Calcium in PDB 5h06: Crystal Structure of Amyp in Complex with Maltose

The structure of Crystal Structure of Amyp in Complex with Maltose, PDB code: 5h06 was solved by C.He, Y.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.94 / 1.95
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	79.870, 130.532, 217.530, 90.00, 90.00, 90.00
R / Rfree (%)	16.4 / 21.2

The binding sites of Calcium atom in the Crystal Structure of Amyp in Complex with Maltose (pdb code 5h06). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Crystal Structure of Amyp in Complex with Maltose, PDB code: 5h06:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in the Crystal Structure of Amyp in Complex with Maltose


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 Amyp in Complex with Maltose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca702 b:28.9 occ:1.00 OD1 A:ASN25 2.3 9.8 1.0 OD2 A:ASP44 2.4 11.6 1.0 O A:ILE30 2.4 9.9 1.0 O A:LYS42 2.5 10.2 1.0 O A:ASP27 2.5 15.9 1.0 CG A:ASN25 3.4 11.9 1.0 C A:ASP27 3.4 11.9 1.0 CG A:ASP44 3.4 12.1 1.0 C A:ILE30 3.5 17.4 1.0 C A:LYS42 3.6 12.8 1.0 CB A:LYS42 3.7 13.1 1.0 N A:ASP27 3.9 12.0 1.0 CB A:ASP44 4.0 5.7 1.0 CG1 A:ILE30 4.0 12.7 1.0 CA A:ASN25 4.0 12.1 1.0 CA A:LYS42 4.1 11.4 1.0 CB A:ASN25 4.1 10.3 1.0 N A:ASP28 4.2 9.0 1.0 CA A:ASP27 4.2 9.5 1.0 CA A:ASP28 4.2 11.9 1.0 C A:ASN25 4.3 8.8 1.0 CA A:GLY31 4.3 14.3 1.0 N A:ILE30 4.3 17.6 1.0 N A:GLY31 4.4 11.6 1.0 N A:GLY26 4.4 8.8 1.0 ND2 A:ASN25 4.4 13.4 1.0 OD1 A:ASP44 4.4 11.1 1.0 CE A:LYS42 4.4 18.2 1.0 CA A:ILE30 4.4 13.2 1.0 CB A:ASP27 4.7 12.2 1.0 C A:ASP28 4.7 17.3 1.0 N A:GLY43 4.7 5.4 1.0 C A:GLY43 4.7 9.3 1.0 CG A:LYS42 4.8 13.1 1.0 N A:ASP44 4.8 9.1 1.0 CB A:ILE30 4.9 9.9 1.0 O A:GLY43 5.0 9.2 1.0 CA A:GLY43 5.0 5.0 1.0 O A:ASN25 5.0 12.6 1.0

Calcium binding site 2 out of 8 in the Crystal Structure of Amyp in Complex with Maltose


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 Amyp in Complex with Maltose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca703 b:10.6 occ:1.00 OE1 A:GLU347 2.3 11.2 1.0 O A:LEU348 2.3 10.3 1.0 OE1 A:GLN306 2.3 8.7 1.0 OD1 A:ASP303 2.3 8.7 1.0 O A:TYR351 2.3 7.5 1.0 O A:HOH1039 2.3 10.4 1.0 C A:LEU348 3.3 9.6 1.0 CD A:GLN306 3.4 10.6 1.0 CD A:GLU347 3.5 14.7 1.0 C A:TYR351 3.5 8.6 1.0 CG A:ASP303 3.5 9.1 1.0 N A:LEU348 3.7 8.9 1.0 NE2 A:GLN306 3.9 9.9 1.0 N A:TYR351 4.0 9.1 1.0 CB A:GLU347 4.0 7.8 1.0 CA A:LEU348 4.1 11.8 1.0 C A:GLU347 4.2 10.4 1.0 N A:GLU349 4.2 14.3 1.0 CA A:TYR351 4.2 12.9 1.0 O A:HOH1086 4.2 33.6 1.0 OD2 A:ASP303 4.3 7.4 1.0 CG A:GLU347 4.3 10.4 1.0 O A:HOH1277 4.4 24.3 1.0 OE2 A:GLU347 4.4 15.8 1.0 CA A:GLU349 4.4 12.6 1.0 CB A:ASP303 4.5 6.8 1.0 N A:ALA352 4.6 7.6 1.0 CB A:TYR351 4.6 8.5 1.0 N A:GLY350 4.6 10.4 1.0 CA A:GLU347 4.6 10.1 1.0 CB A:LEU348 4.6 7.1 1.0 CA A:ASP303 4.7 6.5 1.0 CG A:GLN306 4.7 9.5 1.0 C A:GLU349 4.7 14.6 1.0 CB A:ALA352 4.7 7.8 1.0 CA A:ALA352 4.7 10.6 1.0 CD2 A:TYR351 4.8 8.4 1.0 O A:GLU347 4.8 9.2 1.0 O A:HOH1007 4.8 21.2 1.0 CB A:GLN306 5.0 8.2 1.0

Calcium binding site 3 out of 8 in the Crystal Structure of Amyp in Complex with Maltose


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 Amyp in Complex with Maltose within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca702 b:24.5 occ:1.00 OD2 B:ASP44 2.3 11.6 1.0 O B:ILE30 2.4 13.3 1.0 OD1 B:ASN25 2.4 13.0 1.0 O B:LYS42 2.5 12.1 1.0 O B:ASP27 2.5 14.0 1.0 CG B:ASP44 3.3 14.5 1.0 C B:ASP27 3.3 15.1 1.0 CG B:ASN25 3.4 14.9 1.0 C B:ILE30 3.5 16.5 1.0 C B:LYS42 3.6 12.1 1.0 N B:ASP27 3.8 11.7 1.0 CB B:ASP44 3.8 12.7 1.0 CB B:LYS42 3.8 12.7 1.0 CG1 B:ILE30 3.9 13.9 1.0 CA B:ASN25 4.0 13.3 1.0 CA B:ASP27 4.1 13.2 1.0 CB B:ASN25 4.1 11.9 1.0 CA B:LYS42 4.2 12.9 1.0 N B:ASP28 4.2 11.4 1.0 N B:ILE30 4.3 15.4 1.0 CA B:ASP28 4.3 17.1 1.0 N B:GLY26 4.3 15.9 1.0 CA B:GLY31 4.3 16.5 1.0 ND2 B:ASN25 4.3 17.1 1.0 C B:ASN25 4.3 15.1 1.0 N B:GLY31 4.3 13.9 1.0 OD1 B:ASP44 4.4 10.3 1.0 CA B:ILE30 4.4 13.4 1.0 CB B:ASP27 4.5 10.9 1.0 CE B:LYS42 4.6 18.4 1.0 C B:ASP28 4.7 15.7 1.0 C B:GLY43 4.7 7.5 1.0 N B:GLY43 4.7 6.9 1.0 CB B:ILE30 4.8 12.7 1.0 N B:ASP44 4.8 11.7 1.0 O B:GLY43 4.8 8.4 1.0 CD1 B:ILE30 4.9 11.2 1.0 CA B:ASP44 4.9 9.2 1.0 CG B:LYS42 5.0 17.9 1.0 CA B:GLY43 5.0 7.3 1.0 C B:GLY26 5.0 15.3 1.0

Calcium binding site 4 out of 8 in the Crystal Structure of Amyp in Complex with Maltose


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 Amyp in Complex with Maltose within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca703 b:10.0 occ:1.00 OE1 B:GLN306 2.2 10.2 1.0 OD1 B:ASP303 2.3 9.0 1.0 OE1 B:GLU347 2.3 13.8 1.0 O B:LEU348 2.3 8.1 1.0 O B:TYR351 2.3 9.4 1.0 O B:HOH1172 2.4 11.4 1.0 C B:LEU348 3.3 12.2 1.0 CD B:GLN306 3.3 14.4 1.0 C B:TYR351 3.5 9.5 1.0 CG B:ASP303 3.5 6.1 1.0 CD B:GLU347 3.5 19.8 1.0 N B:LEU348 3.8 9.8 1.0 NE2 B:GLN306 3.8 14.7 1.0 N B:TYR351 3.9 11.3 1.0 CB B:GLU347 3.9 12.5 1.0 CA B:LEU348 4.1 11.1 1.0 C B:GLU347 4.2 10.5 1.0 OD2 B:ASP303 4.2 10.1 1.0 CA B:TYR351 4.2 14.9 1.0 N B:GLU349 4.2 14.3 1.0 CG B:GLU347 4.3 7.5 1.0 O B:HOH1184 4.3 27.4 1.0 CA B:GLU349 4.4 13.9 1.0 OE2 B:GLU347 4.5 16.1 1.0 N B:ALA352 4.6 6.8 1.0 CB B:ASP303 4.6 9.0 1.0 N B:GLY350 4.6 11.9 1.0 O B:HOH1278 4.6 27.3 1.0 CB B:TYR351 4.6 8.7 1.0 CA B:GLU347 4.6 10.6 1.0 CG B:GLN306 4.6 10.7 1.0 C B:GLU349 4.7 11.2 1.0 CA B:ASP303 4.7 6.7 1.0 CB B:LEU348 4.7 7.8 1.0 O B:GLU347 4.8 13.5 1.0 O B:HOH883 4.8 21.5 1.0 CD2 B:TYR351 4.8 8.5 1.0 CA B:ALA352 4.8 12.0 1.0 CB B:ALA352 4.9 10.2 1.0 CB B:GLN306 4.9 9.7 1.0

Calcium binding site 5 out of 8 in the Crystal Structure of Amyp in Complex with Maltose


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 Amyp in Complex with Maltose within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca702 b:32.2 occ:1.00 OD2 C:ASP44 2.3 13.2 1.0 OD1 C:ASN25 2.3 10.1 1.0 O C:ILE30 2.4 11.6 1.0 O C:ASP27 2.5 12.5 1.0 O C:LYS42 2.5 10.5 1.0 C C:ASP27 3.3 16.8 1.0 CG C:ASP44 3.3 14.5 1.0 CG C:ASN25 3.4 13.0 1.0 C C:ILE30 3.5 18.2 1.0 C C:LYS42 3.7 10.3 1.0 N C:ASP27 3.7 18.0 1.0 CB C:LYS42 3.9 12.6 1.0 CB C:ASP44 3.9 10.0 1.0 CG1 C:ILE30 4.0 13.7 1.0 CA C:ASN25 4.0 15.9 1.0 CA C:ASP27 4.0 20.6 1.0 N C:ASP28 4.1 17.7 1.0 CB C:ASN25 4.1 13.7 1.0 CA C:ASP28 4.2 14.6 1.0 N C:ILE30 4.3 14.3 1.0 CA C:LYS42 4.3 12.0 1.0 C C:ASN25 4.3 15.2 1.0 OD1 C:ASP44 4.3 14.3 1.0 N C:GLY26 4.3 12.5 1.0 N C:GLY31 4.3 13.5 1.0 ND2 C:ASN25 4.3 11.0 1.0 CA C:ILE30 4.4 16.0 1.0 CA C:GLY31 4.4 13.5 1.0 CB C:ASP27 4.5 14.5 1.0 C C:ASP28 4.6 14.7 1.0 CE C:LYS42 4.7 17.1 1.0 C C:GLY43 4.7 10.6 1.0 N C:GLY43 4.8 9.6 1.0 CB C:ILE30 4.8 12.3 1.0 N C:ASP44 4.8 11.8 1.0 C C:GLY26 4.9 21.1 1.0 N C:ALA29 4.9 15.5 1.0 O C:ASN25 5.0 13.8 1.0 O C:GLY43 5.0 11.1 1.0 CG C:LYS42 5.0 11.4 1.0 CD1 C:ILE30 5.0 12.2 1.0

Calcium binding site 6 out of 8 in the Crystal Structure of Amyp in Complex with Maltose


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 Amyp in Complex with Maltose within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca703 b:12.2 occ:1.00 OE1 C:GLU347 2.2 13.1 1.0 O C:TYR351 2.3 11.9 1.0 OD1 C:ASP303 2.3 9.2 1.0 O C:HOH1107 2.3 12.9 1.0 O C:LEU348 2.4 14.2 1.0 OE1 C:GLN306 2.4 11.3 1.0 C C:LEU348 3.4 13.2 1.0 CD C:GLN306 3.4 14.8 1.0 CD C:GLU347 3.4 14.9 1.0 C C:TYR351 3.5 10.1 1.0 CG C:ASP303 3.5 9.3 1.0 N C:LEU348 3.7 8.2 1.0 NE2 C:GLN306 3.9 11.1 1.0 N C:TYR351 3.9 13.7 1.0 CB C:GLU347 4.0 11.5 1.0 CA C:LEU348 4.1 9.1 1.0 CG C:GLU347 4.2 13.2 1.0 CA C:TYR351 4.2 10.9 1.0 C C:GLU347 4.3 14.0 1.0 O C:HOH1238 4.3 27.5 1.0 OD2 C:ASP303 4.3 7.2 1.0 N C:GLU349 4.3 18.9 1.0 OE2 C:GLU347 4.4 15.1 1.0 CA C:GLU349 4.5 17.5 1.0 N C:ALA352 4.5 10.2 1.0 CB C:ASP303 4.5 5.2 1.0 CB C:ALA352 4.6 9.7 1.0 CB C:TYR351 4.6 9.0 1.0 CA C:ASP303 4.6 7.7 1.0 N C:GLY350 4.6 13.2 1.0 CA C:GLU347 4.7 9.0 1.0 CA C:ALA352 4.7 6.9 1.0 CB C:LEU348 4.7 10.8 1.0 CG C:GLN306 4.7 15.5 1.0 C C:GLU349 4.8 13.6 1.0 CD2 C:TYR351 4.8 7.0 1.0 O C:HOH1068 4.8 25.1 1.0 O C:HOH815 4.8 27.8 1.0 O C:GLU347 4.9 12.7 1.0 CB C:GLN306 4.9 12.8 1.0

Calcium binding site 7 out of 8 in the Crystal Structure of Amyp in Complex with Maltose


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 Amyp in Complex with Maltose within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca702 b:27.6 occ:1.00 OD2 D:ASP44 2.3 14.8 1.0 O D:ILE30 2.4 14.2 1.0 OD1 D:ASN25 2.4 10.5 1.0 O D:LYS42 2.5 12.0 1.0 O D:ASP27 2.5 14.8 1.0 CG D:ASP44 3.3 12.2 1.0 C D:ASP27 3.3 15.0 1.0 C D:ILE30 3.4 16.1 1.0 CG D:ASN25 3.5 11.7 1.0 C D:LYS42 3.6 12.6 1.0 CG1 D:ILE30 3.8 12.7 1.0 CB D:ASP44 3.8 10.1 1.0 N D:ASP27 3.8 14.4 1.0 CB D:LYS42 3.9 10.3 1.0 CA D:ASN25 4.1 10.2 1.0 CA D:ASP27 4.1 9.6 1.0 N D:ASP28 4.1 14.2 1.0 CB D:ASN25 4.2 10.2 1.0 CA D:LYS42 4.2 11.6 1.0 CA D:ASP28 4.2 14.8 1.0 N D:ILE30 4.3 11.7 1.0 N D:GLY31 4.3 12.6 1.0 CA D:GLY31 4.3 14.7 1.0 N D:GLY26 4.3 9.2 1.0 CA D:ILE30 4.3 11.1 1.0 C D:ASN25 4.3 14.1 1.0 OD1 D:ASP44 4.3 12.2 1.0 ND2 D:ASN25 4.4 12.8 1.0 CB D:ASP27 4.6 9.6 1.0 CE D:LYS42 4.6 20.7 1.0 C D:GLY43 4.7 10.3 1.0 CB D:ILE30 4.7 18.9 1.0 N D:GLY43 4.7 6.9 1.0 C D:ASP28 4.7 15.8 1.0 CD1 D:ILE30 4.7 19.1 1.0 N D:ASP44 4.7 9.0 1.0 O D:GLY43 4.9 7.5 1.0 CA D:ASP44 4.9 9.6 1.0 CA D:GLY43 4.9 9.3 1.0 C D:GLY26 5.0 17.5 1.0 CG D:LYS42 5.0 16.1 1.0

Calcium binding site 8 out of 8 in the Crystal Structure of Amyp in Complex with Maltose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of Amyp in Complex with Maltose within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca703 b:10.9 occ:1.00 OE1 D:GLU347 2.3 12.8 1.0 O D:TYR351 2.3 7.8 1.0 OD1 D:ASP303 2.3 8.1 1.0 OE1 D:GLN306 2.3 14.5 1.0 O D:LEU348 2.4 8.7 1.0 O D:HOH1175 2.4 12.2 1.0 C D:LEU348 3.3 10.7 1.0 CD D:GLN306 3.4 13.2 1.0 C D:TYR351 3.5 11.3 1.0 CD D:GLU347 3.5 13.7 1.0 CG D:ASP303 3.5 7.6 1.0 N D:LEU348 3.7 9.7 1.0 NE2 D:GLN306 3.9 12.8 1.0 N D:TYR351 4.0 14.0 1.0 CB D:GLU347 4.0 11.4 1.0 CA D:LEU348 4.1 8.3 1.0 CA D:TYR351 4.2 13.9 1.0 C D:GLU347 4.2 17.6 1.0 OD2 D:ASP303 4.3 10.1 1.0 N D:GLU349 4.3 9.0 1.0 CG D:GLU347 4.3 11.2 1.0 OE2 D:GLU347 4.4 18.6 1.0 O D:HOH864 4.4 27.4 1.0 N D:ALA352 4.5 8.3 1.0 CA D:GLU349 4.5 14.2 1.0 CB D:ASP303 4.5 10.1 1.0 CB D:TYR351 4.6 9.4 1.0 CB D:ALA352 4.6 7.3 1.0 CB D:LEU348 4.6 11.5 1.0 CA D:GLU347 4.6 10.1 1.0 O D:HOH935 4.6 29.2 1.0 CA D:ASP303 4.7 7.2 1.0 CA D:ALA352 4.7 7.9 1.0 N D:GLY350 4.7 14.7 1.0 C D:GLU349 4.7 12.9 1.0 CG D:GLN306 4.7 10.7 1.0 CD2 D:TYR351 4.7 8.8 1.0 O D:GLU347 4.8 10.3 1.0 CB D:GLN306 5.0 9.1 1.0

Y.Liu, J.Yu, F.Li, H.Peng, X.Zhang, Y.Xiao, C.He. Crystal Structure of A Raw-Starch-Degrading Bacterial Alpha-Amylase Belonging to Subfamily 37 of the Glycoside Hydrolase Family GH13 Sci Rep V. 7 44067 2017.
ISSN: ESSN 2045-2322
PubMed: 28303907
DOI: 10.1038/SREP44067