Calcium in PDB 5yne: Crystal Structure of Pullulanase From Klebsiella Pneumoniae Complex at 10 Mm Alpha-Cyclodextrin

The structure of Crystal Structure of Pullulanase From Klebsiella Pneumoniae Complex at 10 Mm Alpha-Cyclodextrin, PDB code: 5yne was solved by N.Saka, H.Iwamoto, N.Takahashi, K.Mizutani, B.Mikami, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.75 / 2.20
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	89.210, 89.210, 299.647, 90.00, 90.00, 90.00
R / Rfree (%)	18.1 / 24.2

The binding sites of Calcium atom in the Crystal Structure of Pullulanase From Klebsiella Pneumoniae Complex at 10 Mm Alpha-Cyclodextrin (pdb code 5yne). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Crystal Structure of Pullulanase From Klebsiella Pneumoniae Complex at 10 Mm Alpha-Cyclodextrin, PDB code: 5yne:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in the Crystal Structure of Pullulanase From Klebsiella Pneumoniae Complex at 10 Mm Alpha-Cyclodextrin


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 Pullulanase From Klebsiella Pneumoniae Complex at 10 Mm Alpha-Cyclodextrin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1101 b:18.6 occ:1.00 OD1 A:ASP893 2.3 24.2 1.0 O A:TYR555 2.4 17.6 1.0 O A:ALA550 2.4 21.2 1.0 O A:HOH1382 2.5 18.9 1.0 OD1 A:ASP553 2.5 17.0 1.0 O A:HOH1313 2.5 18.9 1.0 O A:HOH1539 2.6 17.1 1.0 C A:ALA550 3.5 24.3 1.0 CG A:ASP893 3.5 20.7 1.0 CG A:ASP553 3.5 19.3 1.0 C A:TYR555 3.6 16.1 1.0 CA A:ALA550 3.9 20.8 1.0 OD2 A:ASP553 3.9 17.6 1.0 OD2 A:ASP893 4.1 19.1 1.0 N A:TYR555 4.2 16.3 1.0 CA A:TYR555 4.3 14.7 1.0 CB A:ALA550 4.3 16.9 1.0 O A:HOH1483 4.4 25.8 1.0 O A:ASP553 4.4 15.9 1.0 CB A:TYR555 4.5 15.2 1.0 O A:ASP893 4.6 15.3 1.0 N A:ASN556 4.7 15.2 1.0 N A:GLN551 4.7 23.1 1.0 N A:ASP553 4.7 22.2 1.0 O A:HOH1630 4.7 25.6 1.0 CB A:ASP893 4.7 17.7 1.0 C A:ASP553 4.8 18.1 1.0 CA A:ASP893 4.8 17.9 1.0 ND2 A:ASN556 4.8 17.6 1.0 CB A:ASP553 4.8 18.9 1.0 CB A:ASN556 4.9 17.5 1.0 O A:THR484 4.9 25.1 1.0 O A:HOH1383 5.0 25.5 1.0 C A:ASP893 5.0 19.9 1.0

Calcium binding site 2 out of 5 in the Crystal Structure of Pullulanase From Klebsiella Pneumoniae Complex at 10 Mm Alpha-Cyclodextrin


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 Pullulanase From Klebsiella Pneumoniae Complex at 10 Mm Alpha-Cyclodextrin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1102 b:17.8 occ:1.00 OE2 A:GLU487 2.3 12.2 1.0 OD1 A:ASP481 2.3 14.2 1.0 O A:LEU482 2.3 16.7 1.0 O A:HOH1290 2.3 12.4 1.0 OE2 A:GLU568 2.4 13.5 1.0 O A:HOH1426 2.5 14.3 1.0 CD A:GLU568 3.2 16.6 1.0 CD A:GLU487 3.3 18.3 1.0 OE1 A:GLU568 3.4 16.4 1.0 C A:LEU482 3.5 13.8 1.0 CG A:ASP481 3.5 14.5 1.0 N A:LEU482 3.7 13.7 1.0 CG A:GLU487 3.9 12.5 1.0 OG A:SER388 4.0 12.8 1.0 C A:ASP481 4.2 16.2 1.0 CA A:LEU482 4.2 15.0 1.0 OE1 A:GLU487 4.2 17.8 1.0 O A:HOH1346 4.2 12.1 1.0 OD2 A:ASP481 4.2 13.7 1.0 CA A:ASP481 4.3 10.7 1.0 N A:GLY569 4.4 12.5 1.0 O A:HOH1398 4.4 15.9 1.0 CB A:ASP481 4.5 12.1 1.0 CG A:LEU482 4.5 17.8 1.0 N A:ALA483 4.6 15.3 1.0 O A:VAL485 4.6 13.8 1.0 CG A:GLU568 4.7 11.6 1.0 CD1 A:LEU482 4.8 16.4 1.0 CA A:GLU568 4.8 15.1 1.0 CA A:ALA483 4.9 18.8 1.0 O A:ASP481 4.9 16.1 1.0 CB A:LEU482 4.9 11.6 1.0

Calcium binding site 3 out of 5 in the Crystal Structure of Pullulanase From Klebsiella Pneumoniae Complex at 10 Mm Alpha-Cyclodextrin


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 Pullulanase From Klebsiella Pneumoniae Complex at 10 Mm Alpha-Cyclodextrin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1103 b:46.9 occ:1.00 O A:ASP162 2.3 47.0 1.0 OD1 A:ASP148 2.4 36.0 1.0 O A:THR150 2.4 40.8 1.0 O A:HOH1209 2.6 33.9 1.0 OD2 A:ASP148 2.6 42.4 1.0 OD1 A:ASP162 2.6 52.6 1.0 CG A:ASP148 2.9 38.1 1.0 CG A:ASP162 3.4 49.6 1.0 C A:ASP162 3.4 41.0 1.0 C A:THR150 3.5 37.2 1.0 CB A:THR150 3.9 33.9 1.0 CA A:ASP162 4.0 44.0 1.0 OD2 A:ASP162 4.0 58.7 1.0 O A:HOH1579 4.0 45.3 1.0 CA A:THR150 4.1 36.8 1.0 N A:THR150 4.2 28.5 1.0 CB A:ASP162 4.3 51.0 1.0 OE1 A:GLU45 4.3 39.5 1.0 CB A:ASP148 4.4 33.0 1.0 O A:HOH1267 4.5 31.6 1.0 N A:SER163 4.5 38.5 1.0 CG2 A:THR150 4.6 31.1 1.0 N A:VAL151 4.6 33.5 1.0 CA A:SER163 4.8 43.3 1.0 CA A:VAL151 4.9 26.9 1.0 OE1 A:GLN48 5.0 39.7 1.0 OG1 A:THR150 5.0 33.5 1.0

Calcium binding site 4 out of 5 in the Crystal Structure of Pullulanase From Klebsiella Pneumoniae Complex at 10 Mm Alpha-Cyclodextrin


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 Pullulanase From Klebsiella Pneumoniae Complex at 10 Mm Alpha-Cyclodextrin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1104 b:53.4 occ:1.00 O A:HOH1201 2.2 29.3 1.0 O A:HOH1309 2.3 31.4 1.0 O A:HOH1322 2.4 28.4 1.0 O A:HOH1719 2.4 34.4 1.0 O A:HOH1239 2.4 31.1 1.0 O A:HOH1730 2.6 33.9 1.0 O A:ASN711 3.9 32.3 0.6 NE2 A:GLN712 4.1 27.6 1.0 OD2 A:ASP714 4.2 33.1 1.0 OD1 A:ASP714 4.2 29.8 1.0 OE2 A:GLU633 4.3 28.6 1.0 ND2 A:ASN711 4.3 41.3 0.4 O A:HOH1662 4.3 35.3 1.0 NE A:ARG715 4.3 25.3 1.0 OE1 A:GLU639 4.3 26.3 1.0 OE1 A:GLN712 4.4 33.0 1.0 O A:ASN711 4.5 30.6 0.4 OE2 A:GLU639 4.6 28.7 1.0 CD A:GLN712 4.6 34.0 1.0 CG A:ASP714 4.6 42.1 1.0 NH2 A:ARG715 4.7 26.4 1.0 ND2 A:ASN711 4.8 42.7 0.6 CD A:GLU639 4.9 30.1 1.0 CG A:ASN711 4.9 42.9 0.4 OE1 A:GLU633 5.0 30.3 1.0

Calcium binding site 5 out of 5 in the Crystal Structure of Pullulanase From Klebsiella Pneumoniae Complex at 10 Mm Alpha-Cyclodextrin


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 Pullulanase From Klebsiella Pneumoniae Complex at 10 Mm Alpha-Cyclodextrin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1105 b:58.3 occ:1.00 OE1 A:GLN1070 2.2 42.3 1.0 OD2 A:ASP994 2.2 24.7 1.0 O A:ASP1003 2.3 41.9 1.0 OG A:SER1001 2.4 22.0 1.0 O A:VAL1006 2.4 37.8 1.0 CD A:GLN1070 3.0 45.6 1.0 CB A:SER1001 3.1 21.9 1.0 NE2 A:GLN1070 3.2 41.7 1.0 CG A:ASP994 3.2 29.1 1.0 O A:ASP994 3.5 39.7 1.0 C A:ASP1003 3.5 36.7 1.0 C A:VAL1006 3.6 35.8 1.0 CB A:ASP994 3.8 32.3 1.0 CA A:SER1001 3.9 22.7 1.0 N A:ASP1003 4.1 31.1 1.0 OD1 A:ASP1007 4.1 35.1 1.0 OD1 A:ASP994 4.2 26.2 1.0 CA A:ASP1003 4.2 31.4 1.0 CA A:ASP1007 4.3 28.2 1.0 CG A:GLN1070 4.3 43.2 1.0 C A:SER1001 4.3 34.1 1.0 N A:ASP1007 4.3 37.0 1.0 N A:VAL1006 4.4 35.8 1.0 C A:ASP994 4.5 42.2 1.0 N A:SER1004 4.5 38.0 0.9 CB A:ASP1003 4.5 36.2 1.0 CA A:SER1004 4.6 48.6 0.9 CA A:VAL1006 4.6 36.7 1.0 O A:SER1001 4.7 44.0 1.0 C A:SER1004 4.7 42.4 0.9 N A:LEU1002 4.7 31.5 1.0 CB A:GLN1070 4.8 44.4 1.0 CA A:ASP994 4.8 37.2 1.0 CG A:ASP1007 4.9 43.8 1.0 O A:SER1004 5.0 47.9 0.9

N.Saka, H.Iwamoto, D.Malle, N.Takahashi, K.Mizutani, B.Mikami. Elucidation of the Mechanism of Interaction Between Klebsiella Pneumoniae Pullulanase and Cyclodextrin Acta Crystallogr D Struct V. 74 1115 2018BIOL.
ISSN: ISSN 2059-7983
PubMed: 30387770
DOI: 10.1107/S2059798318014523