Calcium in PDB 5ynd: Crystal Structure of Pullulanase From Klebsiella Pneumoniae Complex at 1 Mm Gamma-Cyclodextrin

The structure of Crystal Structure of Pullulanase From Klebsiella Pneumoniae Complex at 1 Mm Gamma-Cyclodextrin, PDB code: 5ynd 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)	44.39 / 2.23
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	88.773, 88.773, 298.379, 90.00, 90.00, 90.00
R / Rfree (%)	19.1 / 24.3

The binding sites of Calcium atom in the Crystal Structure of Pullulanase From Klebsiella Pneumoniae Complex at 1 Mm Gamma-Cyclodextrin (pdb code 5ynd). 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 1 Mm Gamma-Cyclodextrin, PDB code: 5ynd:
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 1 Mm Gamma-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 1 Mm Gamma-Cyclodextrin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1101 b:33.7 occ:1.00 OD1 A:ASP893 2.3 33.5 1.0 O A:TYR555 2.3 31.6 1.0 OD1 A:ASP553 2.4 32.5 1.0 O A:ALA550 2.5 35.2 1.0 O A:HOH1242 2.5 33.5 1.0 O A:HOH1369 2.5 29.5 1.0 O A:HOH1444 2.6 31.9 1.0 C A:TYR555 3.5 31.0 1.0 C A:ALA550 3.5 39.0 1.0 CG A:ASP553 3.5 36.5 1.0 CG A:ASP893 3.5 32.8 1.0 CA A:ALA550 3.9 39.8 1.0 OD2 A:ASP553 3.9 34.0 1.0 N A:TYR555 4.1 30.1 1.0 OD2 A:ASP893 4.1 38.6 1.0 CA A:TYR555 4.2 25.9 1.0 CB A:TYR555 4.4 28.6 1.0 CB A:ALA550 4.4 27.1 1.0 O A:ASP553 4.4 28.9 1.0 O A:ASP893 4.5 32.0 1.0 N A:ASN556 4.6 24.4 1.0 ND2 A:ASN556 4.6 27.2 1.0 N A:ASP553 4.7 33.9 1.0 N A:GLN551 4.7 37.8 1.0 C A:ASP553 4.7 35.4 1.0 CB A:ASP893 4.7 29.2 1.0 CA A:ASP893 4.7 29.2 1.0 CB A:ASP553 4.8 32.9 1.0 CB A:ASN556 4.8 25.2 1.0 CA A:ASN556 4.9 23.7 1.0 C A:ASP893 5.0 36.7 1.0 CA A:ASP553 5.0 29.8 1.0

Calcium binding site 2 out of 5 in the Crystal Structure of Pullulanase From Klebsiella Pneumoniae Complex at 1 Mm Gamma-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 1 Mm Gamma-Cyclodextrin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1102 b:38.5 occ:1.00 O A:LEU482 2.2 24.3 1.0 O A:HOH1230 2.2 24.4 1.0 OE2 A:GLU487 2.3 29.3 1.0 O A:HOH1350 2.3 28.8 1.0 OD1 A:ASP481 2.3 25.5 1.0 OE2 A:GLU568 2.4 29.3 1.0 CD A:GLU568 3.2 27.9 1.0 CD A:GLU487 3.3 27.9 1.0 OE1 A:GLU568 3.4 28.5 1.0 C A:LEU482 3.4 24.2 1.0 CG A:ASP481 3.5 24.8 1.0 N A:LEU482 3.7 25.6 1.0 CG A:GLU487 3.8 29.8 1.0 OG A:SER388 4.0 29.5 1.0 CA A:LEU482 4.1 28.9 1.0 OD2 A:ASP481 4.2 31.1 1.0 C A:ASP481 4.2 26.8 1.0 O A:HOH1290 4.3 30.9 1.0 OE1 A:GLU487 4.3 34.7 1.0 CA A:ASP481 4.4 20.2 1.0 O A:VAL485 4.4 29.6 1.0 O A:HOH1288 4.4 23.6 1.0 N A:GLY569 4.5 28.1 1.0 CG A:LEU482 4.5 31.2 1.0 N A:ALA483 4.5 29.3 1.0 CB A:ASP481 4.5 25.9 1.0 CG A:GLU568 4.7 21.9 1.0 CA A:ALA483 4.7 29.8 1.0 CA A:GLU568 4.8 24.5 1.0 CB A:LEU482 4.9 31.1 1.0 CD2 A:LEU482 5.0 32.2 1.0

Calcium binding site 3 out of 5 in the Crystal Structure of Pullulanase From Klebsiella Pneumoniae Complex at 1 Mm Gamma-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 1 Mm Gamma-Cyclodextrin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1103 b:90.7 occ:1.00 OD2 A:ASP148 2.4 55.8 1.0 O A:HOH1203 2.4 48.4 1.0 CG A:ASP148 3.4 56.8 1.0 O A:ASP162 3.5 49.6 1.0 OD1 A:ASP148 3.7 59.7 1.0 OE1 A:GLU45 3.9 51.0 1.0 OD2 A:ASP162 4.1 80.7 1.0 OD1 A:ASP162 4.1 72.0 1.0 O A:THR150 4.3 58.4 1.0 CG A:ASP162 4.3 73.2 1.0 OE1 A:GLN48 4.4 51.5 1.0 NE2 A:GLN48 4.5 65.6 1.0 C A:ASP162 4.5 56.9 1.0 CD A:GLU45 4.6 55.1 1.0 CB A:SER163 4.6 55.6 1.0 CB A:ASP148 4.7 42.5 1.0 CG A:GLU45 4.7 50.0 1.0 CB A:THR150 4.9 52.3 1.0 CD A:GLN48 4.9 54.9 1.0

Calcium binding site 4 out of 5 in the Crystal Structure of Pullulanase From Klebsiella Pneumoniae Complex at 1 Mm Gamma-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 1 Mm Gamma-Cyclodextrin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1104 b:73.6 occ:1.00 OD2 A:ASP994 2.3 44.0 1.0 O A:VAL1006 2.5 46.2 1.0 OG A:SER1001 2.6 54.6 1.0 O A:ASP1003 2.6 53.9 1.0 OE1 A:GLN1070 2.7 66.1 1.0 CB A:SER1001 2.9 36.9 1.0 CD A:GLN1070 3.2 60.7 1.0 CG A:ASP994 3.3 45.6 1.0 O A:ASP994 3.4 44.1 1.0 OD1 A:ASP1007 3.5 56.3 1.0 C A:VAL1006 3.5 48.1 1.0 NE2 A:GLN1070 3.6 56.4 1.0 CA A:SER1001 3.7 46.2 1.0 C A:ASP1003 3.8 60.0 1.0 CA A:ASP1007 3.9 42.5 1.0 CB A:ASP994 3.9 44.2 1.0 CG A:GLN1070 4.0 61.3 1.0 N A:ASP1007 4.0 40.8 1.0 OD1 A:ASP994 4.2 35.0 1.0 CG A:GLN1074 4.4 59.5 1.0 C A:ASP994 4.4 55.9 1.0 CB A:GLN1070 4.4 60.2 1.0 CG A:ASP1007 4.5 61.1 1.0 C A:SER1001 4.5 52.9 1.0 N A:ASP1003 4.5 48.5 1.0 N A:VAL1006 4.6 46.3 1.0 CA A:ASP1003 4.6 47.2 1.0 CA A:VAL1006 4.7 51.4 1.0 CB A:ASP1007 4.7 54.4 1.0 N A:SER1004 4.7 55.1 1.0 CA A:SER1004 4.8 64.9 1.0 NE2 A:GLN1074 4.8 63.4 1.0 CA A:ASP994 4.8 46.4 1.0 C A:ASP1007 4.8 41.3 1.0 CB A:ASP1003 4.9 49.0 1.0 N A:SER1001 4.9 44.1 1.0 O A:SER1001 4.9 44.6 1.0

Calcium binding site 5 out of 5 in the Crystal Structure of Pullulanase From Klebsiella Pneumoniae Complex at 1 Mm Gamma-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 1 Mm Gamma-Cyclodextrin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1105 b:69.1 occ:1.00 O A:HOH1484 2.2 46.5 1.0 O A:HOH1211 2.3 37.4 1.0 O A:HOH1215 2.4 42.8 1.0 O A:HOH1338 2.5 47.7 1.0 OD2 A:ASP714 3.3 46.5 1.0 OE2 A:GLU633 3.4 43.2 1.0 NE A:ARG715 3.7 40.3 1.0 NH2 A:ARG715 3.9 36.0 1.0 OD1 A:ASP714 3.9 43.1 1.0 CG A:ASP714 4.0 46.4 1.0 CD A:GLU633 4.3 49.0 1.0 CZ A:ARG715 4.3 40.6 1.0 OE1 A:GLU633 4.5 45.7 1.0 OE1 A:GLN712 4.5 46.8 1.0 O A:ASN711 4.5 39.2 0.5 OE1 A:GLU639 4.7 42.6 1.0 CG A:ARG715 4.7 45.5 1.0 CD A:ARG715 4.7 37.7 1.0 OE2 A:GLU639 4.8 40.0 1.0 O A:ASN711 4.8 43.9 0.5

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