Sodium in PDB 3mor: Crystal Structure of Cathepsin B From Trypanosoma Brucei

The structure of Crystal Structure of Cathepsin B From Trypanosoma Brucei, PDB code: 3mor was solved by K.Cupelli, T.Stehle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.00 / 2.55
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	53.910, 75.490, 75.600, 90.00, 104.80, 90.00
R / Rfree (%)	20.2 / 24.3

The structure of Crystal Structure of Cathepsin B From Trypanosoma Brucei also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Crystal Structure of Cathepsin B From Trypanosoma Brucei (pdb code 3mor). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Cathepsin B From Trypanosoma Brucei, PDB code: 3mor:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Cathepsin B From Trypanosoma Brucei


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 Cathepsin B From Trypanosoma Brucei within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1 b:19.5 occ:1.00 O A:GLN238 2.9 10.2 1.0 OD2 A:ASP242 3.4 10.6 1.0 N A:ASP242 3.4 6.2 1.0 CA A:GLY239 3.7 6.8 1.0 CG A:ASP242 3.7 10.0 1.0 C A:GLY239 3.8 7.4 1.0 N A:ASP241 3.8 6.8 1.0 CB A:ASP241 3.8 5.1 1.0 C A:GLN238 3.9 9.5 1.0 CB A:ASP242 3.9 6.7 1.0 O A:GLY239 4.0 6.7 1.0 CA A:ASP241 4.1 6.2 1.0 CA A:ASP242 4.2 6.2 1.0 C A:ASP241 4.2 6.6 1.0 N A:GLU240 4.3 6.7 1.0 N A:GLY239 4.3 8.0 1.0 OD1 A:ASP242 4.5 15.9 1.0 C A:GLU240 4.7 7.6 1.0 CG A:ASP241 5.0 7.1 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Cathepsin B From Trypanosoma Brucei


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 Cathepsin B From Trypanosoma Brucei within 5.0Å range: probe atom residue distance (Å) B Occ B:Na341 b:20.7 occ:1.00 O B:GLN238 3.0 12.2 1.0 N B:ASP242 3.5 7.1 1.0 OD2 B:ASP242 3.6 8.6 1.0 CA B:GLY239 3.7 7.8 1.0 CG B:ASP242 3.8 8.0 1.0 C B:GLY239 3.8 7.8 1.0 N B:ASP241 3.9 7.5 1.0 CB B:ASP242 3.9 7.8 1.0 CB B:ASP241 4.0 7.5 1.0 C B:GLN238 4.0 11.2 1.0 O B:GLY239 4.2 8.3 1.0 N B:GLU240 4.2 7.0 1.0 CA B:ASP241 4.2 7.7 1.0 CA B:ASP242 4.3 6.8 1.0 C B:ASP241 4.3 7.3 1.0 N B:GLY239 4.4 9.2 1.0 OD1 B:ASP242 4.6 12.5 1.0 C B:GLU240 4.8 7.9 1.0

R.Koopmann, K.Cupelli, L.Redecke, K.Nass, D.P.Deponte, T.A.White, F.Stellato, D.Rehders, M.Liang, J.Andreasson, A.Aquila, S.Bajt, M.Barthelmess, A.Barty, M.J.Bogan, C.Bostedt, S.Boutet, J.D.Bozek, C.Caleman, N.Coppola, J.Davidsson, R.B.Doak, T.Ekeberg, S.W.Epp, B.Erk, H.Fleckenstein, L.Foucar, H.Graafsma, L.Gumprecht, J.Hajdu, C.Y.Hampton, A.Hartmann, R.Hartmann, G.Hauser, H.Hirsemann, P.Holl, M.S.Hunter, S.Kassemeyer, R.A.Kirian, L.Lomb, F.R.Maia, N.Kimmel, A.V.Martin, M.Messerschmidt, C.Reich, D.Rolles, B.Rudek, A.Rudenko, I.Schlichting, J.Schulz, M.M.Seibert, R.L.Shoeman, R.G.Sierra, H.Soltau, S.Stern, L.Struder, N.Timneanu, J.Ullrich, X.Wang, G.Weidenspointner, U.Weierstall, G.J.Williams, C.B.Wunderer, P.Fromme, J.C.Spence, T.Stehle, H.N.Chapman, C.Betzel, M.Duszenko. In Vivo Protein Crystallization Opens New Routes in Structural Biology. Nat.Methods V. 9 259 2012.
ISSN: ISSN 1548-7091
PubMed: 22286384
DOI: 10.1038/NMETH.1859