Calcium in PDB 5yn7: Crystal Structure of Pullulanase From Klebsiella Pneumoniae Complex at 0.1 Mm Beta-Cyclodextrin

The structure of Crystal Structure of Pullulanase From Klebsiella Pneumoniae Complex at 0.1 Mm Beta-Cyclodextrin, PDB code: 5yn7 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)	48.41 / 2.59
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	89.283, 89.283, 301.706, 90.00, 90.00, 90.00
R / Rfree (%)	19.1 / 25.3

The binding sites of Calcium atom in the Crystal Structure of Pullulanase From Klebsiella Pneumoniae Complex at 0.1 Mm Beta-Cyclodextrin (pdb code 5yn7). 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 0.1 Mm Beta-Cyclodextrin, PDB code: 5yn7:
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 0.1 Mm Beta-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 0.1 Mm Beta-Cyclodextrin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1101 b:32.1 occ:1.00 O A:HOH1330 2.4 32.2 1.0 O A:HOH1255 2.4 33.6 1.0 O A:TYR555 2.4 36.5 1.0 OD1 A:ASP893 2.4 34.9 1.0 O A:HOH1385 2.5 31.5 1.0 O A:ALA550 2.5 35.2 1.0 OD1 A:ASP553 2.5 37.7 1.0 C A:ALA550 3.5 40.2 1.0 CG A:ASP553 3.5 34.5 1.0 C A:TYR555 3.6 35.5 1.0 CG A:ASP893 3.7 41.4 1.0 CA A:ALA550 3.8 37.3 1.0 OD2 A:ASP553 3.8 38.3 1.0 N A:TYR555 4.1 32.6 1.0 CA A:TYR555 4.2 36.6 1.0 CB A:ALA550 4.3 28.7 1.0 OD2 A:ASP893 4.3 36.5 1.0 CB A:TYR555 4.3 35.0 1.0 O A:ASP553 4.4 28.1 1.0 O A:HOH1377 4.4 32.8 1.0 O A:ASP893 4.6 39.2 1.0 N A:ASN556 4.7 39.5 1.0 N A:GLN551 4.7 39.9 1.0 N A:ASP553 4.7 34.1 1.0 C A:ASP553 4.7 36.0 1.0 CA A:ASP893 4.8 39.3 1.0 ND2 A:ASN556 4.8 33.6 1.0 CB A:ASP893 4.8 33.1 1.0 CB A:ASP553 4.8 35.1 1.0 CB A:ASN556 4.9 38.3 1.0 O A:HOH1328 4.9 40.6 1.0 C A:ASP893 5.0 42.0 1.0 CA A:ASN556 5.0 41.5 1.0

Calcium binding site 2 out of 5 in the Crystal Structure of Pullulanase From Klebsiella Pneumoniae Complex at 0.1 Mm Beta-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 0.1 Mm Beta-Cyclodextrin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1102 b:35.8 occ:1.00 OD1 A:ASP481 2.2 29.3 1.0 O A:HOH1232 2.3 35.4 1.0 O A:LEU482 2.4 33.7 1.0 OE2 A:GLU568 2.4 39.1 1.0 OE2 A:GLU487 2.5 37.5 1.0 O A:HOH1380 2.7 34.0 1.0 CD A:GLU568 3.2 38.5 1.0 OE1 A:GLU568 3.3 37.4 1.0 CD A:GLU487 3.4 39.4 1.0 CG A:ASP481 3.4 35.3 1.0 C A:LEU482 3.5 34.0 1.0 N A:LEU482 3.5 30.3 1.0 CG A:GLU487 4.0 36.3 1.0 C A:ASP481 4.0 34.5 1.0 CA A:LEU482 4.1 32.4 1.0 OG A:SER388 4.2 42.6 1.0 CA A:ASP481 4.2 37.5 1.0 OD2 A:ASP481 4.2 38.7 1.0 O A:HOH1275 4.3 32.7 1.0 N A:GLY569 4.3 34.3 1.0 OE1 A:GLU487 4.3 40.2 1.0 CG A:LEU482 4.4 34.9 1.0 CB A:ASP481 4.4 29.3 1.0 CD1 A:LEU482 4.4 38.4 1.0 O A:HOH1215 4.5 34.4 1.0 CG A:GLU568 4.6 28.2 1.0 N A:ALA483 4.6 35.5 1.0 O A:VAL485 4.6 38.9 1.0 CA A:GLU568 4.7 30.7 1.0 O A:ASP481 4.8 38.6 1.0 CB A:LEU482 4.8 34.7 1.0 CA A:ALA483 4.9 33.7 1.0 CB A:GLU568 5.0 30.4 1.0

Calcium binding site 3 out of 5 in the Crystal Structure of Pullulanase From Klebsiella Pneumoniae Complex at 0.1 Mm Beta-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 0.1 Mm Beta-Cyclodextrin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1103 b:51.5 occ:1.00 O A:HOH1245 2.3 35.4 1.0 O A:HOH1408 2.3 39.6 1.0 O A:HOH1324 2.4 35.3 1.0 O A:HOH1260 2.4 36.8 1.0 O A:HOH1211 2.4 44.3 1.0 OE1 A:GLU639 3.9 35.9 1.0 OE2 A:GLU639 4.1 41.9 1.0 NE A:ARG715 4.2 41.5 1.0 OE1 A:GLN712 4.3 39.7 1.0 NE2 A:GLN712 4.4 50.3 1.0 CD A:GLU639 4.5 40.7 1.0 OE2 A:GLU633 4.5 48.1 1.0 NH2 A:ARG715 4.6 44.1 1.0 OE1 A:GLU633 4.7 48.9 1.0 CD A:GLN712 4.7 47.4 1.0 OD2 A:ASP714 4.7 43.7 1.0 O A:ASN711 4.8 53.5 1.0 OD1 A:ASP714 4.8 44.6 1.0 CZ A:ARG715 4.9 45.3 1.0

Calcium binding site 4 out of 5 in the Crystal Structure of Pullulanase From Klebsiella Pneumoniae Complex at 0.1 Mm Beta-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 0.1 Mm Beta-Cyclodextrin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1104 b:59.1 occ:1.00 O A:THR150 2.4 59.2 1.0 O A:ASP162 2.4 51.5 1.0 OD2 A:ASP148 2.5 55.5 1.0 OD1 A:ASP148 2.7 59.7 1.0 CG A:ASP148 2.9 59.4 1.0 OD1 A:ASP162 3.0 59.2 1.0 C A:THR150 3.5 54.7 1.0 C A:ASP162 3.5 59.4 1.0 CG A:ASP162 3.6 62.1 1.0 CB A:THR150 3.8 61.3 1.0 OE2 A:GLU45 4.0 59.0 1.0 CA A:THR150 4.1 56.9 1.0 OD2 A:ASP162 4.1 59.0 1.0 CA A:ASP162 4.1 58.6 1.0 N A:THR150 4.3 60.1 1.0 CG2 A:THR150 4.3 55.7 1.0 CB A:ASP162 4.4 56.4 1.0 CB A:ASP148 4.4 65.2 1.0 N A:VAL151 4.6 52.6 1.0 N A:SER163 4.6 52.9 1.0 OE1 A:GLN48 4.7 67.3 1.0 NE2 A:GLN48 4.9 63.6 1.0 CA A:SER163 4.9 55.6 1.0 CA A:VAL151 4.9 55.4 1.0 OG1 A:THR150 4.9 46.7 1.0

Calcium binding site 5 out of 5 in the Crystal Structure of Pullulanase From Klebsiella Pneumoniae Complex at 0.1 Mm Beta-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 0.1 Mm Beta-Cyclodextrin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1105 b:64.6 occ:1.00 OD2 A:ASP994 2.2 51.2 1.0 O A:VAL1006 2.4 53.0 1.0 NE2 A:GLN1070 2.5 65.0 1.0 OG A:SER1001 2.5 40.6 1.0 O A:ASP1003 2.7 46.5 1.0 CD A:GLN1070 2.9 59.4 1.0 CB A:SER1001 2.9 41.6 1.0 CG A:ASP994 3.1 52.6 1.0 OE1 A:GLN1070 3.3 50.7 1.0 O A:ASP994 3.5 53.4 1.0 C A:VAL1006 3.5 47.5 1.0 OD1 A:ASP1007 3.6 67.2 1.0 CA A:SER1001 3.7 55.7 1.0 CB A:ASP994 3.7 41.9 1.0 CG A:GLN1070 3.7 52.8 1.0 C A:ASP1003 3.9 56.0 1.0 OD1 A:ASP994 4.0 52.0 1.0 CA A:ASP1007 4.0 49.7 1.0 N A:ASP1007 4.1 44.1 1.0 C A:SER1001 4.4 53.0 1.0 C A:ASP994 4.4 50.9 1.0 N A:ASP1003 4.4 44.9 1.0 CG A:ASP1007 4.5 64.3 1.0 CG A:GLN1074 4.5 64.3 1.0 CB A:GLN1070 4.6 51.8 1.0 N A:VAL1006 4.6 51.0 1.0 CA A:ASP1003 4.6 51.1 1.0 CA A:ASP994 4.7 47.5 1.0 CA A:VAL1006 4.7 48.4 1.0 N A:LEU1002 4.7 48.6 1.0 CB A:ASP1007 4.8 57.1 1.0 N A:SER1004 4.9 50.8 1.0 CB A:ASP1003 4.9 44.6 1.0 C A:ASP1007 4.9 50.7 1.0 N A:SER1001 4.9 54.1 1.0 CA A:SER1004 5.0 53.3 1.0

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