Calcium in PDB 4ktr: Crystal Structure of 2-O-Alpha-Glucosylglycerol Phosphorylase in Complex with Isofagomine and Glycerol

The structure of Crystal Structure of 2-O-Alpha-Glucosylglycerol Phosphorylase in Complex with Isofagomine and Glycerol, PDB code: 4ktr was solved by K.K.Touhara, T.Nihira, M.Kitaoka, H.Nakai, S.Fushinobu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.99 / 2.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	109.003, 263.213, 138.793, 90.00, 105.45, 90.00
R / Rfree (%)	16.7 / 22.8

The binding sites of Calcium atom in the Crystal Structure of 2-O-Alpha-Glucosylglycerol Phosphorylase in Complex with Isofagomine and Glycerol (pdb code 4ktr). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the Crystal Structure of 2-O-Alpha-Glucosylglycerol Phosphorylase in Complex with Isofagomine and Glycerol, PDB code: 4ktr:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in the Crystal Structure of 2-O-Alpha-Glucosylglycerol Phosphorylase in Complex with Isofagomine and Glycerol


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 2-O-Alpha-Glucosylglycerol Phosphorylase in Complex with Isofagomine and Glycerol within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca813 b:44.8 occ:1.00 O F:HOH1147 2.2 35.0 1.0 OD2 F:ASP154 2.3 48.6 1.0 O A:HOH1081 2.4 53.6 1.0 OE2 A:GLU615 2.4 38.3 1.0 O A:HOH938 2.5 39.7 1.0 OE1 A:GLU615 2.5 37.1 1.0 O F:HOH1078 2.8 44.4 1.0 CD A:GLU615 2.8 34.9 1.0 CG F:ASP154 3.4 50.6 1.0 CB F:ASP154 3.9 39.5 1.0 O A:GLU615 4.2 38.7 1.0 CG A:GLU615 4.3 32.6 1.0 OD1 F:ASP87 4.4 57.9 1.0 OD1 F:ASP154 4.5 57.0 1.0 NE2 A:HIS620 4.6 32.4 1.0 O F:HOH901 4.7 23.4 1.0 C A:GLU615 4.7 39.9 1.0 CA A:PRO616 4.8 33.5 1.0 CD2 A:HIS620 4.8 30.7 1.0

Calcium binding site 2 out of 7 in the Crystal Structure of 2-O-Alpha-Glucosylglycerol Phosphorylase in Complex with Isofagomine and Glycerol


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 2-O-Alpha-Glucosylglycerol Phosphorylase in Complex with Isofagomine and Glycerol within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca809 b:43.1 occ:1.00 O B:HOH1202 2.2 43.8 1.0 OD2 D:ASP154 2.3 44.9 1.0 OE2 B:GLU615 2.5 34.2 1.0 O D:HOH1055 2.5 42.4 1.0 O B:HOH1107 2.5 43.4 1.0 OE1 B:GLU615 2.6 37.9 1.0 O D:HOH1166 2.6 38.0 1.0 CD B:GLU615 2.9 32.5 1.0 CG D:ASP154 3.4 56.7 1.0 CB D:ASP154 3.9 47.0 1.0 O B:GLU615 4.2 37.6 1.0 O B:HOH1077 4.4 53.3 1.0 CG B:GLU615 4.4 33.4 1.0 O B:HOH1155 4.5 51.8 1.0 OD1 D:ASP154 4.5 57.0 1.0 C B:GLU615 4.7 34.4 1.0 CA B:PRO616 4.8 34.6 1.0 O D:HOH937 4.8 23.8 1.0 OD1 D:ASP87 4.8 57.0 1.0 NE2 B:HIS620 4.8 31.6 1.0 N B:PRO616 5.0 36.6 1.0

Calcium binding site 3 out of 7 in the Crystal Structure of 2-O-Alpha-Glucosylglycerol Phosphorylase in Complex with Isofagomine and Glycerol


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 2-O-Alpha-Glucosylglycerol Phosphorylase in Complex with Isofagomine and Glycerol within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca810 b:36.9 occ:1.00 O A:HOH1076 2.2 45.7 1.0 OD2 A:ASP154 2.3 36.9 1.0 O C:HOH1148 2.3 40.5 1.0 OE1 C:GLU615 2.4 33.3 1.0 O C:HOH973 2.5 30.9 1.0 O A:HOH979 2.5 35.4 1.0 OE2 C:GLU615 2.7 31.8 1.0 CD C:GLU615 2.9 30.0 1.0 CG A:ASP154 3.3 40.4 1.0 CB A:ASP154 3.7 33.4 1.0 O C:HOH1041 4.2 47.1 1.0 O C:GLU615 4.2 29.8 1.0 O A:HOH1052 4.4 51.4 1.0 CG C:GLU615 4.4 26.6 1.0 OD1 A:ASP154 4.4 36.6 1.0 O C:HOH990 4.5 48.5 1.0 OD1 A:ASP87 4.6 56.6 1.0 NE2 C:HIS620 4.6 32.6 1.0 O A:HOH901 4.7 18.2 1.0 C C:GLU615 4.7 28.9 1.0 CA C:PRO616 4.7 34.3 1.0 O C:HOH947 4.8 38.9 1.0 CD2 C:HIS620 4.9 30.2 1.0 N C:PRO616 4.9 29.9 1.0

Calcium binding site 4 out of 7 in the Crystal Structure of 2-O-Alpha-Glucosylglycerol Phosphorylase in Complex with Isofagomine and Glycerol


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of 2-O-Alpha-Glucosylglycerol Phosphorylase in Complex with Isofagomine and Glycerol within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca813 b:54.0 occ:1.00 O D:HOH1176 2.2 44.7 1.0 O D:HOH1247 2.4 55.7 1.0 OE2 D:GLU213 2.4 52.1 1.0 O D:HOH1232 2.4 47.1 1.0 OD2 D:ASP214 2.5 55.9 1.0 O D:HOH1248 2.6 57.3 1.0 CG D:ASP214 3.4 49.5 1.0 CD D:GLU213 3.5 50.0 1.0 OD1 D:ASP214 3.7 44.8 1.0 OE1 D:GLU213 4.0 40.5 1.0 O D:ASP214 4.2 48.0 1.0 O D:HOH1208 4.4 60.5 1.0 N D:ASP214 4.5 36.5 1.0 CG D:GLU213 4.7 43.8 1.0 CB D:ASP214 4.8 44.3 1.0 C D:ASP214 5.0 44.4 1.0

Calcium binding site 5 out of 7 in the Crystal Structure of 2-O-Alpha-Glucosylglycerol Phosphorylase in Complex with Isofagomine and Glycerol


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of 2-O-Alpha-Glucosylglycerol Phosphorylase in Complex with Isofagomine and Glycerol within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca814 b:45.4 occ:1.00 O D:HOH1067 2.4 38.9 1.0 O D:HOH1047 2.5 45.6 1.0 OD2 H:ASP154 2.5 53.0 1.0 O D:HOH1118 2.5 41.8 1.0 OE1 D:GLU615 2.5 39.5 1.0 OE2 D:GLU615 2.7 40.4 1.0 CD D:GLU615 3.0 37.5 1.0 CG H:ASP154 3.5 52.6 1.0 CB H:ASP154 3.8 47.6 1.0 O D:GLU615 4.1 37.4 1.0 O H:HOH1117 4.4 53.7 1.0 CG D:GLU615 4.5 35.5 1.0 O D:HOH1196 4.5 53.6 1.0 O H:HOH1096 4.5 53.9 1.0 CA D:PRO616 4.5 40.6 1.0 C D:GLU615 4.6 36.0 1.0 NE2 D:HIS620 4.6 35.6 1.0 O H:HOH901 4.6 20.3 1.0 OD1 H:ASP154 4.6 57.4 1.0 OD1 H:ASP87 4.7 55.1 1.0 N D:PRO616 4.8 38.5 1.0 CD2 D:HIS620 4.9 34.1 1.0 O D:HOH1168 4.9 56.9 1.0

Calcium binding site 6 out of 7 in the Crystal Structure of 2-O-Alpha-Glucosylglycerol Phosphorylase in Complex with Isofagomine and Glycerol


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of 2-O-Alpha-Glucosylglycerol Phosphorylase in Complex with Isofagomine and Glycerol within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca808 b:54.8 occ:1.00 O E:HOH1082 2.3 45.5 1.0 O E:HOH1070 2.3 51.3 1.0 O E:HOH1002 2.4 43.8 1.0 OD2 B:ASP154 2.4 58.4 1.0 OE2 E:GLU615 2.5 39.9 1.0 OE1 E:GLU615 2.5 52.1 1.0 O B:HOH1203 2.6 49.0 1.0 CD E:GLU615 2.8 46.5 1.0 CG B:ASP154 3.5 55.7 1.0 CB B:ASP154 4.0 51.0 1.0 O E:GLU615 4.2 46.9 1.0 CG E:GLU615 4.4 41.6 1.0 CA E:PRO616 4.6 46.0 1.0 OD1 B:ASP154 4.6 58.1 1.0 C E:GLU615 4.6 46.8 1.0 NE2 E:HIS620 4.7 45.6 1.0 O B:HOH929 4.7 25.4 1.0 OD1 B:ASP87 4.7 63.6 1.0 N E:PRO616 4.8 45.6 1.0 CD2 E:HIS620 4.9 42.8 1.0 O E:HOH941 4.9 43.9 1.0

Calcium binding site 7 out of 7 in the Crystal Structure of 2-O-Alpha-Glucosylglycerol Phosphorylase in Complex with Isofagomine and Glycerol


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of 2-O-Alpha-Glucosylglycerol Phosphorylase in Complex with Isofagomine and Glycerol within 5.0Å range: probe atom residue distance (Å) B Occ G:Ca806 b:55.3 occ:1.00 OD2 C:ASP154 2.1 54.3 1.0 O G:HOH1097 2.3 55.6 1.0 O C:HOH1186 2.3 48.9 1.0 OE1 G:GLU615 2.4 48.1 1.0 OE2 G:GLU615 2.5 46.5 1.0 O G:HOH995 2.6 52.4 1.0 CD G:GLU615 2.8 49.6 1.0 CG C:ASP154 3.2 64.9 1.0 CB C:ASP154 3.7 57.0 1.0 O G:HOH1061 4.0 59.9 1.0 OD1 C:ASP154 4.2 70.0 1.0 O G:GLU615 4.3 43.9 1.0 CG G:GLU615 4.3 40.7 1.0 NH1 G:ARG644 4.6 82.4 1.0 O C:HOH907 4.7 29.2 1.0 C G:GLU615 4.7 47.4 1.0 NE2 G:HIS620 4.7 43.1 1.0 OD1 C:ASP87 4.8 63.7 1.0 CA G:PRO616 4.8 48.8 1.0 N G:PRO616 5.0 45.8 1.0

K.K.Touhara, T.Nihira, M.Kitaoka, H.Nakai, S.Fushinobu. Structural Basis For Reversible Phosphorolysis and Hydrolysis Reactions of 2-O-Alpha-Glucosylglycerol Phosphorylase J.Biol.Chem. 2014.
ISSN: ESSN 1083-351X
PubMed: 24828502
DOI: 10.1074/JBC.M114.573212