Magnesium in PDB 8ic6: Exo-Beta-D-Arabinanase EXOMA2 From Microbacterium Arabinogalactanolyticum in Complex with Tris

The structure of Exo-Beta-D-Arabinanase EXOMA2 From Microbacterium Arabinogalactanolyticum in Complex with Tris, PDB code: 8ic6 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)	48.80 / 1.75
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	66.552, 97.511, 139.978, 90, 100.55, 90
R / Rfree (%)	13.8 / 17.4

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

Chlorine

(Cl)

1 atom

Pages:

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

Binding sites:

The binding sites of Magnesium atom in the Exo-Beta-D-Arabinanase EXOMA2 From Microbacterium Arabinogalactanolyticum in Complex with Tris (pdb code 8ic6). 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-Arabinanase EXOMA2 From Microbacterium Arabinogalactanolyticum in Complex with Tris, PDB code: 8ic6:
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-Arabinanase EXOMA2 From Microbacterium Arabinogalactanolyticum in Complex with Tris


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-Arabinanase EXOMA2 From Microbacterium Arabinogalactanolyticum in Complex with Tris within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg901 b:23.4 occ:1.00 OD2 B:ASP201 2.0 20.0 1.0 O B:HOH1124 2.1 26.9 1.0 O B:HOH1557 2.1 23.0 1.0 O B:HOH1305 2.1 21.9 1.0 O B:HOH1159 2.1 19.8 1.0 O B:HOH1390 2.2 24.0 1.0 CG B:ASP201 3.1 19.2 1.0 CB B:ASP201 3.5 20.3 1.0 O B:HOH1432 4.0 38.4 1.0 OD2 B:ASP199 4.1 23.8 1.0 OD1 B:ASP201 4.2 19.7 1.0 O B:HOH1102 4.3 25.0 1.0 CG2 B:THR213 4.3 19.4 1.0 OD2 B:ASP360 4.3 25.6 1.0 OD1 B:ASP199 4.3 21.5 1.0 O B:HOH1011 4.3 31.1 1.0 NH1 B:ARG188 4.4 89.6 1.0 CG B:ASP199 4.5 21.3 1.0 O B:HOH1464 4.6 17.1 1.0 O B:PHE200 4.7 18.9 1.0 CA B:ASP201 4.7 19.6 1.0 O B:HOH1437 4.8 32.4 1.0 NH2 B:ARG188 4.9 65.1 1.0 OH B:TYR211 4.9 20.0 1.0

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


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-Arabinanase EXOMA2 From Microbacterium Arabinogalactanolyticum in Complex with Tris within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg902 b:18.0 occ:1.00 O B:HOH1620 2.0 17.8 1.0 O B:HOH1296 2.0 16.7 1.0 O B:HOH1580 2.1 19.3 1.0 NE2 B:HIS749 2.1 16.2 1.0 O B:HOH1632 2.2 23.1 1.0 O B:HOH1019 2.2 19.8 1.0 CD2 B:HIS749 3.1 17.7 1.0 CE1 B:HIS749 3.2 16.3 1.0 O B:HOH1578 3.9 21.6 1.0 OD1 B:ASP688 4.0 23.6 1.0 OD2 B:ASP688 4.1 21.6 1.0 CG B:HIS749 4.3 16.4 1.0 O B:HOH1746 4.3 30.1 1.0 ND1 B:HIS749 4.3 16.1 1.0 O B:HOH1547 4.4 22.4 1.0 O A:HOH1776 4.4 18.6 1.0 O B:HOH1182 4.4 20.7 1.0 CG B:ASP688 4.5 22.0 1.0 O B:HOH1542 4.5 37.4 1.0 O B:HOH1220 4.5 28.8 1.0 CB B:ALA748 4.7 17.4 1.0

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


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-Arabinanase EXOMA2 From Microbacterium Arabinogalactanolyticum in Complex with Tris within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg903 b:22.9 occ:1.00 OD1 B:ASP541 2.0 21.9 1.0 OD1 B:ASP545 2.0 21.2 1.0 OD2 B:ASP549 2.0 24.2 1.0 O B:LEU547 2.0 22.2 1.0 OD1 B:ASP543 2.1 27.8 1.0 O B:HOH1056 2.1 24.6 1.0 CG B:ASP545 2.9 24.1 1.0 CG B:ASP543 3.0 27.9 1.0 CG B:ASP541 3.1 23.1 1.0 CG B:ASP549 3.1 23.6 1.0 C B:LEU547 3.2 23.9 1.0 OD2 B:ASP543 3.3 32.0 1.0 OD2 B:ASP545 3.3 21.2 1.0 CB B:ASP549 3.7 21.8 1.0 N B:LEU547 3.7 22.0 1.0 CA B:LEU547 3.8 23.3 1.0 OD2 B:ASP541 3.9 27.9 1.0 N B:ASP545 4.0 26.7 1.0 CB B:ASP541 4.0 22.4 1.0 CB B:LEU547 4.0 21.8 1.0 N B:ASP543 4.1 31.5 1.0 CA B:ASP541 4.1 24.9 1.0 CB B:ASP545 4.2 24.5 1.0 OD1 B:ASP549 4.3 24.5 1.0 CB B:ASP543 4.3 30.0 1.0 N B:LEU548 4.3 22.1 1.0 N B:HIS542 4.3 26.8 1.0 N B:ASP549 4.4 18.5 1.0 N B:GLY544 4.5 32.2 1.0 N B:GLY546 4.5 22.6 1.0 CA B:ASP545 4.5 22.9 1.0 C B:ASP541 4.5 26.7 1.0 C B:LEU548 4.5 17.6 1.0 CA B:ASP543 4.5 31.5 1.0 C B:ASP543 4.6 29.8 1.0 CA B:LEU548 4.6 19.9 1.0 C B:ASP545 4.7 22.8 1.0 CA B:ASP549 4.7 21.3 1.0 C B:GLY546 4.7 23.3 1.0 O B:LEU548 4.9 22.8 1.0

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


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-Arabinanase EXOMA2 From Microbacterium Arabinogalactanolyticum in Complex with Tris within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg904 b:18.2 occ:1.00 O B:LEU250 2.0 20.2 1.0 OD1 B:ASP248 2.0 22.0 1.0 O B:ASP244 2.0 19.1 1.0 OD1 B:ASP244 2.0 18.4 1.0 O B:HOH1170 2.1 22.3 1.0 O B:HOH1156 2.1 22.9 1.0 C B:ASP244 3.0 21.1 1.0 CG B:ASP248 3.0 24.6 1.0 C B:LEU250 3.0 18.6 1.0 CG B:ASP244 3.2 16.7 1.0 OD2 B:ASP248 3.3 21.4 1.0 CA B:ASP244 3.5 18.1 1.0 N B:LEU250 3.9 20.9 1.0 CB B:ASP244 3.9 17.9 1.0 CA B:LEU250 3.9 19.8 1.0 N B:LEU251 4.0 18.5 1.0 O B:HOH1326 4.1 37.0 1.0 N B:LEU245 4.1 17.7 1.0 OD2 B:ASP244 4.1 21.1 1.0 CB B:LEU250 4.2 20.7 1.0 OD2 B:ASP247 4.2 29.0 1.0 CA B:LEU251 4.3 20.1 1.0 CB B:ASP248 4.4 22.9 1.0 N B:ASP248 4.4 24.9 1.0 CB B:ASP247 4.5 24.9 1.0 CA B:LEU245 4.6 19.7 1.0 O B:HOH1622 4.6 39.7 1.0 O B:HOH1768 4.6 45.5 1.0 CA B:ASP248 4.8 22.6 1.0 N B:GLY249 4.9 22.8 1.0 CG B:ASP247 4.9 29.1 1.0 N B:ASP244 4.9 20.2 1.0 C B:ASP248 5.0 24.7 1.0 C B:LEU245 5.0 22.0 1.0 C B:LEU251 5.0 22.5 1.0

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


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-Arabinanase EXOMA2 From Microbacterium Arabinogalactanolyticum in Complex with Tris within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg905 b:34.0 occ:1.00 O B:HOH1213 1.9 28.5 1.0 O B:HOH1184 2.1 27.4 1.0 O B:HOH1498 2.1 33.8 1.0 O B:HOH1775 2.1 32.1 1.0 NE2 B:HIS436 2.2 21.7 1.0 O B:HOH1576 2.3 46.5 1.0 CE1 B:HIS436 3.1 23.9 1.0 CD2 B:HIS436 3.2 21.1 1.0 O B:LYS46 4.0 17.8 1.0 O B:HOH1690 4.1 43.9 1.0 OD2 B:ASP435 4.2 17.8 1.0 CB B:ASP435 4.3 16.0 1.0 ND1 B:HIS436 4.3 24.0 1.0 CG B:HIS436 4.3 20.7 1.0 CG B:ASP435 4.6 17.9 1.0 O B:HOH1703 4.6 36.0 1.0

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


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-Arabinanase EXOMA2 From Microbacterium Arabinogalactanolyticum in Complex with Tris within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg906 b:33.2 occ:1.00 O B:HOH1664 2.0 37.7 1.0 O B:HOH1132 2.1 34.4 1.0 O B:HOH1050 2.1 30.1 1.0 O B:ASP688 4.0 20.3 1.0 O B:GLY672 4.1 20.1 1.0 OD1 B:ASP673 4.3 20.4 1.0 O B:HOH1101 4.3 27.1 1.0 CB B:ASP673 4.7 16.1 1.0 O B:HOH1122 5.0 34.8 1.0 C B:GLY672 5.0 19.2 1.0

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


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-Arabinanase EXOMA2 From Microbacterium Arabinogalactanolyticum in Complex with Tris within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg907 b:38.2 occ:1.00 O B:GLU539 2.0 27.1 1.0 O B:HOH1541 2.1 30.3 1.0 NE2 B:HIS542 2.1 33.7 1.0 O B:HOH1609 2.1 37.7 1.0 O B:HOH1555 2.2 38.5 1.0 O B:HOH1035 2.2 36.9 1.0 CE1 B:HIS542 3.1 32.7 1.0 CD2 B:HIS542 3.1 30.2 1.0 C B:GLU539 3.2 27.0 1.0 CA B:GLU539 3.8 23.8 1.0 O B:HOH1089 4.0 40.2 1.0 ND1 B:HIS542 4.2 32.3 1.0 CG B:HIS542 4.2 30.6 1.0 OE1 B:GLU539 4.2 31.0 1.0 N B:TRP540 4.2 21.3 1.0 CB B:GLU539 4.3 24.0 1.0 CA B:TRP540 4.4 23.3 1.0 O B:HOH1171 4.6 38.1 1.0 CD1 B:TRP540 4.8 25.1 1.0

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


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-Arabinanase EXOMA2 From Microbacterium Arabinogalactanolyticum in Complex with Tris within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg908 b:40.2 occ:1.00 OD1 B:ASP814 2.0 35.1 1.0 O B:HOH1468 2.1 34.5 1.0 O B:HOH1537 2.1 33.1 1.0 O B:HOH1211 2.2 27.5 1.0 CG B:ASP814 3.2 40.0 1.0 OD2 B:ASP814 3.9 32.8 1.0 O B:HOH1691 4.0 50.2 1.0 N B:ASP814 4.1 36.1 1.0 OD1 B:ASP815 4.1 41.4 1.0 OD1 B:ASP796 4.2 37.5 1.0 CB B:ASP814 4.4 39.1 1.0 OD2 B:ASP796 4.4 33.0 1.0 O B:HOH1751 4.6 49.2 1.0 CG B:ASP815 4.6 37.3 1.0 N B:ASP815 4.6 35.9 1.0 CG B:ASP796 4.7 30.4 1.0 CA B:ASP814 4.8 42.4 1.0 CA B:GLY813 5.0 34.5 1.0

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


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-Arabinanase EXOMA2 From Microbacterium Arabinogalactanolyticum in Complex with Tris within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg901 b:19.3 occ:1.00 OD2 A:ASP201 2.0 16.5 1.0 O A:HOH1153 2.0 18.3 1.0 O A:HOH1551 2.1 19.7 1.0 O A:HOH1370 2.1 17.6 1.0 O A:HOH1639 2.1 17.0 1.0 O A:HOH1040 2.2 18.7 1.0 CG A:ASP201 3.2 19.8 1.0 CB A:ASP201 3.7 19.0 1.0 OD2 A:ASP199 4.0 22.7 1.0 O A:HOH1692 4.1 36.5 1.0 OD1 A:ASP199 4.1 19.2 1.0 OD1 A:ASP201 4.2 16.8 1.0 O A:HOH1207 4.3 19.0 1.0 OD2 A:ASP360 4.3 19.7 1.0 CG A:ASP199 4.3 22.2 1.0 CG2 A:THR213 4.3 19.8 1.0 O A:PHE200 4.6 18.8 1.0 O A:HOH1161 4.6 27.6 1.0 OH A:TYR211 4.8 18.2 1.0 CA A:ASP201 4.8 18.0 1.0 NH1 A:ARG188 4.8 28.9 1.0

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


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-Arabinanase EXOMA2 From Microbacterium Arabinogalactanolyticum in Complex with Tris within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg902 b:21.0 occ:1.00 O A:HOH1536 2.0 23.0 1.0 O A:HOH1494 2.1 20.3 1.0 O A:HOH1653 2.1 20.4 1.0 O A:HOH1667 2.1 21.2 1.0 O A:HOH1238 2.1 23.9 1.0 NE2 A:HIS749 2.2 17.5 1.0 CD2 A:HIS749 3.2 16.5 1.0 CE1 A:HIS749 3.2 19.1 1.0 O A:HOH1527 3.8 22.1 1.0 OD2 A:ASP688 4.2 27.4 1.0 OD1 A:ASP688 4.2 25.7 1.0 O A:HOH1834 4.2 26.7 1.0 O A:HOH1330 4.3 23.0 1.0 O A:HOH1747 4.3 30.6 1.0 ND1 A:HIS749 4.3 17.0 1.0 O A:HOH1457 4.3 30.7 1.0 CG A:HIS749 4.3 16.1 1.0 O B:HOH1723 4.3 19.9 1.0 O A:HOH1698 4.3 30.0 1.0 CG A:ASP688 4.6 24.7 1.0 O A:HOH1264 4.8 18.0 1.0 CB A:ALA748 4.8 18.7 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.