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

Protein crystallography data

The structure of Crystal Structure of Pullulanase From Klebsiella Pneumoniae Complex at 1 Mm Alpha-Cyclodextrin, PDB code: 5yna 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) 44.15 / 1.96
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 89.278, 89.278, 299.375, 90.00, 90.00, 90.00
R / Rfree (%) 19.8 / 24

Calcium Binding Sites:

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

Calcium binding site 1 out of 5 in 5yna

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

b:29.9
occ:1.00
 OD1 A:ASP893 2.3 37.9 1.0
O A:TYR555 2.4 27.8 1.0
O A:HOH1391 2.4 26.1 1.0
OD1 A:ASP553 2.4 28.7 1.0
O A:ALA550 2.5 30.7 1.0
O A:HOH1360 2.6 29.7 1.0
O A:HOH1537 2.6 29.1 1.0
CG A:ASP553 3.5 31.7 1.0
C A:ALA550 3.5 33.3 1.0
CG A:ASP893 3.5 31.0 1.0
C A:TYR555 3.6 25.9 1.0
OD2 A:ASP553 3.8 29.1 1.0
CA A:ALA550 3.9 31.1 1.0
OD2 A:ASP893 4.1 29.2 1.0
N A:TYR555 4.2 26.3 1.0
CA A:TYR555 4.2 25.1 1.0
CB A:ALA550 4.2 28.2 1.0
CB A:TYR555 4.4 21.2 1.0
O A:HOH1433 4.5 41.4 1.0
O A:ASP553 4.5 28.0 1.0
O A:ASP893 4.5 26.4 1.0
N A:ASN556 4.7 25.4 1.0
O A:HOH1596 4.7 37.8 1.0
N A:GLN551 4.7 30.0 1.0
N A:ASP553 4.7 28.2 1.0
CB A:ASP893 4.7 27.1 1.0
CA A:ASP893 4.8 25.3 1.0
C A:ASP553 4.8 30.9 1.0
CB A:ASP553 4.8 32.7 1.0
ND2 A:ASN556 4.9 30.0 1.0
O A:HOH1320 4.9 33.2 1.0
CB A:ASN556 4.9 29.1 1.0
C A:ASP893 5.0 30.1 1.0
CA A:ASN556 5.0 25.5 1.0
O A:THR484 5.0 33.2 1.0

Calcium binding site 2 out of 5 in 5yna

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

b:31.6
occ:1.00
 OD1 A:ASP481 2.2 21.9 1.0
OE2 A:GLU487 2.2 27.2 1.0
O A:HOH1296 2.3 24.7 1.0
OE2 A:GLU568 2.3 24.3 1.0
O A:LEU482 2.3 24.4 1.0
O A:HOH1509 2.3 26.3 1.0
CD A:GLU568 3.2 26.1 1.0
CD A:GLU487 3.3 26.7 1.0
CG A:ASP481 3.3 24.9 1.0
OE1 A:GLU568 3.4 25.4 1.0
C A:LEU482 3.4 23.9 1.0
N A:LEU482 3.6 25.7 1.0
CG A:GLU487 3.9 25.6 1.0
OG A:SER388 4.0 24.9 1.0
OD2 A:ASP481 4.0 25.8 1.0
C A:ASP481 4.1 27.1 1.0
CA A:LEU482 4.1 27.2 1.0
OE1 A:GLU487 4.2 25.9 1.0
CA A:ASP481 4.2 20.9 1.0
O A:HOH1306 4.3 24.8 1.0
N A:GLY569 4.3 22.9 1.0
CB A:ASP481 4.4 22.4 1.0
O A:HOH1422 4.5 28.9 1.0
CG A:LEU482 4.5 29.1 1.0
N A:ALA483 4.5 24.3 1.0
CG A:GLU568 4.6 25.4 1.0
O A:VAL485 4.6 21.0 1.0
CA A:GLU568 4.7 27.4 1.0
CA A:ALA483 4.8 27.8 1.0
O A:ASP481 4.8 24.1 1.0
CB A:LEU482 4.9 27.8 1.0
CB A:GLU568 5.0 24.1 1.0

Calcium binding site 3 out of 5 in 5yna

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

b:67.9
occ:1.00
 O A:HOH1484 2.2 45.3 1.0
O A:HOH1371 2.3 46.7 1.0
O A:HOH1241 2.3 38.1 1.0
O A:HOH1681 2.4 42.2 1.0
O A:HOH1347 2.6 40.5 1.0
O A:HOH1406 3.6 43.6 1.0
OE1 A:GLU639 3.9 37.9 1.0
OE2 A:GLU639 4.0 41.2 1.0
OE1 A:GLN712 4.2 43.6 1.0
NE2 A:GLN712 4.3 39.6 1.0
ND2 A:ASN711 4.3 58.8 1.0
CD A:GLU639 4.3 34.2 1.0
CD A:GLN712 4.6 45.8 1.0
NE A:ARG715 4.6 39.2 1.0
O A:ASN711 4.6 45.0 1.0
OE1 A:GLU633 4.8 44.4 1.0
NH2 A:ARG715 4.8 35.6 1.0
OD1 A:ASP714 4.8 42.1 1.0
OD2 A:ASP714 4.9 40.6 1.0
OE2 A:GLU633 4.9 42.1 1.0

Calcium binding site 4 out of 5 in 5yna

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

b:64.8
occ:1.00
 OE1 A:GLN1070 2.2 52.3 1.0
OD2 A:ASP994 2.2 34.1 1.0
O A:ASP1003 2.3 51.2 1.0
OG A:SER1001 2.4 41.5 1.0
O A:VAL1006 2.4 49.8 1.0
CG A:ASP994 3.1 41.9 1.0
CB A:SER1001 3.1 42.1 1.0
CD A:GLN1070 3.1 56.5 1.0
C A:ASP1003 3.4 44.0 1.0
O A:ASP994 3.4 53.0 1.0
C A:VAL1006 3.6 47.3 1.0
CB A:ASP994 3.6 36.5 1.0
NE2 A:GLN1070 3.6 45.7 1.0
CA A:SER1001 3.8 41.0 1.0
N A:ASP1003 3.9 42.7 1.0
OD1 A:ASP994 4.1 38.9 1.0
CA A:ASP1003 4.1 44.0 1.0
C A:SER1001 4.1 50.2 1.0
OD1 A:ASP1007 4.2 56.0 1.0
CA A:ASP1007 4.2 41.1 1.0
N A:ASP1007 4.3 48.3 1.0
CG A:GLN1070 4.4 55.7 1.0
CB A:ASP1003 4.4 47.2 1.0
C A:ASP994 4.4 54.5 1.0
N A:SER1004 4.5 49.8 0.3
N A:SER1004 4.5 49.8 0.7
N A:VAL1006 4.5 49.7 1.0
N A:LEU1002 4.5 46.3 1.0
O A:SER1001 4.6 57.4 1.0
CA A:ASP994 4.6 46.7 1.0
CA A:VAL1006 4.7 52.3 1.0
CA A:SER1004 4.7 52.7 0.7
CA A:SER1004 4.7 52.6 0.3
C A:SER1004 4.8 52.0 0.7
CB A:GLN1070 5.0 54.7 1.0
CG A:ASP1007 5.0 61.0 1.0

Calcium binding site 5 out of 5 in 5yna

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

b:85.1
occ:1.00
 OD2 A:ASP148 2.2 49.2 1.0
CG A:ASP148 3.2 55.3 1.0
O A:ASP162 3.3 57.8 1.0
OD1 A:ASP162 3.5 76.8 1.0
OD1 A:ASP148 3.6 53.5 1.0
NE2 A:GLN48 3.8 44.8 1.0
OE1 A:GLU45 3.8 55.1 1.0
O A:THR150 4.0 53.4 1.0
CG A:ASP162 4.1 70.2 1.0
OD2 A:ASP162 4.2 72.2 1.0
OE1 A:GLN48 4.3 51.1 1.0
C A:ASP162 4.4 47.2 1.0
CD A:GLN48 4.5 47.7 1.0
CB A:ASP148 4.6 50.5 1.0
CD A:GLU45 4.6 50.9 1.0
CB A:THR150 4.6 48.5 1.0
CG A:GLU45 4.8 51.1 1.0
CG2 A:THR150 5.0 39.0 1.0
CB A:SER163 5.0 50.6 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: Wed Jul 9 12:00:37 2025

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