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

Protein crystallography data

The structure of Crystal Structure of Pullulanase From Klebsiella Pneumoniae Complex at 1 Mm Beta-Cyclodextrin, PDB code: 5ync 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) 49.68 / 2.32
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 88.925, 88.925, 299.527, 90.00, 90.00, 90.00
R / Rfree (%) 18.7 / 25.4

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Pullulanase From Klebsiella Pneumoniae Complex at 1 Mm Beta-Cyclodextrin (pdb code 5ync). 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 Beta-Cyclodextrin, PDB code: 5ync:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 5ync

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Calcium binding site 1 out of 5 in the Crystal Structure of Pullulanase From Klebsiella Pneumoniae Complex at 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 1 Mm Beta-Cyclodextrin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1101

b:25.3
occ:1.00
 OD1 A:ASP893 2.4 24.4 1.0
O A:HOH1341 2.4 25.6 1.0
O A:TYR555 2.4 21.7 1.0
OD1 A:ASP553 2.5 26.9 1.0
O A:ALA550 2.5 29.7 1.0
O A:HOH1348 2.5 26.0 1.0
O A:HOH1470 2.5 22.7 1.0
C A:ALA550 3.5 32.6 1.0
CG A:ASP553 3.5 27.3 1.0
CG A:ASP893 3.6 27.6 1.0
C A:TYR555 3.6 22.7 1.0
OD2 A:ASP553 3.9 28.5 1.0
CA A:ALA550 3.9 27.9 1.0
OD2 A:ASP893 4.1 29.7 1.0
N A:TYR555 4.2 23.2 1.0
CA A:TYR555 4.2 22.8 1.0
CB A:ALA550 4.3 19.8 1.0
O A:ASP553 4.4 22.1 1.0
CB A:TYR555 4.4 18.9 1.0
O A:ASP893 4.5 23.4 1.0
N A:ASN556 4.7 25.1 1.0
ND2 A:ASN556 4.7 23.9 1.0
N A:GLN551 4.7 36.4 1.0
N A:ASP553 4.7 25.1 1.0
C A:ASP553 4.8 27.1 1.0
CB A:ASP893 4.8 22.6 1.0
O A:HOH1449 4.8 18.4 0.5
CA A:ASP893 4.8 26.4 1.0
CB A:ASP553 4.8 24.5 1.0
CB A:ASN556 4.8 21.0 1.0
O A:HOH1439 4.9 33.5 1.0
O A:THR484 4.9 30.1 1.0
CA A:ASN556 5.0 25.0 1.0
C A:ASP893 5.0 30.2 1.0

Calcium binding site 2 out of 5 in 5ync

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Calcium binding site 2 out of 5 in the Crystal Structure of Pullulanase From Klebsiella Pneumoniae Complex at 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 1 Mm Beta-Cyclodextrin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1102

b:59.1
occ:1.00
 O A:HOH1201 2.3 34.7 1.0
O A:HOH1226 2.3 30.8 1.0
O A:HOH1269 2.4 38.9 1.0
O A:HOH1227 2.5 36.9 1.0
O A:HOH1567 2.7 46.1 1.0
O A:HOH1582 2.8 38.1 1.0
O A:HOH1274 3.9 42.0 1.0
O A:ASN711 4.0 35.1 1.0
OD2 A:ASP714 4.2 41.6 1.0
NE2 A:GLN712 4.2 34.4 1.0
OE1 A:GLN712 4.3 41.6 1.0
OE2 A:GLU639 4.3 39.4 1.0
OD1 A:ASP714 4.4 45.9 1.0
OE1 A:GLU639 4.6 32.4 1.0
CD A:GLN712 4.6 40.2 1.0
OE1 A:GLU633 4.6 40.4 1.0
NE A:ARG715 4.6 34.3 1.0
CG A:ASP714 4.7 47.6 1.0
OD1 A:ASN711 4.7 61.5 1.0
OE2 A:GLU633 4.8 40.2 1.0
NH2 A:ARG715 4.8 28.0 1.0
CD A:GLU639 4.9 36.5 1.0

Calcium binding site 3 out of 5 in 5ync

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Calcium binding site 3 out of 5 in the Crystal Structure of Pullulanase From Klebsiella Pneumoniae Complex at 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 1 Mm Beta-Cyclodextrin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1103

b:69.3
occ:1.00
 O A:ASP162 2.4 60.8 1.0
OD1 A:ASP148 2.5 50.0 1.0
OD2 A:ASP148 2.6 49.8 1.0
O A:THR150 2.6 52.9 1.0
CG A:ASP148 2.9 45.2 1.0
OD1 A:ASP162 2.9 66.4 1.0
CG A:ASP162 3.4 68.1 1.0
C A:ASP162 3.6 59.9 1.0
C A:THR150 3.6 48.7 1.0
CB A:THR150 3.8 46.6 1.0
OE2 A:GLU45 3.8 49.1 1.0
OD2 A:ASP162 3.8 79.0 1.0
CA A:THR150 4.1 50.0 1.0
CA A:ASP162 4.2 57.8 1.0
N A:THR150 4.3 41.5 1.0
CB A:ASP148 4.4 44.2 1.0
CG2 A:THR150 4.4 44.2 1.0
CB A:ASP162 4.4 58.1 1.0
N A:SER163 4.7 48.0 1.0
O A:HOH1383 4.8 45.4 1.0
OG1 A:THR150 4.8 43.0 1.0
N A:VAL151 4.8 51.9 1.0
CD A:GLU45 4.8 52.8 1.0
NE2 A:GLN48 4.9 50.0 1.0
CA A:SER163 4.9 49.4 1.0
OE1 A:GLN48 5.0 51.8 1.0

Calcium binding site 4 out of 5 in 5ync

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Calcium binding site 4 out of 5 in the Crystal Structure of Pullulanase From Klebsiella Pneumoniae Complex at 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 1 Mm Beta-Cyclodextrin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1104

b:65.7
occ:1.00
 OD2 A:ASP994 2.2 36.6 1.0
OG A:SER1001 2.4 39.3 1.0
OE1 A:GLN1070 2.4 53.7 1.0
O A:ASP1003 2.5 52.3 1.0
O A:VAL1006 2.5 48.4 1.0
CB A:SER1001 2.8 28.2 1.0
NE2 A:GLN1070 3.0 52.9 1.0
CD A:GLN1070 3.0 56.2 1.0
CG A:ASP994 3.2 42.7 1.0
O A:ASP994 3.4 45.9 1.0
C A:VAL1006 3.6 43.5 1.0
CA A:SER1001 3.7 40.1 1.0
C A:ASP1003 3.7 46.4 1.0
CB A:ASP994 3.7 41.4 1.0
OD1 A:ASP1007 4.0 55.5 1.0
CA A:ASP1007 4.1 42.9 1.0
OD1 A:ASP994 4.2 36.3 1.0
C A:SER1001 4.2 45.8 1.0
N A:ASP1007 4.3 45.8 1.0
N A:ASP1003 4.3 36.1 1.0
CG A:GLN1070 4.4 58.0 1.0
C A:ASP994 4.4 50.0 1.0
CA A:ASP1003 4.5 42.9 1.0
N A:VAL1006 4.6 50.3 1.0
CG A:ASP1007 4.6 55.3 1.0
O A:SER1001 4.6 54.1 1.0
N A:SER1004 4.7 46.4 1.0
CA A:ASP994 4.7 46.9 1.0
CB A:ASP1003 4.7 37.2 1.0
CA A:SER1004 4.7 57.9 1.0
CA A:VAL1006 4.7 46.0 1.0
N A:LEU1002 4.8 40.1 1.0
C A:SER1004 4.8 52.4 1.0
O A:SER1004 4.9 59.5 1.0
CB A:GLN1070 4.9 55.4 1.0
N A:SER1001 4.9 36.0 1.0
CB A:ASP1007 5.0 50.7 1.0

Calcium binding site 5 out of 5 in 5ync

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Calcium binding site 5 out of 5 in the Crystal Structure of Pullulanase From Klebsiella Pneumoniae Complex at 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 1 Mm Beta-Cyclodextrin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1105

b:31.7
occ:1.00
 O A:HOH1302 2.3 22.6 1.0
OE2 A:GLU487 2.3 25.4 1.0
O A:LEU482 2.3 22.2 1.0
OD1 A:ASP481 2.3 21.9 1.0
OE2 A:GLU568 2.4 24.4 1.0
O A:HOH1370 2.5 21.8 1.0
CD A:GLU568 3.2 23.1 1.0
CD A:GLU487 3.3 23.6 1.0
OE1 A:GLU568 3.3 21.9 1.0
C A:LEU482 3.5 21.1 1.0
CG A:ASP481 3.5 22.0 1.0
N A:LEU482 3.7 22.0 1.0
CG A:GLU487 3.8 24.4 1.0
OG A:SER388 4.0 20.4 1.0
C A:ASP481 4.1 24.2 1.0
OD2 A:ASP481 4.2 21.8 1.0
CA A:LEU482 4.2 23.3 1.0
OE1 A:GLU487 4.2 23.5 1.0
O A:HOH1316 4.2 17.9 1.0
N A:GLY569 4.3 22.2 1.0
CA A:ASP481 4.3 17.8 1.0
O A:HOH1318 4.4 24.6 1.0
CB A:ASP481 4.5 20.9 1.0
CG A:LEU482 4.5 27.5 1.0
N A:ALA483 4.5 22.2 1.0
O A:VAL485 4.6 23.6 1.0
CG A:GLU568 4.7 17.9 1.0
CA A:ALA483 4.8 25.6 1.0
CA A:GLU568 4.8 24.1 1.0
O A:ASP481 4.9 22.9 1.0
CB A:LEU482 5.0 20.5 1.0

Reference:

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
Page generated: Mon Jul 15 15:29:33 2024

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