Sodium in PDB 4kca: Crystal Structure of Endo-1,5-Alpha-L-Arabinanase From A Bovine Ruminal Metagenomic Library

All present enzymatic activity of Crystal Structure of Endo-1,5-Alpha-L-Arabinanase From A Bovine Ruminal Metagenomic Library:
3.2.1.99;

The structure of Crystal Structure of Endo-1,5-Alpha-L-Arabinanase From A Bovine Ruminal Metagenomic Library, PDB code: 4kca was solved by C.R.Santos, C.C.Polo, M.C.M.F.Costa, A.F.Z.Nascimento, D.W.S.Wong, M.T.Murakami, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.84 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	99.909, 114.318, 167.201, 90.00, 90.00, 90.00
R / Rfree (%)	18.7 / 21.6

The structure of Crystal Structure of Endo-1,5-Alpha-L-Arabinanase From A Bovine Ruminal Metagenomic Library also contains other interesting chemical elements:

Iodine

(I)

63 atoms

The binding sites of Sodium atom in the Crystal Structure of Endo-1,5-Alpha-L-Arabinanase From A Bovine Ruminal Metagenomic Library (pdb code 4kca). 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 Endo-1,5-Alpha-L-Arabinanase From A Bovine Ruminal Metagenomic Library, PDB code: 4kca:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Endo-1,5-Alpha-L-Arabinanase From A Bovine Ruminal Metagenomic Library


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 Endo-1,5-Alpha-L-Arabinanase From A Bovine Ruminal Metagenomic Library within 5.0Å range: probe atom residue distance (Å) B Occ A:Na735 b:41.2 occ:1.00 O A:HOH918 2.3 24.8 1.0 O A:HOH813 2.4 29.7 1.0 O A:HOH992 2.4 33.3 1.0 O A:HOH1082 2.5 24.4 1.0 O A:HOH874 3.0 45.7 1.0 NE2 A:HIS475 3.3 26.3 1.0 CD2 A:HIS475 3.6 23.1 1.0 O A:HOH929 3.7 33.6 1.0 O A:PRO309 3.8 20.5 1.0 OG A:SER128 4.0 33.2 1.0 O A:SER378 4.1 19.9 1.0 CD2 A:TYR379 4.3 23.1 1.0 O A:ASN476 4.4 21.4 1.0 CE1 A:HIS475 4.5 22.3 1.0 CA A:ALA377 4.6 17.6 1.0 C A:ALA377 4.7 18.6 1.0 C A:PRO309 4.7 19.9 1.0 O A:ALA377 4.7 18.1 1.0 CB A:ALA377 4.8 18.9 1.0 O A:ASP308 4.9 19.4 1.0 CG A:HIS475 4.9 22.2 1.0 CE2 A:TYR379 4.9 26.1 1.0 C A:ASP308 4.9 19.2 1.0 O A:ALA218 5.0 24.1 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Endo-1,5-Alpha-L-Arabinanase From A Bovine Ruminal Metagenomic Library


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 Endo-1,5-Alpha-L-Arabinanase From A Bovine Ruminal Metagenomic Library within 5.0Å range: probe atom residue distance (Å) B Occ B:Na732 b:40.1 occ:1.00 O B:HOH1068 2.2 30.1 1.0 O B:HOH873 2.4 26.2 1.0 O B:HOH845 2.5 30.4 1.0 O B:HOH864 2.5 24.7 1.0 O B:HOH1061 2.9 49.4 1.0 NE2 B:HIS475 3.3 27.1 1.0 CD2 B:HIS475 3.6 23.7 1.0 O B:PRO309 3.8 21.5 1.0 O B:HOH977 4.1 33.5 1.0 O B:SER378 4.1 20.3 1.0 OG B:SER128 4.1 30.2 1.0 CD2 B:TYR379 4.2 25.7 1.0 O B:ASN476 4.3 22.6 1.0 CE1 B:HIS475 4.5 23.8 1.0 CA B:ALA377 4.6 19.6 1.0 C B:ALA377 4.6 20.4 1.0 O B:ALA377 4.6 20.2 1.0 C B:PRO309 4.7 20.5 1.0 CB B:ALA377 4.8 20.2 1.0 CG B:HIS475 4.8 22.7 1.0 CE2 B:TYR379 4.9 27.0 1.0 O B:ASP308 4.9 20.7 1.0

C.R.Santos, C.C.Polo, M.C.Costa, A.F.Nascimento, A.N.Meza, J.Cota, Z.B.Hoffmam, R.V.Honorato, P.S.Oliveira, G.H.Goldman, H.J.Gilbert, R.A.Prade, R.Ruller, F.M.Squina, D.W.Wong, M.T.Murakami. Mechanistic Strategies For Catalysis Adopted By Evolutionary Distinct Family 43 Arabinanases. J.Biol.Chem. V. 289 7362 2014.
ISSN: ISSN 0021-9258
PubMed: 24469445
DOI: 10.1074/JBC.M113.537167