Sodium in PDB 8ic1: Endo-Alpha-D-Arabinanase ENDOMA1 D51N Mutant From Microbacterium Arabinogalactanolyticum in Complex with Arabinooligosaccharides

The structure of Endo-Alpha-D-Arabinanase ENDOMA1 D51N Mutant From Microbacterium Arabinogalactanolyticum in Complex with Arabinooligosaccharides, PDB code: 8ic1 was solved by J.Li, C.Nakashima, A.Ishiwata, K.Fujita, S.Fushinobu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.65 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	114.708, 137.731, 148.589, 90, 90, 90
R / Rfree (%)	15.9 / 19

The structure of Endo-Alpha-D-Arabinanase ENDOMA1 D51N Mutant From Microbacterium Arabinogalactanolyticum in Complex with Arabinooligosaccharides also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Sodium atom in the Endo-Alpha-D-Arabinanase ENDOMA1 D51N Mutant From Microbacterium Arabinogalactanolyticum in Complex with Arabinooligosaccharides (pdb code 8ic1). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Endo-Alpha-D-Arabinanase ENDOMA1 D51N Mutant From Microbacterium Arabinogalactanolyticum in Complex with Arabinooligosaccharides, PDB code: 8ic1:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Endo-Alpha-D-Arabinanase ENDOMA1 D51N Mutant From Microbacterium Arabinogalactanolyticum in Complex with Arabinooligosaccharides


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Endo-Alpha-D-Arabinanase ENDOMA1 D51N Mutant From Microbacterium Arabinogalactanolyticum in Complex with Arabinooligosaccharides within 5.0Å range: probe atom residue distance (Å) B Occ A:Na505 b:23.5 occ:1.00 OD1 A:ASP85 2.2 38.3 1.0 OD2 A:ASP80 2.3 19.1 1.0 O A:HOH878 2.4 41.6 1.0 O A:ASP82 2.5 23.8 1.0 O A:GLY86 2.8 25.9 1.0 OD1 A:ASP80 2.8 19.3 1.0 CG A:ASP80 2.9 22.1 1.0 CG A:ASP85 3.4 36.8 1.0 C A:ASP82 3.4 22.9 1.0 C A:GLY86 3.5 20.2 1.0 N A:GLY86 3.9 20.2 1.0 C A:ASP85 3.9 21.2 1.0 OD2 A:ASP82 4.0 45.6 1.0 CB A:ASP82 4.0 31.9 1.0 OD2 A:ASP85 4.0 42.3 1.0 CA A:ASP82 4.1 27.7 1.0 CA A:GLY86 4.1 21.8 1.0 CG A:ASP82 4.2 42.2 1.0 O A:ASP85 4.2 23.0 1.0 N A:MET87 4.2 17.8 1.0 CB A:ASP80 4.4 20.3 1.0 N A:ASP82 4.4 25.3 1.0 N A:LEU83 4.4 17.4 1.0 CA A:MET87 4.4 15.2 1.0 CB A:ASP85 4.5 28.0 1.0 CA A:ASP85 4.5 21.5 1.0 CA A:LEU83 4.6 18.7 1.0 N A:LEU88 4.6 15.6 1.0 N A:ASP85 4.6 17.5 1.0 O A:HOH927 4.6 38.9 1.0 OD1 A:ASP82 4.9 37.8 1.0 C A:LEU83 5.0 17.7 1.0

Sodium binding site 2 out of 4 in the Endo-Alpha-D-Arabinanase ENDOMA1 D51N Mutant From Microbacterium Arabinogalactanolyticum in Complex with Arabinooligosaccharides


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Endo-Alpha-D-Arabinanase ENDOMA1 D51N Mutant From Microbacterium Arabinogalactanolyticum in Complex with Arabinooligosaccharides within 5.0Å range: probe atom residue distance (Å) B Occ B:Na507 b:25.4 occ:1.00 OD1 B:ASP85 2.2 42.6 1.0 OD2 B:ASP80 2.4 19.8 1.0 O B:HOH892 2.4 43.0 1.0 O B:ASP82 2.5 28.7 1.0 O B:GLY86 2.6 21.6 1.0 OD1 B:ASP80 2.9 21.4 1.0 CG B:ASP80 2.9 21.4 1.0 CG B:ASP85 3.3 46.2 1.0 C B:GLY86 3.4 19.3 1.0 C B:ASP82 3.4 22.5 1.0 N B:GLY86 3.8 21.0 1.0 OD2 B:ASP85 3.9 55.8 1.0 C B:ASP85 3.9 25.0 1.0 CB B:ASP82 4.0 32.1 1.0 CA B:ASP82 4.1 25.6 1.0 CA B:GLY86 4.1 19.4 1.0 OD2 B:ASP82 4.2 45.8 1.0 O B:ASP85 4.2 27.0 1.0 N B:MET87 4.2 18.1 1.0 CG B:ASP82 4.3 43.7 1.0 N B:ASP82 4.4 23.3 1.0 CB B:ASP80 4.4 19.5 1.0 N B:LEU83 4.4 19.9 1.0 O A:HOH907 4.4 35.7 1.0 CB B:ASP85 4.5 31.6 1.0 CA B:MET87 4.5 16.1 1.0 CA B:ASP85 4.5 25.1 1.0 CA B:LEU83 4.5 20.0 1.0 N B:ASP85 4.6 21.3 1.0 N B:LEU88 4.7 15.7 1.0 O B:HOH868 4.7 39.6 1.0 C B:LEU83 4.9 20.9 1.0

Sodium binding site 3 out of 4 in the Endo-Alpha-D-Arabinanase ENDOMA1 D51N Mutant From Microbacterium Arabinogalactanolyticum in Complex with Arabinooligosaccharides


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Endo-Alpha-D-Arabinanase ENDOMA1 D51N Mutant From Microbacterium Arabinogalactanolyticum in Complex with Arabinooligosaccharides within 5.0Å range: probe atom residue distance (Å) B Occ C:Na506 b:29.4 occ:1.00 OD1 C:ASP85 2.3 47.8 1.0 OD2 C:ASP80 2.3 19.8 1.0 O C:ASP82 2.4 31.6 1.0 O C:GLY86 2.6 24.9 1.0 O C:HOH881 2.7 48.6 1.0 OD1 C:ASP80 2.9 23.5 1.0 CG C:ASP80 2.9 20.9 1.0 C C:GLY86 3.4 23.5 1.0 C C:ASP82 3.4 26.4 1.0 CG C:ASP85 3.5 46.8 1.0 N C:GLY86 3.8 22.3 1.0 CB C:ASP82 3.8 35.1 1.0 C C:ASP85 3.9 26.0 1.0 OD2 C:ASP82 4.0 48.1 1.0 CA C:GLY86 4.0 25.9 1.0 O C:ASP85 4.1 25.9 1.0 CA C:ASP82 4.1 30.5 1.0 CG C:ASP82 4.1 43.4 1.0 N C:MET87 4.2 20.3 1.0 OD2 C:ASP85 4.3 55.8 1.0 N C:LEU83 4.4 20.8 1.0 CB C:ASP80 4.4 22.3 1.0 N C:ASP82 4.4 27.3 1.0 CA C:ASP85 4.5 27.8 1.0 CA C:MET87 4.5 20.5 1.0 N C:ASP85 4.5 23.6 1.0 O D:HOH803 4.5 37.5 1.0 CA C:LEU83 4.5 22.1 1.0 CB C:ASP85 4.6 35.1 1.0 N C:LEU88 4.6 19.0 1.0 C C:LEU83 4.9 23.8 1.0

Sodium binding site 4 out of 4 in the Endo-Alpha-D-Arabinanase ENDOMA1 D51N Mutant From Microbacterium Arabinogalactanolyticum in Complex with Arabinooligosaccharides


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Endo-Alpha-D-Arabinanase ENDOMA1 D51N Mutant From Microbacterium Arabinogalactanolyticum in Complex with Arabinooligosaccharides within 5.0Å range: probe atom residue distance (Å) B Occ D:Na506 b:28.0 occ:1.00 OD1 D:ASP85 2.2 43.1 1.0 OD2 D:ASP80 2.3 27.0 1.0 O D:ASP82 2.4 26.0 1.0 O D:GLY86 2.6 28.9 1.0 O D:HOH871 2.6 51.6 1.0 O D:HOH853 2.7 53.6 1.0 CG D:ASP80 2.9 28.9 1.0 OD1 D:ASP80 2.9 29.3 1.0 C D:GLY86 3.3 25.8 1.0 CG D:ASP85 3.4 43.0 1.0 C D:ASP82 3.5 30.9 1.0 N D:GLY86 3.8 28.0 1.0 C D:ASP85 3.9 34.0 1.0 OD2 D:ASP85 4.0 57.9 1.0 CA D:GLY86 4.0 29.6 1.0 O D:ASP85 4.2 30.1 1.0 N D:MET87 4.2 21.8 1.0 CB D:ASP82 4.2 38.9 1.0 CA D:ASP82 4.3 32.3 1.0 O D:HOH884 4.3 51.0 1.0 OD2 D:ASP82 4.3 61.2 1.0 CB D:ASP80 4.4 26.1 1.0 N D:LEU83 4.4 25.0 1.0 CA D:MET87 4.5 21.2 1.0 CA D:LEU83 4.5 23.6 1.0 N D:ASP85 4.5 24.2 1.0 CA D:ASP85 4.5 31.6 1.0 CG D:ASP82 4.5 44.6 1.0 N D:ASP82 4.5 27.9 1.0 CB D:ASP85 4.5 36.4 1.0 N D:LEU88 4.7 23.4 1.0 C D:LEU83 4.8 27.0 1.0

M.Shimokawa, A.Ishiwata, T.Kashima, C.Nakashima, J.Li, R.Fukushima, T.Arakawa, C.Yamada, S.Fiushinobu, K.Fujita. Identification and Characterization of Endo- and Exo-Hydrolases Cleaving the Alpha- and Beta-D-Arabinofuranosidic Bonds of Lipoarabinomannan and Arabinogalactan of Mycobacteria To Be Published.