Magnesium in PDB 8ic7: Exo-Beta-D-Arabinofuranosidase EXOMA2 From Microbacterium Arabinogalactanolyticum in Complex with Beta-D-Arabinofuranose

The structure of Exo-Beta-D-Arabinofuranosidase EXOMA2 From Microbacterium Arabinogalactanolyticum in Complex with Beta-D-Arabinofuranose, PDB code: 8ic7 was solved by R.Fukushima, T.Kashima, 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)	45.87 / 1.35
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	66.763, 97.249, 139.681, 90, 101.25, 90
R / Rfree (%)	15.9 / 18.2

The structure of Exo-Beta-D-Arabinofuranosidase EXOMA2 From Microbacterium Arabinogalactanolyticum in Complex with Beta-D-Arabinofuranose also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Magnesium atom in the Exo-Beta-D-Arabinofuranosidase EXOMA2 From Microbacterium Arabinogalactanolyticum in Complex with Beta-D-Arabinofuranose (pdb code 8ic7). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 15 binding sites of Magnesium where determined in the Exo-Beta-D-Arabinofuranosidase EXOMA2 From Microbacterium Arabinogalactanolyticum in Complex with Beta-D-Arabinofuranose, PDB code: 8ic7:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 15 in the Exo-Beta-D-Arabinofuranosidase EXOMA2 From Microbacterium Arabinogalactanolyticum in Complex with Beta-D-Arabinofuranose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Exo-Beta-D-Arabinofuranosidase EXOMA2 From Microbacterium Arabinogalactanolyticum in Complex with Beta-D-Arabinofuranose within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg901 b:21.3 occ:1.00 O B:HOH1744 2.0 32.5 1.0 O B:HOH1330 2.0 30.5 1.0 O B:HOH1058 2.1 25.1 1.0 O B:GLY672 4.1 17.9 1.0 O B:ASP688 4.1 18.7 1.0 O B:HOH1199 4.1 27.4 1.0 OD2 B:ASP673 4.3 18.1 1.0 CB B:ASP673 4.8 16.7 1.0 C B:GLY672 5.0 14.8 1.0

Magnesium binding site 2 out of 15 in the Exo-Beta-D-Arabinofuranosidase EXOMA2 From Microbacterium Arabinogalactanolyticum in Complex with Beta-D-Arabinofuranose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Exo-Beta-D-Arabinofuranosidase EXOMA2 From Microbacterium Arabinogalactanolyticum in Complex with Beta-D-Arabinofuranose within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg902 b:41.8 occ:1.00 O B:HOH1623 1.9 38.2 1.0 O B:HOH1597 2.0 40.9 1.0 O B:HOH1091 2.0 40.8 1.0 O B:HOH1603 2.0 43.3 1.0 O B:HOH1799 2.1 43.8 1.0 O B:HOH1575 2.2 26.9 1.0 OD2 B:ASP790 4.1 31.2 1.0 CA B:VAL792 4.3 20.4 1.0 O B:HOH1347 4.4 17.4 1.0 O B:PHE727 4.4 18.1 1.0 O B:HOH1741 4.5 39.1 1.0 CA B:GLY729 4.6 15.9 1.0 O B:PRO791 4.6 17.9 1.0 O B:VAL792 4.6 19.7 1.0 O B:HOH1016 4.7 30.8 1.0 O B:LEU726 4.7 16.3 1.0 N B:GLY729 4.7 15.9 1.0 O B:HOH1515 4.8 19.4 1.0 O B:HOH1224 4.8 24.1 1.0 O B:ASP790 4.8 17.5 1.0 CG B:ASP790 4.8 28.7 1.0 CG2 B:VAL792 4.9 25.0 1.0 CB B:VAL792 4.9 22.7 1.0 OD1 B:ASP790 5.0 31.9 1.0 C B:VAL792 5.0 20.0 1.0

Magnesium binding site 3 out of 15 in the Exo-Beta-D-Arabinofuranosidase EXOMA2 From Microbacterium Arabinogalactanolyticum in Complex with Beta-D-Arabinofuranose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Exo-Beta-D-Arabinofuranosidase EXOMA2 From Microbacterium Arabinogalactanolyticum in Complex with Beta-D-Arabinofuranose within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg903 b:21.3 occ:1.00 OD2 B:ASP201 2.0 19.8 1.0 O B:HOH1190 2.0 19.6 1.0 O B:HOH1107 2.1 24.7 1.0 O B:HOH1283 2.1 20.2 1.0 O B:HOH1563 2.2 22.9 1.0 O B:HOH1344 2.2 25.5 1.0 CG B:ASP201 3.1 16.4 1.0 CB B:ASP201 3.6 19.0 1.0 OD2 B:ASP199 4.1 23.8 1.0 O B:HOH1694 4.1 43.8 1.0 O B:HOH1586 4.1 34.4 1.0 OD1 B:ASP201 4.2 19.1 1.0 O B:HOH1212 4.2 26.1 1.0 OD1 B:ASP199 4.3 20.8 1.0 OD2 B:ASP360 4.3 23.2 1.0 CG2 B:THR213 4.3 16.7 1.0 O B:HOH1485 4.5 18.6 1.0 O B:HOH1022 4.5 30.5 1.0 NH1 B:ARG188 4.5 54.9 1.0 CG B:ASP199 4.5 22.3 1.0 NH2 B:ARG188 4.5 67.2 1.0 O B:PHE200 4.6 18.6 1.0 CA B:ASP201 4.8 17.9 1.0 O B:HOH1326 4.8 29.0 1.0 OH B:TYR211 4.8 20.3 1.0 CZ B:ARG188 4.8 62.6 1.0

Magnesium binding site 4 out of 15 in the Exo-Beta-D-Arabinofuranosidase EXOMA2 From Microbacterium Arabinogalactanolyticum in Complex with Beta-D-Arabinofuranose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Exo-Beta-D-Arabinofuranosidase EXOMA2 From Microbacterium Arabinogalactanolyticum in Complex with Beta-D-Arabinofuranose within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg904 b:16.8 occ:1.00 O B:HOH1391 2.0 16.8 1.0 O B:HOH1115 2.0 18.8 1.0 O B:HOH1625 2.0 17.9 1.0 O B:HOH1576 2.1 23.0 1.0 O B:HOH1617 2.1 17.2 1.0 NE2 B:HIS749 2.2 15.6 1.0 CE1 B:HIS749 3.2 15.3 1.0 CD2 B:HIS749 3.2 16.0 1.0 O B:HOH1537 3.9 19.8 1.0 OD1 B:ASP688 4.1 19.2 1.0 OD2 B:ASP688 4.1 22.7 1.0 O B:HOH1742 4.2 36.8 1.0 ND1 B:HIS749 4.3 13.9 1.0 CG B:HIS749 4.3 13.3 1.0 O B:HOH1794 4.3 27.9 1.0 O A:HOH1765 4.4 19.0 1.0 O B:HOH1549 4.4 23.7 1.0 O B:HOH1138 4.4 17.3 1.0 O B:HOH1262 4.5 24.2 1.0 CG B:ASP688 4.5 19.3 1.0 CB B:ALA748 4.7 14.5 1.0

Magnesium binding site 5 out of 15 in the Exo-Beta-D-Arabinofuranosidase EXOMA2 From Microbacterium Arabinogalactanolyticum in Complex with Beta-D-Arabinofuranose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Exo-Beta-D-Arabinofuranosidase EXOMA2 From Microbacterium Arabinogalactanolyticum in Complex with Beta-D-Arabinofuranose within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg905 b:28.6 occ:1.00 O B:HOH1628 2.0 38.0 1.0 O B:HOH1194 2.0 29.0 1.0 O B:HOH1767 2.0 31.3 1.0 O B:HOH1162 2.1 31.2 1.0 NE2 B:HIS436 2.2 18.7 1.0 O B:HOH1562 2.5 48.7 1.0 CE1 B:HIS436 3.1 18.2 1.0 CD2 B:HIS436 3.2 17.1 1.0 O B:LYS46 4.1 15.1 1.0 ND1 B:HIS436 4.3 19.3 1.0 CG B:HIS436 4.3 17.2 1.0 OD2 B:ASP435 4.4 18.2 1.0 CB B:ASP435 4.4 14.5 1.0 CG B:ASP435 4.8 15.6 1.0

Magnesium binding site 6 out of 15 in the Exo-Beta-D-Arabinofuranosidase EXOMA2 From Microbacterium Arabinogalactanolyticum in Complex with Beta-D-Arabinofuranose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Exo-Beta-D-Arabinofuranosidase EXOMA2 From Microbacterium Arabinogalactanolyticum in Complex with Beta-D-Arabinofuranose within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg906 b:18.3 occ:1.00 OD1 B:ASP244 2.0 18.8 1.0 O B:ASP244 2.1 17.7 1.0 O B:HOH1186 2.1 19.0 1.0 O B:LEU250 2.1 16.7 1.0 OD1 B:ASP248 2.1 19.2 1.0 O B:HOH1116 2.1 21.2 1.0 C B:ASP244 3.0 17.8 1.0 CG B:ASP248 3.1 21.3 1.0 C B:LEU250 3.2 17.0 1.0 CG B:ASP244 3.2 18.9 1.0 OD2 B:ASP248 3.4 21.0 1.0 CA B:ASP244 3.5 16.4 1.0 CB B:ASP244 3.8 17.5 1.0 N B:LEU250 3.9 17.0 1.0 CA B:LEU250 4.0 18.1 1.0 N B:LEU251 4.0 17.5 1.0 OD2 B:ASP244 4.2 18.3 1.0 N B:LEU245 4.2 16.9 1.0 O B:HOH1436 4.2 33.8 1.0 CA B:LEU251 4.3 17.1 1.0 OD2 B:ASP247 4.3 21.8 1.0 CB B:LEU250 4.4 19.9 1.0 CB B:ASP248 4.4 20.5 1.0 N B:ASP248 4.4 20.9 1.0 CB B:ASP247 4.6 20.0 1.0 CA B:LEU245 4.6 18.6 1.0 CA B:ASP248 4.8 18.9 1.0 N B:GLY249 4.8 18.8 1.0 N B:ASP244 4.9 16.0 1.0 O B:HOH1584 4.9 40.3 1.0 CG B:ASP247 4.9 22.9 1.0 CD2 B:LEU251 5.0 18.2 1.0

Magnesium binding site 7 out of 15 in the Exo-Beta-D-Arabinofuranosidase EXOMA2 From Microbacterium Arabinogalactanolyticum in Complex with Beta-D-Arabinofuranose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Exo-Beta-D-Arabinofuranosidase EXOMA2 From Microbacterium Arabinogalactanolyticum in Complex with Beta-D-Arabinofuranose within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg907 b:21.6 occ:1.00 OD1 B:ASP541 2.0 20.8 1.0 OD1 B:ASP545 2.1 19.9 1.0 O B:HOH1141 2.1 24.1 1.0 OD2 B:ASP549 2.1 22.9 1.0 OD1 B:ASP543 2.1 24.6 1.0 O B:LEU547 2.1 18.4 1.0 CG B:ASP545 3.0 22.9 1.0 CG B:ASP543 3.1 27.8 1.0 CG B:ASP541 3.1 21.4 1.0 CG B:ASP549 3.2 23.9 1.0 C B:LEU547 3.2 18.1 1.0 OD2 B:ASP543 3.4 28.9 1.0 OD2 B:ASP545 3.5 24.6 1.0 CB B:ASP549 3.7 20.1 1.0 N B:LEU547 3.8 18.1 1.0 CA B:LEU547 3.9 19.3 1.0 OD2 B:ASP541 3.9 23.9 1.0 N B:ASP545 4.0 26.9 1.0 CB B:ASP541 4.0 22.6 1.0 CB B:LEU547 4.0 18.3 1.0 CA B:ASP541 4.1 20.9 1.0 N B:ASP543 4.1 32.8 1.0 N B:HIS542 4.2 25.9 1.0 CB B:ASP545 4.2 24.8 1.0 OD1 B:ASP549 4.3 23.9 1.0 N B:LEU548 4.3 18.7 1.0 CB B:ASP543 4.4 29.9 1.0 N B:GLY546 4.4 21.8 1.0 N B:GLY544 4.5 29.3 1.0 N B:ASP549 4.5 18.4 1.0 CA B:ASP545 4.5 23.6 1.0 C B:ASP541 4.5 25.6 1.0 C B:LEU548 4.5 17.2 1.0 CA B:ASP543 4.6 31.3 1.0 C B:ASP543 4.6 29.9 1.0 CA B:LEU548 4.6 18.4 1.0 CA B:ASP549 4.7 19.3 1.0 C B:ASP545 4.7 22.8 1.0 C B:GLY546 4.7 19.2 1.0 O B:LEU548 5.0 17.9 1.0

Magnesium binding site 8 out of 15 in the Exo-Beta-D-Arabinofuranosidase EXOMA2 From Microbacterium Arabinogalactanolyticum in Complex with Beta-D-Arabinofuranose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Exo-Beta-D-Arabinofuranosidase EXOMA2 From Microbacterium Arabinogalactanolyticum in Complex with Beta-D-Arabinofuranose within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg908 b:33.7 occ:1.00 O B:GLU539 2.0 22.5 1.0 O B:HOH1506 2.0 30.6 1.0 NE2 B:HIS542 2.1 32.5 1.0 O B:HOH1432 2.1 34.5 1.0 O B:HOH1585 2.2 33.6 1.0 O B:HOH1609 2.3 34.9 1.0 CE1 B:HIS542 3.0 31.5 1.0 CD2 B:HIS542 3.1 27.1 1.0 C B:GLU539 3.1 22.0 1.0 CA B:GLU539 3.9 21.7 1.0 ND1 B:HIS542 4.1 28.6 1.0 CG B:HIS542 4.1 28.1 1.0 N B:TRP540 4.2 21.6 1.0 CB B:GLU539 4.3 23.5 1.0 CA B:TRP540 4.4 19.7 1.0 OE1 B:GLU539 4.4 30.4 1.0 O B:HOH1204 4.6 37.1 1.0 CD1 B:TRP540 4.7 22.0 1.0

Magnesium binding site 9 out of 15 in the Exo-Beta-D-Arabinofuranosidase EXOMA2 From Microbacterium Arabinogalactanolyticum in Complex with Beta-D-Arabinofuranose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Exo-Beta-D-Arabinofuranosidase EXOMA2 From Microbacterium Arabinogalactanolyticum in Complex with Beta-D-Arabinofuranose within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg901 b:20.7 occ:1.00 O A:HOH1461 2.0 26.2 1.0 OD1 A:ASP845 2.0 19.5 1.0 O A:HOH1171 2.1 19.8 1.0 O A:HOH1534 2.1 25.2 1.0 O A:HOH1531 2.1 23.4 1.0 CG A:ASP845 3.1 20.3 1.0 OD2 A:ASP845 3.5 19.5 1.0 O A:HOH1685 4.1 35.9 1.0 O A:LEU844 4.1 17.9 1.0 O A:HOH1297 4.2 19.0 1.0 OD2 A:ASP827 4.3 44.6 1.0 OD1 A:ASP827 4.3 31.8 1.0 C A:LEU844 4.3 20.8 1.0 CB A:ASP845 4.4 19.3 1.0 N A:ASP845 4.6 19.5 1.0 CB A:HIS843 4.6 23.5 1.0 CA A:ASP845 4.7 18.4 1.0 CG A:ASP827 4.7 27.8 1.0 N A:LEU844 4.9 20.5 1.0 CB A:ALA825 4.9 21.1 1.0 ND1 A:HIS843 4.9 33.6 1.0 O A:HOH1389 4.9 25.0 1.0

Magnesium binding site 10 out of 15 in the Exo-Beta-D-Arabinofuranosidase EXOMA2 From Microbacterium Arabinogalactanolyticum in Complex with Beta-D-Arabinofuranose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Exo-Beta-D-Arabinofuranosidase EXOMA2 From Microbacterium Arabinogalactanolyticum in Complex with Beta-D-Arabinofuranose within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg902 b:22.0 occ:1.00 OD2 A:ASP845 2.0 19.5 1.0 O A:HOH1389 2.1 25.0 1.0 O A:HOH1124 2.1 22.4 1.0 O A:HOH1585 2.1 26.4 1.0 CG A:ASP845 3.1 20.3 1.0 CB A:ASP845 3.7 19.3 1.0 O A:HOH1297 4.2 19.0 1.0 OD1 A:ASP845 4.2 19.5 1.0 OE2 A:GLU848 4.3 24.1 1.0 O A:HOH1406 4.5 31.2 1.0 CD A:GLU848 4.9 22.0 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.