Calcium in PDB 1k1y: Crystal Structure of Thermococcus Litoralis 4-Alpha-Glucanotransferase Complexed with Acarbose

All present enzymatic activity of Crystal Structure of Thermococcus Litoralis 4-Alpha-Glucanotransferase Complexed with Acarbose:
2.4.1.25;

The structure of Crystal Structure of Thermococcus Litoralis 4-Alpha-Glucanotransferase Complexed with Acarbose, PDB code: 1k1y was solved by H.Imamura, S.Fushinobu, T.Kumasaka, M.Yamamoto, B.S.Jeon, T.Wakagi, H.Matsuzawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.85 / 2.40
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	137.610, 160.968, 70.202, 90.00, 90.00, 90.00
R / Rfree (%)	19.8 / 25.6

The binding sites of Calcium atom in the Crystal Structure of Thermococcus Litoralis 4-Alpha-Glucanotransferase Complexed with Acarbose (pdb code 1k1y). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of Thermococcus Litoralis 4-Alpha-Glucanotransferase Complexed with Acarbose, PDB code: 1k1y:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of Thermococcus Litoralis 4-Alpha-Glucanotransferase Complexed with Acarbose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Thermococcus Litoralis 4-Alpha-Glucanotransferase Complexed with Acarbose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1601 b:43.8 occ:1.00 OD2 A:ASP394 2.6 33.0 1.0 OE2 A:GLU400 2.6 25.3 1.0 O A:ARG398 2.7 32.8 1.0 OD1 A:ASP392 2.7 36.5 1.0 OE1 A:GLU400 2.7 25.3 1.0 OD2 A:ASP396 2.7 58.1 1.0 CD A:GLU400 3.0 25.3 1.0 CG A:ASP396 3.1 58.1 1.0 OD1 A:ASP396 3.3 58.1 1.0 CG A:ASP392 3.5 36.5 1.0 C A:ARG398 3.5 32.8 1.0 CG A:ASP394 3.7 33.0 1.0 N A:ASP396 3.9 37.8 1.0 N A:ARG398 3.9 32.8 1.0 OD2 A:ASP392 4.1 36.5 1.0 NE2 A:HIS415 4.1 52.9 1.0 CA A:ASP392 4.1 35.5 1.0 OD1 A:ASP394 4.2 33.0 1.0 CA A:ARG398 4.2 32.8 1.0 CB A:ASP396 4.2 58.1 1.0 N A:VAL393 4.3 31.2 1.0 CE1 A:HIS415 4.3 52.9 1.0 CB A:ASP392 4.3 36.5 1.0 N A:ASP394 4.4 35.8 1.0 N A:ALA399 4.4 47.0 1.0 N A:PHE395 4.4 32.9 1.0 CA A:ASP396 4.5 37.8 1.0 C A:ASP392 4.5 35.5 1.0 CG A:GLU400 4.5 25.3 1.0 N A:GLY397 4.5 39.8 1.0 C A:ALA399 4.6 47.0 1.0 CA A:ALA399 4.6 47.0 1.0 C A:ASP396 4.7 37.8 1.0 N A:GLU400 4.7 29.1 1.0 CB A:ARG398 4.8 79.4 1.0 C A:ASP394 4.8 35.8 1.0 C A:PHE395 4.9 32.9 1.0 CB A:ASP394 4.9 33.0 1.0 CA A:ASP394 4.9 35.8 1.0 CA A:PHE395 5.0 32.9 1.0 O A:ALA399 5.0 47.0 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of Thermococcus Litoralis 4-Alpha-Glucanotransferase Complexed with Acarbose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Thermococcus Litoralis 4-Alpha-Glucanotransferase Complexed with Acarbose within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1602 b:32.5 occ:1.00 O B:ARG398 2.5 33.8 1.0 OD1 B:ASP394 2.5 42.8 1.0 OE2 B:GLU400 2.6 32.6 1.0 OD1 B:ASP396 2.7 39.4 1.0 OD1 B:ASP392 2.7 33.9 1.0 OE1 B:GLU400 2.7 32.6 1.0 CD B:GLU400 3.0 32.6 1.0 CG B:ASP396 3.2 39.4 1.0 OD2 B:ASP396 3.3 39.4 1.0 CG B:ASP394 3.5 42.8 1.0 C B:ARG398 3.5 33.8 1.0 CG B:ASP392 3.8 33.9 1.0 OD2 B:ASP394 4.0 42.8 1.0 NE2 B:HIS415 4.0 74.9 1.0 N B:ARG398 4.0 33.8 1.0 N B:ASP394 4.2 25.2 1.0 CA B:ARG398 4.2 33.8 1.0 N B:ASP396 4.3 33.1 1.0 CE1 B:HIS415 4.3 74.9 1.0 CB B:ASP396 4.3 39.4 1.0 N B:VAL393 4.4 25.8 1.0 NZ B:LYS413 4.4 45.5 1.0 CA B:ASP392 4.4 30.7 1.0 CB B:ARG398 4.5 82.7 1.0 CG B:GLU400 4.5 32.6 1.0 CB B:ASP392 4.5 33.9 1.0 N B:ALA399 4.5 31.6 1.0 C B:ALA399 4.7 31.6 1.0 CB B:ASP394 4.7 42.8 1.0 C B:ASP392 4.7 30.7 1.0 CA B:ASP394 4.7 25.2 1.0 OD2 B:ASP392 4.7 33.9 1.0 CA B:ASP396 4.7 33.1 1.0 N B:PHE395 4.8 32.4 1.0 C B:ASP394 4.8 25.2 1.0 CA B:ALA399 4.8 31.6 1.0 N B:GLY397 4.9 39.3 1.0 N B:GLU400 4.9 37.0 1.0 O B:ALA399 4.9 31.6 1.0 CD2 B:HIS415 5.0 74.9 1.0 C B:ASP396 5.0 33.1 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of Thermococcus Litoralis 4-Alpha-Glucanotransferase Complexed with Acarbose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Thermococcus Litoralis 4-Alpha-Glucanotransferase Complexed with Acarbose within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1603 b:43.8 occ:1.00 OE1 B:GLU60 2.9 49.0 1.0 CD B:GLU60 3.8 49.0 1.0 OE2 B:GLU60 4.0 49.0 1.0 O B:GLU60 4.7 56.3 1.0

H.Imamura, S.Fushinobu, M.Yamamoto, T.Kumasaka, B.S.Jeon, T.Wakagi, H.Matsuzawa. Crystal Structures of 4-Alpha-Glucanotransferase From Thermococcus Litoralis and Its Complex with An Inhibitor J.Biol.Chem. V. 278 19378 2003.
ISSN: ISSN 0021-9258
PubMed: 12618437
DOI: 10.1074/JBC.M213134200