Sodium in PDB 8b4f: Crystal Structure of Human Cathepsin L Forming A Thiohemiacetal with N-Boc-2-Aminoacetaldehyde

The structure of Crystal Structure of Human Cathepsin L Forming A Thiohemiacetal with N-Boc-2-Aminoacetaldehyde, PDB code: 8b4f 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)	49.42 / 1.90
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	57.21, 62.26, 67.63, 105.44, 93.41, 115.9
R / Rfree (%)	17.8 / 21

The binding sites of Sodium atom in the Crystal Structure of Human Cathepsin L Forming A Thiohemiacetal with N-Boc-2-Aminoacetaldehyde (pdb code 8b4f). 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 Forming A Thiohemiacetal with N-Boc-2-Aminoacetaldehyde, PDB code: 8b4f:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of Human Cathepsin L Forming A Thiohemiacetal with N-Boc-2-Aminoacetaldehyde


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 Forming A Thiohemiacetal with N-Boc-2-Aminoacetaldehyde within 5.0Å range: probe atom residue distance (Å) B Occ A:Na307 b:51.6 occ:1.00 OD2 A:ASP79 2.4 29.5 1.0 HG2 A:GLN75 3.2 52.9 1.0 CG A:ASP79 3.4 30.0 1.0 HG3 A:GLN75 3.5 52.9 1.0 HG3 A:GLN60 3.5 23.6 1.0 HE21 A:GLN60 3.7 33.0 1.0 CG A:GLN75 3.8 44.0 1.0 OD1 A:ASP79 3.8 31.8 1.0 CD A:GLN75 4.3 61.2 1.0 OE1 A:GLN75 4.4 53.1 1.0 CG A:GLN60 4.4 19.6 1.0 NE2 A:GLN60 4.5 27.4 1.0 HA A:GLN60 4.5 34.5 1.0 HG2 A:GLN60 4.7 23.6 1.0 CB A:ASP79 4.7 31.5 1.0 HB3 A:ASP79 4.8 37.9 1.0 HB2 A:ASP79 5.0 37.9 1.0 CD A:GLN60 5.0 18.3 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of Human Cathepsin L Forming A Thiohemiacetal with N-Boc-2-Aminoacetaldehyde


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 Forming A Thiohemiacetal with N-Boc-2-Aminoacetaldehyde within 5.0Å range: probe atom residue distance (Å) B Occ A:Na308 b:49.0 occ:1.00 HO1 A:PEG305 2.1 57.5 1.0 OE1 A:GLN21 2.4 41.9 1.0 H42 A:PEG305 2.5 61.6 1.0 H31 A:PEG305 2.7 53.9 1.0 H21 A:PEG305 2.8 42.3 1.0 O1 A:PEG305 2.9 47.9 1.0 C4 A:PEG305 3.0 51.3 1.0 O4 A:PEG305 3.0 47.4 1.0 C3 A:PEG305 3.1 44.9 1.0 O2 A:PEG305 3.3 55.3 1.0 C2 A:PEG305 3.3 35.1 1.0 CD A:GLN21 3.4 49.5 1.0 HE22 A:GLN21 3.5 61.7 1.0 C1 A:PEG305 3.5 46.3 1.0 HO4 A:PEG305 3.9 57.0 1.0 NE2 A:GLN21 3.9 51.3 1.0 H11 A:PEG305 3.9 55.6 1.0 H41 A:PEG305 4.0 61.6 1.0 HA A:GLN21 4.1 34.4 1.0 H32 A:PEG305 4.1 53.9 1.0 H22 A:PEG305 4.3 42.3 1.0 H12 A:PEG305 4.5 55.6 1.0 HE21 A:GLN21 4.7 61.7 1.0 CG A:GLN21 4.8 39.8 1.0 HB3 A:GLN21 4.8 37.7 1.0 CA A:GLN21 4.9 28.6 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of Human Cathepsin L Forming A Thiohemiacetal with N-Boc-2-Aminoacetaldehyde


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 Forming A Thiohemiacetal with N-Boc-2-Aminoacetaldehyde within 5.0Å range: probe atom residue distance (Å) B Occ C:Na306 b:44.7 occ:1.00 OE1 C:GLU141 2.3 36.9 1.0 H32 D:PEG302 2.5 54.9 1.0 OD1 D:ASN18 2.9 24.6 1.0 H D:GLY20 2.9 27.2 1.0 O D:GLY20 3.0 23.0 1.0 CD C:GLU141 3.1 39.0 1.0 OE2 C:GLU141 3.1 35.8 1.0 HA D:TRP189 3.1 19.1 1.0 HG2 D:GLN19 3.2 31.6 1.0 N D:GLY20 3.3 22.6 1.0 HA2 D:GLY20 3.4 34.8 1.0 HD1 D:TRP189 3.5 25.8 1.0 HG3 D:GLN19 3.6 31.6 1.0 C D:GLY20 3.6 23.8 1.0 C3 D:PEG302 3.6 45.7 1.0 CA D:GLY20 3.6 28.9 1.0 CG D:GLN19 3.8 26.2 1.0 CD1 D:TRP189 3.8 21.4 1.0 CG D:ASN18 3.9 25.8 1.0 H D:GLN19 4.0 28.6 1.0 CA D:TRP189 4.0 15.8 1.0 O2 D:PEG302 4.0 45.5 1.0 HB3 D:TRP189 4.1 24.7 1.0 HD22 D:ASN18 4.1 30.7 1.0 H41 D:PEG302 4.2 56.5 1.0 C D:GLN19 4.2 25.0 1.0 CG D:TRP189 4.2 19.1 1.0 H31 D:PEG302 4.2 54.9 1.0 O D:SER188 4.3 19.3 1.0 N D:GLN19 4.3 23.7 1.0 CB D:TRP189 4.3 20.5 1.0 C4 D:PEG302 4.3 47.0 1.0 HE21 D:GLN21 4.4 70.1 1.0 HE2 C:PHE145 4.4 36.4 1.0 ND2 D:ASN18 4.4 25.5 1.0 CG C:GLU141 4.5 31.0 1.0 NE1 D:TRP189 4.6 24.6 1.0 HA3 D:GLY20 4.6 34.8 1.0 HE22 D:GLN21 4.6 70.1 1.0 O4 D:PEG302 4.7 45.7 1.0 CA D:GLN19 4.7 26.3 1.0 C D:TRP189 4.7 22.0 1.0 NE2 D:GLN21 4.7 58.3 1.0 N D:GLN21 4.7 24.9 1.0 HB3 C:GLU141 4.7 41.9 1.0 CD D:GLN19 4.7 22.1 1.0 O D:TRP189 4.8 18.0 1.0 HZ C:PHE145 4.8 33.1 1.0 HA D:ASN18 4.8 28.5 1.0 HB2 C:GLU141 4.8 41.9 1.0 HE1 D:TRP189 4.8 29.6 1.0 CB D:GLN19 4.9 24.2 1.0 HA D:GLN21 4.9 34.0 1.0 HG2 C:GLU141 4.9 37.4 1.0 C D:ASN18 5.0 20.4 1.0 CB C:GLU141 5.0 34.8 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. Crystal Structure of Human Cathepsin L Forming A Thiohemiacetal with N-Boc-2-Aminoacetaldehyde To Be Published.