Sodium in PDB 8a4u: Crystal Structure of Human Cathepsin L with CAA0225

The structure of Crystal Structure of Human Cathepsin L with CAA0225, PDB code: 8a4u 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)	44.14 / 1.90
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	57, 62.87, 65.18, 104.04, 95.83, 116.05
R / Rfree (%)	17.8 / 21

The binding sites of Sodium atom in the Crystal Structure of Human Cathepsin L with CAA0225 (pdb code 8a4u). 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 Human Cathepsin L with CAA0225, PDB code: 8a4u:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of Human Cathepsin L with CAA0225


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 with CAA0225 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na302 b:28.6 occ:1.00 O A:HOH403 2.3 26.3 1.0 O A:GLU96 2.4 28.8 1.0 O A:ASP55 2.6 27.3 1.0 HA A:ASP55 3.0 34.8 1.0 HA A:SER97 3.3 35.3 1.0 C A:GLU96 3.4 32.1 1.0 C A:ASP55 3.5 29.8 1.0 HG2 A:GLU95 3.6 44.0 1.0 CA A:ASP55 3.7 29.0 1.0 HG3 A:GLU95 3.7 44.0 1.0 O A:HOH446 3.8 25.8 1.0 HB3 A:ASP55 3.9 34.0 1.0 OE1 A:GLU95 4.0 39.2 1.0 CG A:GLU95 4.0 36.7 1.0 CA A:SER97 4.0 29.4 1.0 N A:SER97 4.1 31.3 1.0 H A:GLU96 4.1 39.9 1.0 CB A:ASP55 4.3 28.2 1.0 N A:GLU96 4.4 33.2 1.0 O A:VAL54 4.4 27.6 1.0 C A:SER97 4.5 29.4 1.0 CA A:GLU96 4.5 38.2 1.0 CD A:GLU95 4.5 38.2 1.0 H A:CYS98 4.6 35.3 1.0 N A:CYS98 4.6 29.4 1.0 HA A:GLU96 4.7 46.0 1.0 N A:CYS56 4.8 26.0 1.0 OD1 A:ASP55 4.9 34.0 1.0 O A:HOH473 4.9 74.6 1.0 H A:SER97 4.9 37.6 1.0 N A:ASP55 4.9 25.8 1.0 HA A:CYS56 5.0 30.2 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of Human Cathepsin L with CAA0225


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 with CAA0225 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na303 b:51.9 occ:1.00 O C:HOH453 2.3 42.4 1.0 O C:GLY43 2.6 40.6 1.0 O C:HOH457 2.6 31.6 1.0 O A:GLY43 2.7 43.1 1.0 O A:HOH471 2.9 23.7 1.0 HE1 A:PHE39 3.1 38.5 1.0 HA C:ARG44 3.2 51.1 1.0 HE1 C:PHE39 3.2 45.2 1.0 HA A:ARG44 3.4 45.5 1.0 C C:GLY43 3.7 41.4 1.0 H C:LEU45 3.8 40.3 1.0 C A:GLY43 3.9 40.8 1.0 CE1 A:PHE39 4.0 32.1 1.0 CE1 C:PHE39 4.0 37.7 1.0 CA C:ARG44 4.1 42.6 1.0 H A:LEU45 4.2 35.6 1.0 HG2 C:ARG44 4.3 66.3 1.0 CA A:ARG44 4.3 37.8 1.0 N C:ARG44 4.3 39.7 1.0 HZ A:PHE39 4.5 39.9 1.0 N A:ARG44 4.5 38.5 1.0 N C:LEU45 4.5 33.5 1.0 HG3 C:ARG44 4.5 66.3 1.0 HZ C:PHE39 4.6 48.6 1.0 CZ A:PHE39 4.7 33.2 1.0 HD1 C:PHE39 4.8 43.4 1.0 HG3 A:ARG44 4.8 57.2 1.0 CG C:ARG44 4.8 55.2 1.0 CZ C:PHE39 4.8 40.5 1.0 C C:ARG44 4.8 37.8 1.0 HD1 A:PHE39 4.8 35.7 1.0 CA C:GLY43 4.8 42.0 1.0 N A:LEU45 4.8 29.7 1.0 HA3 C:GLY43 4.9 50.4 1.0 CD1 C:PHE39 4.9 36.1 1.0 CD1 A:PHE39 4.9 29.7 1.0 HA2 C:GLY43 4.9 50.4 1.0 CA A:GLY43 5.0 41.5 1.0 HA3 A:GLY43 5.0 49.8 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of Human Cathepsin L with CAA0225


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 with CAA0225 within 5.0Å range: probe atom residue distance (Å) B Occ C:Na302 b:32.9 occ:1.00 O C:HOH461 2.4 36.2 1.0 O C:GLU96 2.6 30.0 1.0 O C:HOH402 2.6 36.8 1.0 O C:ASP55 2.6 26.3 1.0 HA C:ASP55 3.0 32.7 1.0 HG2 C:GLU95 3.3 49.7 1.0 C C:ASP55 3.5 26.8 1.0 HA C:SER97 3.5 38.2 1.0 C C:GLU96 3.6 31.1 1.0 CA C:ASP55 3.7 27.2 1.0 O C:HOH451 3.7 27.0 1.0 OE2 C:GLU95 3.8 47.4 1.0 HG3 C:GLU95 4.0 49.7 1.0 HB3 C:ASP55 4.0 34.8 1.0 CG C:GLU95 4.0 41.4 1.0 H C:GLU96 4.1 41.9 1.0 CA C:SER97 4.2 31.8 1.0 N C:SER97 4.3 32.4 1.0 CB C:ASP55 4.4 29.0 1.0 O C:VAL54 4.4 20.1 1.0 CD C:GLU95 4.4 46.1 1.0 N C:GLU96 4.4 34.9 1.0 C C:SER97 4.6 31.6 1.0 H C:CYS98 4.6 37.1 1.0 CA C:GLU96 4.6 37.3 1.0 O C:HOH476 4.6 51.6 1.0 N C:CYS56 4.7 27.9 1.0 N C:CYS98 4.7 30.9 1.0 HA C:CYS56 4.8 32.7 1.0 HA C:GLU96 4.8 44.8 1.0 OD1 C:ASP55 4.9 29.3 1.0 N C:ASP55 4.9 26.1 1.0 HB2 C:CYS98 5.0 37.0 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, D.Turk, A.Meents. Structural Elucidation of Antiviral Cathepsin L Inhibitors To Be Published.