Calcium 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:

Sodium

(Na)

4 atoms

The binding sites of Calcium 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 Calcium atom.
In total 4 binding sites of Calcium where determined in the Endo-Alpha-D-Arabinanase ENDOMA1 D51N Mutant From Microbacterium Arabinogalactanolyticum in Complex with Arabinooligosaccharides, PDB code: 8ic1:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium 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 Calcium with other atoms in the Ca 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:Ca506 b:16.5 occ:1.00 O A:SER341 2.3 14.1 1.0 O A:HIS376 2.4 17.8 1.0 OE2 A:GLU343 2.4 15.0 1.0 O A:THR373 2.4 14.8 1.0 OG A:SER341 2.5 15.7 1.0 OD1 A:ASP472 2.5 15.7 1.0 OD2 A:ASP472 2.5 15.9 1.0 CG A:ASP472 2.8 16.1 1.0 C A:SER341 3.3 15.1 1.0 CD A:GLU343 3.5 16.5 1.0 CB A:SER341 3.5 15.1 1.0 C A:HIS376 3.5 14.3 1.0 C A:THR373 3.5 16.0 1.0 CA A:SER341 3.7 16.4 1.0 OG1 A:THR373 3.9 14.5 1.0 CG A:GLU343 4.0 15.9 1.0 O A:HOH752 4.0 15.1 1.0 N A:HIS376 4.1 14.1 1.0 CA A:GLY371 4.3 15.0 1.0 CA A:HIS376 4.3 14.1 1.0 N A:THR373 4.4 15.3 1.0 CB A:ASP472 4.4 15.0 1.0 OD2 A:ASP473 4.4 16.5 1.0 N A:GLY374 4.4 14.2 1.0 CA A:GLY374 4.4 13.6 1.0 CA A:THR373 4.5 13.9 1.0 N A:PHE342 4.5 14.8 1.0 N A:ARG377 4.6 15.4 1.0 OE1 A:GLU343 4.6 16.7 1.0 OD1 A:ASP473 4.6 15.6 1.0 C A:GLY374 4.6 14.4 1.0 CB A:HIS376 4.6 15.3 1.0 CG A:ASP473 4.7 15.4 1.0 N A:PHE372 4.8 15.5 1.0 CA A:ARG377 4.8 15.3 1.0 N A:ASP375 4.8 14.7 1.0 CB A:THR373 4.9 15.1 1.0 CB A:PHE342 5.0 16.3 1.0 N A:GLU343 5.0 14.7 1.0 C A:GLY371 5.0 15.5 1.0

Calcium 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 Calcium with other atoms in the Ca 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:Ca508 b:18.6 occ:1.00 OE2 B:GLU343 2.3 21.5 1.0 O B:HIS376 2.3 17.6 1.0 O B:SER341 2.4 18.0 1.0 O B:THR373 2.4 18.8 1.0 OG B:SER341 2.4 17.3 1.0 OD2 B:ASP472 2.5 17.2 1.0 OD1 B:ASP472 2.5 18.5 1.0 CG B:ASP472 2.9 18.7 1.0 C B:SER341 3.3 16.2 1.0 CD B:GLU343 3.5 22.8 1.0 CB B:SER341 3.5 18.2 1.0 C B:HIS376 3.5 19.2 1.0 C B:THR373 3.5 18.2 1.0 CA B:SER341 3.7 18.4 1.0 OG1 B:THR373 3.9 16.5 1.0 CG B:GLU343 4.0 21.2 1.0 O B:HOH770 4.1 19.4 1.0 N B:HIS376 4.1 19.1 1.0 CA B:GLY371 4.2 18.2 1.0 CA B:HIS376 4.3 18.7 1.0 OD2 B:ASP473 4.4 19.6 1.0 CB B:ASP472 4.4 18.4 1.0 N B:THR373 4.4 16.7 1.0 N B:GLY374 4.4 18.2 1.0 CA B:GLY374 4.5 19.4 1.0 OD1 B:ASP473 4.5 20.3 1.0 CA B:THR373 4.5 18.0 1.0 OE1 B:GLU343 4.5 20.8 1.0 CB B:HIS376 4.5 18.5 1.0 N B:PHE342 4.6 20.1 1.0 N B:ARG377 4.6 17.8 1.0 C B:GLY374 4.6 20.7 1.0 CG B:ASP473 4.7 19.1 1.0 N B:PHE372 4.8 18.6 1.0 CB B:THR373 4.8 17.3 1.0 N B:ASP375 4.8 20.9 1.0 CA B:ARG377 4.9 19.2 1.0 C B:GLY371 5.0 17.2 1.0 CB B:PHE342 5.0 17.2 1.0 N B:GLU343 5.0 17.3 1.0

Calcium 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 Calcium with other atoms in the Ca 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:Ca507 b:15.5 occ:1.00 OE2 C:GLU343 2.3 16.5 1.0 O C:SER341 2.4 16.5 1.0 O C:HIS376 2.4 17.6 1.0 OD2 C:ASP472 2.4 14.8 1.0 O C:THR373 2.4 16.3 1.0 OG C:SER341 2.4 14.8 1.0 OD1 C:ASP472 2.5 14.7 1.0 CG C:ASP472 2.8 15.2 1.0 C C:SER341 3.4 13.9 1.0 CB C:SER341 3.4 15.3 1.0 CD C:GLU343 3.5 18.5 1.0 C C:HIS376 3.5 16.5 1.0 C C:THR373 3.6 15.6 1.0 CA C:SER341 3.6 15.3 1.0 OG1 C:THR373 3.9 15.6 1.0 CG C:GLU343 4.0 17.0 1.0 O C:HOH753 4.1 14.3 1.0 N C:HIS376 4.1 15.6 1.0 CA C:GLY371 4.2 17.5 1.0 CA C:HIS376 4.3 15.4 1.0 CB C:ASP472 4.3 15.6 1.0 N C:THR373 4.3 15.5 1.0 OD2 C:ASP473 4.4 18.8 1.0 N C:GLY374 4.5 16.3 1.0 CA C:GLY374 4.5 17.8 1.0 CA C:THR373 4.5 16.7 1.0 OE1 C:GLU343 4.6 18.1 1.0 OD1 C:ASP473 4.6 16.7 1.0 N C:PHE342 4.6 15.7 1.0 N C:ARG377 4.6 16.8 1.0 CB C:HIS376 4.6 16.8 1.0 C C:GLY374 4.6 16.2 1.0 N C:PHE372 4.7 16.4 1.0 CG C:ASP473 4.8 16.1 1.0 N C:ASP375 4.8 16.2 1.0 CB C:THR373 4.8 15.4 1.0 CA C:ARG377 4.9 16.0 1.0 C C:GLY371 4.9 17.1 1.0

Calcium 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 Calcium with other atoms in the Ca 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:Ca507 b:19.9 occ:1.00 O D:THR373 2.4 21.6 1.0 O D:SER341 2.4 19.6 1.0 O D:HIS376 2.4 19.8 1.0 OE2 D:GLU343 2.4 18.4 1.0 OG D:SER341 2.5 19.0 1.0 OD1 D:ASP472 2.6 19.0 1.0 OD2 D:ASP472 2.6 20.0 1.0 CG D:ASP472 2.9 20.2 1.0 C D:SER341 3.4 21.1 1.0 CB D:SER341 3.4 22.3 1.0 C D:THR373 3.5 16.8 1.0 C D:HIS376 3.5 18.5 1.0 CD D:GLU343 3.6 19.3 1.0 CA D:SER341 3.7 22.1 1.0 OG1 D:THR373 3.8 19.6 1.0 CG D:GLU343 4.0 18.1 1.0 N D:HIS376 4.1 19.9 1.0 O D:HOH811 4.1 19.5 1.0 CA D:GLY371 4.2 19.0 1.0 CA D:HIS376 4.3 20.4 1.0 N D:THR373 4.4 18.0 1.0 N D:GLY374 4.4 17.6 1.0 CA D:GLY374 4.4 18.6 1.0 OD2 D:ASP473 4.4 20.4 1.0 CB D:ASP472 4.4 20.2 1.0 CA D:THR373 4.4 18.3 1.0 N D:ARG377 4.6 18.1 1.0 OD1 D:ASP473 4.6 20.5 1.0 N D:PHE342 4.6 21.0 1.0 C D:GLY374 4.6 19.3 1.0 OE1 D:GLU343 4.6 21.4 1.0 CB D:HIS376 4.6 20.5 1.0 N D:ASP375 4.8 20.5 1.0 N D:PHE372 4.8 20.6 1.0 CG D:ASP473 4.8 23.7 1.0 CB D:THR373 4.8 19.4 1.0 CA D:ARG377 4.9 18.5 1.0 C D:GLY371 5.0 19.4 1.0 N D:GLU343 5.0 19.8 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.