Calcium in PDB 8hhv: Endo-Alpha-D-Arabinanase ENDOMA1 From Microbacterium Arabinogalactanolyticum

The structure of Endo-Alpha-D-Arabinanase ENDOMA1 From Microbacterium Arabinogalactanolyticum, PDB code: 8hhv was solved by C.Nakashima, J.Li, T.Arakawa, C.Yamada, 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)	46.18 / 1.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	81.285, 128.296, 104.019, 90, 109.38, 90
R / Rfree (%)	17.7 / 21.1

The structure of Endo-Alpha-D-Arabinanase ENDOMA1 From Microbacterium Arabinogalactanolyticum also contains other interesting chemical elements:

Sodium

(Na)

8 atoms

The binding sites of Calcium atom in the Endo-Alpha-D-Arabinanase ENDOMA1 From Microbacterium Arabinogalactanolyticum (pdb code 8hhv). 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 From Microbacterium Arabinogalactanolyticum, PDB code: 8hhv:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Endo-Alpha-D-Arabinanase ENDOMA1 From Microbacterium Arabinogalactanolyticum


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 From Microbacterium Arabinogalactanolyticum within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:12.6 occ:1.00 O A:HIS376 2.3 14.6 1.0 OE2 A:GLU343 2.4 13.3 1.0 O A:THR373 2.4 12.5 1.0 OG A:SER341 2.4 13.8 1.0 O A:SER341 2.5 12.5 1.0 OD2 A:ASP472 2.5 11.5 1.0 OD1 A:ASP472 2.5 12.3 1.0 CG A:ASP472 2.8 13.2 1.0 C A:SER341 3.3 13.1 1.0 CB A:SER341 3.4 14.5 1.0 C A:HIS376 3.5 14.4 1.0 CD A:GLU343 3.6 14.5 1.0 C A:THR373 3.6 10.9 1.0 CA A:SER341 3.6 14.0 1.0 OG1 A:THR373 3.9 11.7 1.0 O A:HOH856 4.1 13.5 1.0 CG A:GLU343 4.1 14.5 1.0 N A:HIS376 4.1 14.1 1.0 CA A:GLY371 4.2 11.8 1.0 CA A:HIS376 4.3 13.9 1.0 OD2 A:ASP473 4.4 15.3 1.0 CB A:ASP472 4.4 11.4 1.0 N A:THR373 4.4 11.2 1.0 N A:GLY374 4.5 12.5 1.0 CA A:THR373 4.5 10.4 1.0 CA A:GLY374 4.5 12.7 1.0 N A:ARG377 4.6 14.2 1.0 CB A:HIS376 4.6 13.7 1.0 N A:PHE342 4.6 12.6 1.0 OD1 A:ASP473 4.6 13.9 1.0 OE1 A:GLU343 4.6 15.4 1.0 C A:GLY374 4.6 11.5 1.0 CG A:ASP473 4.8 14.2 1.0 N A:PHE372 4.8 12.7 1.0 CB A:THR373 4.8 10.2 1.0 CA A:ARG377 4.8 14.0 1.0 N A:ASP375 4.9 13.9 1.0 C A:GLY371 5.0 11.1 1.0

Calcium binding site 2 out of 4 in the Endo-Alpha-D-Arabinanase ENDOMA1 From Microbacterium Arabinogalactanolyticum


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 From Microbacterium Arabinogalactanolyticum within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:11.7 occ:1.00 O B:HIS376 2.4 12.3 1.0 OE2 B:GLU343 2.4 13.9 1.0 OG B:SER341 2.4 12.3 1.0 O B:THR373 2.4 11.5 1.0 O B:SER341 2.4 11.6 1.0 OD2 B:ASP472 2.5 12.0 1.0 OD1 B:ASP472 2.5 10.8 1.0 CG B:ASP472 2.9 10.0 1.0 C B:SER341 3.4 11.0 1.0 CB B:SER341 3.4 11.2 1.0 CD B:GLU343 3.5 13.8 1.0 C B:HIS376 3.5 13.6 1.0 C B:THR373 3.6 10.8 1.0 CA B:SER341 3.7 11.4 1.0 OG1 B:THR373 4.0 11.4 1.0 CG B:GLU343 4.0 12.6 1.0 O B:HOH823 4.2 12.8 1.0 CA B:GLY371 4.2 12.3 1.0 N B:HIS376 4.2 11.6 1.0 CA B:HIS376 4.3 13.2 1.0 CA B:GLY374 4.3 10.5 1.0 N B:THR373 4.4 11.0 1.0 OD2 B:ASP473 4.4 13.8 1.0 CB B:ASP472 4.4 9.9 1.0 N B:GLY374 4.4 10.8 1.0 CA B:THR373 4.5 10.0 1.0 OD1 B:ASP473 4.6 12.1 1.0 CB B:HIS376 4.6 14.0 1.0 N B:PHE342 4.6 11.1 1.0 N B:ARG377 4.6 12.3 1.0 OE1 B:GLU343 4.6 14.1 1.0 C B:GLY374 4.6 10.8 1.0 N B:PHE372 4.7 11.0 1.0 CG B:ASP473 4.7 13.2 1.0 CB B:THR373 4.8 10.5 1.0 CA B:ARG377 4.9 12.6 1.0 C B:GLY371 4.9 12.0 1.0 N B:ASP375 4.9 11.0 1.0 CB B:PHE342 5.0 10.3 1.0

Calcium binding site 3 out of 4 in the Endo-Alpha-D-Arabinanase ENDOMA1 From Microbacterium Arabinogalactanolyticum


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 From Microbacterium Arabinogalactanolyticum within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:15.1 occ:1.00 O C:HIS376 2.3 15.4 1.0 O C:SER341 2.4 18.9 1.0 OE2 C:GLU343 2.4 14.7 1.0 O C:THR373 2.4 13.5 1.0 OD1 C:ASP472 2.5 14.6 1.0 OG C:SER341 2.6 17.1 1.0 OD2 C:ASP472 2.6 16.3 1.0 CG C:ASP472 2.9 15.4 1.0 C C:SER341 3.4 17.8 1.0 C C:HIS376 3.5 15.1 1.0 CB C:SER341 3.5 17.7 1.0 CD C:GLU343 3.5 17.4 1.0 C C:THR373 3.6 13.4 1.0 CA C:SER341 3.7 17.1 1.0 OG1 C:THR373 3.8 13.7 1.0 CG C:GLU343 4.0 16.5 1.0 O C:HOH794 4.1 14.1 1.0 N C:HIS376 4.1 15.8 1.0 CA C:HIS376 4.2 16.5 1.0 CA C:GLY371 4.3 15.1 1.0 CB C:ASP472 4.4 14.6 1.0 OD2 C:ASP473 4.4 16.7 1.0 N C:THR373 4.4 13.8 1.0 CA C:GLY374 4.5 15.6 1.0 N C:GLY374 4.5 12.9 1.0 CA C:THR373 4.5 13.2 1.0 N C:ARG377 4.5 13.3 1.0 CB C:HIS376 4.6 16.8 1.0 N C:PHE342 4.6 16.2 1.0 OE1 C:GLU343 4.6 16.0 1.0 OD1 C:ASP473 4.6 14.7 1.0 C C:GLY374 4.6 12.2 1.0 CA C:ARG377 4.8 14.1 1.0 CG C:ASP473 4.8 16.1 1.0 CB C:THR373 4.9 14.8 1.0 N C:PHE372 4.9 18.9 1.0 N C:ASP375 4.9 14.6 1.0 CB C:PHE342 5.0 17.0 1.0

Calcium binding site 4 out of 4 in the Endo-Alpha-D-Arabinanase ENDOMA1 From Microbacterium Arabinogalactanolyticum


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 From Microbacterium Arabinogalactanolyticum within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca503 b:11.4 occ:1.00 O D:HIS376 2.4 13.5 1.0 O D:THR373 2.4 15.0 1.0 O D:SER341 2.4 12.6 1.0 OE2 D:GLU343 2.5 11.4 1.0 OD2 D:ASP472 2.5 12.8 1.0 OG D:SER341 2.5 11.1 1.0 OD1 D:ASP472 2.6 12.8 1.0 CG D:ASP472 2.9 12.5 1.0 C D:SER341 3.4 11.9 1.0 CB D:SER341 3.5 11.8 1.0 C D:HIS376 3.5 12.8 1.0 CD D:GLU343 3.6 14.4 1.0 C D:THR373 3.6 11.9 1.0 CA D:SER341 3.7 12.4 1.0 OG1 D:THR373 4.0 10.8 1.0 CG D:GLU343 4.0 13.4 1.0 O D:HOH817 4.1 11.2 1.0 N D:HIS376 4.2 13.3 1.0 CA D:GLY371 4.2 13.7 1.0 CA D:HIS376 4.3 14.0 1.0 N D:THR373 4.4 12.2 1.0 OD2 D:ASP473 4.4 14.7 1.0 CA D:GLY374 4.4 12.7 1.0 CB D:ASP472 4.4 11.9 1.0 N D:GLY374 4.4 14.2 1.0 CA D:THR373 4.5 11.7 1.0 OD1 D:ASP473 4.5 14.5 1.0 N D:ARG377 4.6 12.8 1.0 CB D:HIS376 4.6 13.5 1.0 N D:PHE342 4.6 11.6 1.0 OE1 D:GLU343 4.6 14.2 1.0 C D:GLY374 4.7 12.9 1.0 N D:PHE372 4.7 11.3 1.0 CG D:ASP473 4.8 15.8 1.0 CB D:THR373 4.9 13.2 1.0 C D:GLY371 4.9 12.0 1.0 N D:ASP375 4.9 16.1 1.0 CA D:ARG377 4.9 12.3 1.0 CB D:PHE342 5.0 12.3 1.0

M.Shimokawa, A.Ishiwata, T.Kashima, C.Nakashima, J.Li, R.Fukushima, M.Sawai, M.Nakamori, Y.Tanaka, A.Kudoh, S.Morigami, G.Akai, N.Shimizu, T.Arakawa, C.Yamada, K.Tanaka, Y.Ito, S.Fushinobu, 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.