Sodium in PDB 7qkb: Crystal Structure of Human Cathepsin L in Complex with Covalently Bound GC376

The structure of Crystal Structure of Human Cathepsin L in Complex with Covalently Bound GC376, PDB code: 7qkb was solved by P.Y.A.Reinke, S.Falke, J.Lieske, W.Ewert, J.Loboda, A.Rahmani Mashhour, M.Hauser, K.Karnicar, A.Usenik, N.Lindic, M.Lach, H.Boehler, T.Beck, R.Cox, H.N.Chapman, W.Hinrichs, D.Turk, S.Guenther, A.Meents, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.25 / 1.80
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	57.29, 62.45, 67.82, 105.31, 93.52, 115.93
R / Rfree (%)	16.9 / 20.3

The structure of Crystal Structure of Human Cathepsin L in Complex with Covalently Bound GC376 also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Crystal Structure of Human Cathepsin L in Complex with Covalently Bound GC376 (pdb code 7qkb). 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 GC376, PDB code: 7qkb:
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 GC376


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 GC376 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:73.0 occ:1.00 HE2 A:HIS140 2.1 83.3 1.0 OD2 A:ASP137 2.3 61.3 1.0 NE2 A:HIS140 2.8 69.4 1.0 HE1 A:HIS140 3.1 77.6 1.0 H A:SER157 3.1 76.2 1.0 CG A:ASP137 3.2 57.9 1.0 CE1 A:HIS140 3.3 64.7 1.0 HB3 A:SER157 3.3 80.8 1.0 OD1 A:ASP137 3.5 51.6 1.0 HA A:CYS156 3.6 71.8 1.0 O A:ASP155 3.7 62.2 1.0 N A:SER157 3.8 63.5 1.0 HB2 A:SER157 3.9 80.8 1.0 CD2 A:HIS140 4.0 62.0 1.0 CB A:SER157 4.0 67.3 1.0 HD2 A:HIS140 4.3 74.4 1.0 CA A:CYS156 4.4 59.8 1.0 C A:CYS156 4.5 61.0 1.0 ND1 A:HIS140 4.5 61.8 1.0 CA A:SER157 4.5 62.8 1.0 CB A:ASP137 4.5 53.3 1.0 HB2 A:ASP137 4.7 64.0 1.0 C A:ASP155 4.7 64.7 1.0 HB3 A:ASP137 4.8 64.0 1.0 CG A:HIS140 4.9 64.8 1.0 HB3 A:ASP160 4.9 109.0 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of Human Cathepsin L in Complex with Covalently Bound GC376


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 GC376 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na304 b:61.2 occ:1.00 HE2 B:HIS140 1.9 74.5 1.0 OD2 B:ASP137 2.3 64.0 1.0 NE2 B:HIS140 2.5 62.1 1.0 OD1 B:ASP137 2.8 51.7 1.0 CG B:ASP137 2.8 60.3 1.0 HE1 B:HIS140 3.0 84.5 1.0 CE1 B:HIS140 3.1 70.4 1.0 CD2 B:HIS140 3.6 57.3 1.0 H B:SER157 3.7 76.7 1.0 HB3 B:SER157 3.9 87.2 1.0 HD2 B:HIS140 4.0 68.8 1.0 HA B:CYS156 4.0 69.7 1.0 HB2 B:SER157 4.0 87.2 1.0 ND1 B:HIS140 4.2 68.5 1.0 O B:ASP155 4.2 68.3 1.0 CB B:ASP137 4.3 45.5 1.0 N B:SER157 4.3 63.9 1.0 CB B:SER157 4.4 72.6 1.0 HB2 B:ASP137 4.4 54.6 1.0 CG B:HIS140 4.5 61.9 1.0 H B:GLY139 4.6 55.3 1.0 O B:GLY139 4.6 54.5 1.0 HB3 B:ASP137 4.7 54.6 1.0 HA3 B:GLY139 4.7 63.1 1.0 O B:ASP160 4.8 64.1 1.0 CA B:CYS156 4.9 58.0 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of Human Cathepsin L in Complex with Covalently Bound GC376


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 GC376 within 5.0Å range: probe atom residue distance (Å) B Occ C:Na303 b:70.9 occ:1.00 HE2 C:HIS140 1.9 85.4 1.0 OD2 C:ASP137 2.2 65.1 1.0 NE2 C:HIS140 2.4 71.2 1.0 OD1 C:ASP137 2.8 55.3 1.0 CG C:ASP137 2.8 70.5 1.0 HE1 C:HIS140 3.0 86.6 1.0 CE1 C:HIS140 3.0 72.1 1.0 H C:SER157 3.4 103.8 1.0 CD2 C:HIS140 3.5 66.0 1.0 HA C:CYS156 3.8 92.2 1.0 HB3 C:SER157 3.8 99.2 1.0 HB2 C:SER157 3.8 99.2 1.0 HD2 C:HIS140 3.9 79.2 1.0 O C:ASP155 4.0 85.6 1.0 N C:SER157 4.0 86.5 1.0 ND1 C:HIS140 4.1 67.2 1.0 CB C:SER157 4.2 82.7 1.0 CB C:ASP137 4.3 65.2 1.0 CG C:HIS140 4.4 66.5 1.0 HB2 C:ASP137 4.5 78.2 1.0 H C:GLY139 4.5 66.2 1.0 O C:GLY139 4.6 60.9 1.0 CA C:CYS156 4.6 76.8 1.0 HB3 C:ASP137 4.7 78.2 1.0 HA3 C:GLY139 4.7 65.2 1.0 C C:CYS156 4.8 83.6 1.0 CA C:SER157 4.8 84.5 1.0 O C:ASP160 4.9 82.9 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of Human Cathepsin L in Complex with Covalently Bound GC376


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 GC376 within 5.0Å range: probe atom residue distance (Å) B Occ D:Na301 b:33.7 occ:1.00 OD1 D:ASP155 2.0 57.0 1.0 OE1 D:GLU153 2.1 63.9 1.0 ND1 D:HIS140 2.1 55.7 1.0 O D:HOH477 2.2 54.1 1.0 HB3 D:HIS140 2.7 58.5 1.0 CG D:ASP155 2.7 55.0 1.0 OD2 D:ASP155 2.8 65.5 1.0 CG D:HIS140 2.9 46.6 1.0 HG2 D:GLU153 3.0 56.4 1.0 CE1 D:HIS140 3.0 51.2 1.0 CD D:GLU153 3.0 51.0 1.0 HG3 D:GLU153 3.2 56.4 1.0 CG D:GLU153 3.2 47.0 1.0 HE1 D:HIS140 3.2 61.4 1.0 CB D:HIS140 3.3 48.7 1.0 O D:HOH420 3.6 50.0 1.0 CD2 D:HIS140 3.9 50.5 1.0 NE2 D:HIS140 3.9 50.6 1.0 HB2 D:HIS140 4.0 58.5 1.0 HA D:HIS140 4.0 55.3 1.0 H D:ASP155 4.1 53.2 1.0 OE2 D:GLU153 4.2 59.2 1.0 O D:HOH448 4.2 50.4 1.0 CB D:ASP155 4.2 54.2 1.0 CA D:HIS140 4.3 46.0 1.0 HB3 D:ASP155 4.5 65.0 1.0 HE2 D:HIS140 4.7 60.7 1.0 HD2 D:HIS140 4.7 60.6 1.0 HG D:SER142 4.7 62.6 1.0 HB2 D:ASP155 4.7 65.0 1.0 CB D:GLU153 4.8 43.0 1.0 N D:ASP155 4.8 44.3 1.0 H D:GLU141 4.8 50.8 1.0 C D:ASP155 4.8 48.1 1.0 CA D:ASP155 4.8 44.8 1.0 OG D:SER142 4.9 52.2 1.0 O D:ASP155 4.9 47.9 1.0

P.Y.A.Reinke, S.Falke, J.Lieske, W.Ewert, J.Loboda, A.Rahmani Mashhour, M.Hauser, K.Karnicar, A.Usenik, N.Lindic, M.Lach, H.Boehler, T.Beck, R.Cox, H.N.Chapman, W.Hinrichs, D.Turk, S.Guenther, A.Meents. Sulfonated Calpeptin Is A Promising Drug Candidate Against Sars-Cov-2 Infections To Be Published.