU192 3.5 57.5 1.0 N A:TRP193 3.6 26.2 1.0 CA A:GLU192 3.7 35.2 1.0 C A:TRP189 3.7 27.4 1.0 HD21 A:ASN18 3.8 35.3 1.0 HD22 A:ASN18 3.8 35.3 1.0 N A:GLU191 3.8 22.5 1.0 H A:GLU191 3.9 27.0 1.0 O A:GLY190 3.9 25.2 1.0 C A:GLU192 4.0 27.8 1.0 CG A:GLU192 4.0 39.1 1.0 ND2 A:ASN18 4.0 29.4 1.0 HB3 A:GLU192 4.0 41.6 1.0 HB2 A:TRP193 4.0 27.9 1.0 N A:GLY190 4.1 23.8 1.0 HA2 A:GLY190 4.2 22.3 1.0 C A:GLU191 4.4 29.4 1.0 HG2 A:GLU192 4.4 47.0 1.0 HB3 A:TRP193 4.5 27.9 1.0 CB A:TRP193 4.6 23.2 1.0 HA A:GLU192 4.6 42.3 1.0 OE2 A:GLU192 4.6 50.9 1.0 CA A:TRP193 4.7 23.3 1.0 CA A:GLU191 4.7 34.2 1.0 HG3 A:GLU192 4.8 47.0 1.0 HB3 A:TRP189 4.8 25.3 1.0 H A:GLY190 4.9 28.6 1.0 O A:GLU192 5.0 27.5 1.0 CG A:ASN18 5.0 19.2 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of Human Cathepsin L in Complex with Covalently Bound Mg-101


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 Human Cathepsin L in Complex with Covalently Bound Mg-101 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na301 b:34.0 occ:1.00 HH B:TYR76 2.0 28.2 1.0 OD1 B:ASN80 2.5 21.1 1.0 OH B:TYR76 2.6 23.5 1.0 HE1 B:TYR76 2.8 24.4 1.0 HB3 B:CYS56 3.1 26.1 1.0 O B:HOH445 3.2 25.9 1.0 HB3 B:TYR100 3.2 27.6 1.0 CG B:ASN80 3.3 23.1 1.0 CE1 B:TYR76 3.4 20.4 1.0 CZ B:TYR76 3.4 22.6 1.0 HD22 B:ASN80 3.5 28.7 1.0 HB2 B:TYR100 3.6 27.6 1.0 SG B:CYS98 3.7 27.3 1.0 ND2 B:ASN80 3.7 23.9 1.0 CB B:TYR100 3.8 23.0 1.0 HD2 B:TYR100 3.8 31.1 1.0 CB B:CYS56 3.9 21.8 1.0 CG B:TYR100 4.0 23.8 1.0 CD2 B:TYR100 4.0 25.9 1.0 HB2 B:CYS56 4.1 26.1 1.0 HB2 B:ASN80 4.2 28.7 1.0 HD22 B:ASN52 4.2 26.0 1.0 SG B:CYS56 4.2 24.0 1.0 CB B:ASN80 4.4 23.9 1.0 HD21 B:ASN80 4.5 28.7 1.0 CD1 B:TYR76 4.7 21.4 1.0 CE2 B:TYR76 4.7 20.1 1.0 CD1 B:TYR100 4.8 24.3 1.0 CE2 B:TYR100 4.9 22.9 1.0 O B:CYS56 4.9 22.1 1.0 H B:TYR100 4.9 27.2 1.0 HB3 B:ASN80 5.0 28.7 1.0 ND2 B:ASN52 5.0 21.6 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of Human Cathepsin L in Complex with Covalently Bound Mg-101


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 Human Cathepsin L in Complex with Covalently Bound Mg-101 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na302 b:41.4 occ:1.00 OE1 B:GLN75 2.4 26.9 1.0 OE1 B:GLN78 2.5 27.3 1.0 OD2 A:ASP178 2.6 25.6 1.0 HE22 B:GLN75 2.6 31.7 1.0 HB2 A:ASP178 2.7 23.3 1.0 HA2 B:GLY111 3.0 29.3 1.0 CD B:GLN75 3.0 22.8 1.0 NE2 B:GLN75 3.1 26.4 1.0 CB A:ASP178 3.2 19.4 1.0 CG A:ASP178 3.3 22.4 1.0 HB3 A:ASP178 3.3 23.3 1.0 HA3 B:GLY111 3.4 29.3 1.0 CD B:GLN78 3.6 25.2 1.0 CA B:GLY111 3.6 24.4 1.0 HE1 B:PHE112 3.7 19.9 1.0 HE22 B:GLN78 3.8 31.3 1.0 HE21 B:GLN75 3.9 31.7 1.0 HA B:GLN75 4.0 20.0 1.0 HD1 B:PHE112 4.1 25.2 1.0 NE2 B:GLN78 4.2 26.1 1.0 CE1 B:PHE112 4.2 16.6 1.0 H B:PHE112 4.3 26.8 1.0 O A:SER177 4.3 23.6 1.0 CD1 B:PHE112 4.4 21.0 1.0 CG B:GLN75 4.5 20.1 1.0 N B:GLY111 4.5 21.3 1.0 OD1 A:ASP178 4.5 25.9 1.0 HB3 B:GLN78 4.5 26.2 1.0 HB2 B:GLN75 4.6 24.5 1.0 CA A:ASP178 4.7 17.3 1.0 C B:GLY111 4.7 21.9 1.0 N B:PHE112 4.7 22.4 1.0 H B:GLY111 4.8 25.6 1.0 CA B:GLN75 4.9 16.6 1.0 CG B:GLN78 4.9 22.9 1.0 CB B:GLN75 4.9 20.4 1.0 HB2 B:GLN78 4.9 26.2 1.0 C A:SER177 4.9 20.7 1.0 HG2 B:GLN75 4.9 24.1 1.0 HG3 B:GLN75 5.0 24.1 1.0 CB B:GLN78 5.0 21.8 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of Human Cathepsin L in Complex with Covalently Bound Mg-101


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Human Cathepsin L in Complex with Covalently Bound Mg-101 within 5.0Å range: probe atom residue distance (Å) B Occ D:Na303 b:45.8 occ:1.00 OE1 D:GLN75 2.5 31.9 1.0 OE1 D:GLN78 2.7 26.1 1.0 HE22 D:GLN75 2.8 41.8 1.0 O D:HOH460 2.9 32.0 1.0 HA2 D:GLY111 3.1 31.0 1.0 CD D:GLN75 3.2 27.6 1.0 NE2 D:GLN75 3.3 34.9 1.0 HA3 D:GLY111 3.6 31.0 1.0 HE22 D:GLN78 3.7 50.2 1.0 HE2 D:PHE112 3.8 30.4 1.0 CD D:GLN78 3.8 31.9 1.0 CA D:GLY111 3.8 25.8 1.0 HE21 D:GLN75 4.1 41.8 1.0 CE2 D:PHE112 4.1 25.3 1.0 NE2 D:GLN78 4.1 41.8 1.0 HD2 D:PHE112 4.3 30.5 1.0 HA D:GLN75 4.3 29.6 1.0 H D:PHE112 4.3 29.0 1.0 CD2 D:PHE112 4.4 25.4 1.0 CG D:GLN75 4.6 26.5 1.0 HB2 D:GLN75 4.6 30.4 1.0 N D:GLY111 4.8 33.3 1.0 N D:PHE112 4.8 24.2 1.0 C D:GLY111 4.8 26.3 1.0 O D:ALA110 4.8 40.8 1.0 CZ D:PHE112 4.9 26.1 1.0 HB3 D:GLN78 4.9 33.1 1.0 HE21 D:GLN78 5.0 50.2 1.0

S.Falke, J.Lieske, A.Herrmann, S.Guenther, P.Y.A.Reinke, W.Ewert, J.Loboda, K.Karnicar, A.Usenik, N.Lindic, A.Sekirnik, H.N.Chapman, W.Hinrichs, G.Ebert, D.Turk, A.Meents. Structural Elucidation of Antiviral Cathepsin L Inhibitors To Be Published.