Sodium in PDB 3ged: Fingerprint and Structural Analysis of A Apo Scor Enzyme From Clostridium Thermocellum

The structure of Fingerprint and Structural Analysis of A Apo Scor Enzyme From Clostridium Thermocellum, PDB code: 3ged was solved by R.Huether, Z.J.Liu, H.Xu, B.C.Wang, V.Pletnev, Q.Mao, T.Umland, W.Duax, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.68 / 1.70
Space group	I 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	124.287, 124.287, 162.608, 90.00, 90.00, 90.00
R / Rfree (%)	17.9 / 20.8

The binding sites of Sodium atom in the Fingerprint and Structural Analysis of A Apo Scor Enzyme From Clostridium Thermocellum (pdb code 3ged). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Fingerprint and Structural Analysis of A Apo Scor Enzyme From Clostridium Thermocellum, PDB code: 3ged:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Fingerprint and Structural Analysis of A Apo Scor Enzyme From Clostridium Thermocellum


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Fingerprint and Structural Analysis of A Apo Scor Enzyme From Clostridium Thermocellum within 5.0Å range: probe atom residue distance (Å) B Occ A:Na251 b:32.6 occ:1.00 O A:LEU49 2.4 33.1 1.0 O A:ARG46 2.5 36.5 1.0 O A:ALA43 2.5 32.9 1.0 O A:HOH350 2.5 39.2 1.0 O A:HOH360 2.7 45.5 1.0 O A:HOH291 2.9 43.5 1.0 C A:ARG46 3.3 35.3 1.0 C A:ALA43 3.5 31.4 1.0 C A:LEU49 3.6 31.1 1.0 CB A:ALA43 3.9 36.1 1.0 N A:ARG46 3.9 37.9 1.0 CA A:ALA43 4.0 30.9 1.0 CA A:ARG46 4.1 35.0 1.0 N A:PRO47 4.1 39.5 1.0 N A:LEU49 4.1 29.4 1.0 CA A:PRO47 4.2 42.6 1.0 CA A:LEU49 4.3 28.8 1.0 CB A:ARG46 4.3 34.3 1.0 CB A:LEU49 4.3 28.5 1.0 O A:HOH385 4.3 38.3 1.0 C A:PRO47 4.4 41.5 1.0 O A:HOH280 4.4 36.0 1.0 O A:PRO47 4.6 40.0 1.0 N A:LYS44 4.6 33.8 1.0 N A:PHE50 4.6 29.7 1.0 N A:GLU45 4.8 34.5 1.0 CA A:PHE50 4.8 31.9 1.0 CA A:LYS44 4.9 35.1 1.0 C A:LYS44 4.9 37.0 1.0 N A:ASN48 5.0 33.3 1.0

Sodium binding site 2 out of 2 in the Fingerprint and Structural Analysis of A Apo Scor Enzyme From Clostridium Thermocellum


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Fingerprint and Structural Analysis of A Apo Scor Enzyme From Clostridium Thermocellum within 5.0Å range: probe atom residue distance (Å) B Occ B:Na250 b:29.4 occ:1.00 O B:LEU49 2.3 28.9 1.0 O B:ARG46 2.5 33.5 1.0 O B:ALA43 2.5 30.0 1.0 O B:HOH441 2.5 40.1 1.0 O B:HOH472 2.7 37.9 1.0 O B:HOH497 2.9 37.5 1.0 C B:ARG46 3.3 31.7 1.0 C B:ALA43 3.5 32.1 1.0 C B:LEU49 3.5 26.2 1.0 CB B:ALA43 3.8 32.5 1.0 N B:ARG46 4.0 31.3 1.0 CA B:ALA43 4.0 27.3 1.0 CA B:ARG46 4.1 31.8 1.0 N B:LEU49 4.1 25.7 1.0 N B:PRO47 4.1 33.9 1.0 CA B:PRO47 4.2 36.1 1.0 CA B:LEU49 4.2 25.4 1.0 CB B:LEU49 4.3 28.1 1.0 CB B:ARG46 4.3 32.3 1.0 O B:HOH488 4.4 68.0 1.0 C B:PRO47 4.4 38.2 1.0 O B:HOH473 4.4 63.9 1.0 O B:HOH289 4.5 40.5 1.0 N B:PHE50 4.5 26.3 1.0 N B:LYS44 4.6 35.1 1.0 O B:HOH357 4.6 37.8 1.0 O B:PRO47 4.6 34.5 1.0 CA B:PHE50 4.8 25.9 1.0 N B:GLU45 4.8 31.0 1.0 CA B:LYS44 4.9 36.2 1.0 C B:LYS44 4.9 35.8 1.0 N B:ASN48 4.9 33.1 1.0

R.Huether, Z.J.Liu, H.Xu, B.C.Wang, V.Z.Pletnev, Q.Mao, W.L.Duax, T.C.Umland. Sequence Fingerprint and Structural Analysis of the Scor Enzyme A3DFK9 From Clostridium Thermocellum. Proteins V. 78 603 2010.
ISSN: ISSN 0887-3585
PubMed: 19774618
DOI: 10.1002/PROT.22584