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

Protein crystallography data

The structure of Crystal Structure of Pullulanase From Klebsiella Pneumoniae Complex at 10 Mm Gamma-Cyclodextrin, PDB code: 5ynh 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) 49.67 / 2.05
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 89.206, 89.206, 298.980, 90.00, 90.00, 90.00
R / Rfree (%) 20.5 / 25.8

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Pullulanase From Klebsiella Pneumoniae Complex at 10 Mm Gamma-Cyclodextrin (pdb code 5ynh). 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 Gamma-Cyclodextrin, PDB code: 5ynh:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 5ynh

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Calcium binding site 1 out of 5 in the Crystal Structure of Pullulanase From Klebsiella Pneumoniae Complex at 10 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 10 Mm Gamma-Cyclodextrin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1117

b:24.1
occ:1.00
 OD1 A:ASP893 2.3 24.8 1.0
O A:TYR555 2.4 20.5 1.0
O A:ALA550 2.5 23.0 1.0
O A:HOH1418 2.5 22.7 1.0
OD1 A:ASP553 2.5 24.3 1.0
O A:HOH1479 2.6 22.6 1.0
O A:HOH1233 2.6 23.0 1.0
C A:ALA550 3.5 26.1 1.0
CG A:ASP893 3.5 25.1 1.0
CG A:ASP553 3.5 22.3 1.0
C A:TYR555 3.6 19.7 1.0
CA A:ALA550 3.9 25.6 1.0
OD2 A:ASP553 3.9 24.2 1.0
OD2 A:ASP893 4.1 25.1 1.0
N A:TYR555 4.2 19.9 1.0
CA A:TYR555 4.3 19.8 1.0
CB A:ALA550 4.3 22.3 1.0
CB A:TYR555 4.4 19.3 1.0
O A:ASP553 4.4 22.1 1.0
O A:HOH1506 4.4 31.4 1.0
O A:ASP893 4.5 20.3 1.0
O A:HOH1500 4.6 29.1 1.0
N A:ASN556 4.7 20.6 1.0
N A:GLN551 4.7 27.0 1.0
N A:ASP553 4.7 21.1 1.0
CB A:ASP893 4.7 22.8 1.0
CA A:ASP893 4.7 25.2 1.0
C A:ASP553 4.8 25.6 1.0
ND2 A:ASN556 4.8 23.8 1.0
CB A:ASP553 4.8 24.7 1.0
CB A:ASN556 4.9 22.1 1.0
O A:HOH1276 4.9 27.7 1.0
C A:ASP893 5.0 25.8 1.0
O A:THR484 5.0 28.0 1.0
CA A:ASN556 5.0 19.4 1.0

Calcium binding site 2 out of 5 in 5ynh

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Calcium binding site 2 out of 5 in the Crystal Structure of Pullulanase From Klebsiella Pneumoniae Complex at 10 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 10 Mm Gamma-Cyclodextrin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1118

b:54.5
occ:1.00
 O A:ASP162 2.3 48.4 1.0
OD1 A:ASP148 2.4 38.9 1.0
O A:THR150 2.4 44.9 1.0
OD2 A:ASP148 2.5 40.1 1.0
CG A:ASP148 2.8 42.6 1.0
OD1 A:ASP162 2.9 52.6 1.0
C A:ASP162 3.5 46.9 1.0
CG A:ASP162 3.5 52.1 1.0
C A:THR150 3.5 45.9 1.0
OE1 A:GLU45 3.8 41.9 1.0
CB A:THR150 3.8 41.5 1.0
OD2 A:ASP162 4.0 62.1 1.0
CA A:ASP162 4.1 50.0 1.0
CA A:THR150 4.1 44.0 1.0
N A:THR150 4.2 34.4 1.0
CB A:ASP148 4.3 38.7 1.0
O A:HOH1266 4.3 44.0 1.0
CB A:ASP162 4.3 52.1 1.0
CG2 A:THR150 4.4 34.0 1.0
O A:HOH1378 4.5 43.3 1.0
N A:SER163 4.6 48.3 1.0
N A:VAL151 4.7 42.7 1.0
CA A:SER163 4.8 45.8 1.0
CD A:GLU45 4.9 45.4 1.0
OG1 A:THR150 4.9 38.4 1.0
NE2 A:GLN48 5.0 47.6 1.0
OE1 A:GLN48 5.0 41.7 1.0

Calcium binding site 3 out of 5 in 5ynh

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Calcium binding site 3 out of 5 in the Crystal Structure of Pullulanase From Klebsiella Pneumoniae Complex at 10 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 10 Mm Gamma-Cyclodextrin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1119

b:53.4
occ:1.00
 O A:HOH1201 2.2 36.1 1.0
O A:HOH1235 2.3 32.5 1.0
O A:HOH1299 2.3 32.5 1.0
O A:HOH1247 2.4 34.1 1.0
O A:HOH1544 2.5 37.6 1.0
O A:HOH1239 4.0 33.4 1.0
O A:ASN711 4.1 34.0 0.5
NE2 A:GLN712 4.1 30.0 1.0
OD2 A:ASP714 4.2 33.5 1.0
OE1 A:GLN712 4.2 33.4 1.0
O A:ASN711 4.3 33.9 0.5
NE A:ARG715 4.3 30.8 1.0
OE1 A:GLU639 4.3 33.7 1.0
OD1 A:ASP714 4.3 36.7 1.0
OE1 A:GLU633 4.4 39.6 1.0
CD A:GLN712 4.5 36.9 1.0
OE2 A:GLU639 4.5 30.7 1.0
ND2 A:ASN711 4.6 32.9 0.5
NH2 A:ARG715 4.6 33.1 1.0
CG A:ASP714 4.7 42.0 1.0
OE2 A:GLU633 4.7 40.0 1.0
CD A:GLU639 4.8 30.2 1.0
CG A:ASN711 4.9 35.2 0.5
CD A:GLU633 5.0 36.6 1.0
CZ A:ARG715 5.0 33.8 1.0

Calcium binding site 4 out of 5 in 5ynh

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Calcium binding site 4 out of 5 in the Crystal Structure of Pullulanase From Klebsiella Pneumoniae Complex at 10 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 10 Mm Gamma-Cyclodextrin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1120

b:23.6
occ:1.00
 O A:LEU482 2.3 18.6 1.0
O A:HOH1286 2.3 17.3 1.0
OD1 A:ASP481 2.3 18.8 1.0
OE2 A:GLU487 2.3 18.4 1.0
OE2 A:GLU568 2.4 17.8 1.0
O A:HOH1386 2.5 19.3 1.0
CD A:GLU568 3.2 22.1 1.0
CD A:GLU487 3.3 19.9 1.0
OE1 A:GLU568 3.4 18.7 1.0
C A:LEU482 3.5 17.2 1.0
CG A:ASP481 3.5 17.9 1.0
N A:LEU482 3.7 20.5 1.0
CG A:GLU487 3.9 17.9 1.0
OG A:SER388 4.0 17.2 1.0
CA A:LEU482 4.2 18.5 1.0
OE1 A:GLU487 4.2 20.3 1.0
C A:ASP481 4.2 18.6 1.0
OD2 A:ASP481 4.2 18.2 1.0
O A:HOH1267 4.3 19.2 1.0
N A:GLY569 4.3 20.0 1.0
CA A:ASP481 4.3 16.1 1.0
O A:HOH1425 4.4 21.0 1.0
CG A:LEU482 4.4 19.7 1.0
CB A:ASP481 4.5 17.1 1.0
N A:ALA483 4.5 20.9 1.0
O A:VAL485 4.6 18.8 1.0
CG A:GLU568 4.7 18.9 1.0
CA A:ALA483 4.8 21.2 1.0
CA A:GLU568 4.8 19.0 1.0
CB A:LEU482 4.9 20.8 1.0
O A:ASP481 5.0 19.7 1.0

Calcium binding site 5 out of 5 in 5ynh

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Calcium binding site 5 out of 5 in the Crystal Structure of Pullulanase From Klebsiella Pneumoniae Complex at 10 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 10 Mm Gamma-Cyclodextrin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1121

b:64.9
occ:1.00
 OG A:SER1001 2.5 33.4 1.0
OD2 A:ASP994 2.5 32.3 1.0
OE1 A:GLN1070 2.6 51.6 1.0
O A:VAL1006 2.7 46.3 1.0
O A:ASP1003 3.0 47.3 1.0
O A:ASP994 3.0 43.8 1.0
CB A:SER1001 3.0 31.3 1.0
CD A:GLN1070 3.2 51.3 1.0
CG A:ASP994 3.3 35.3 1.0
NE2 A:GLN1070 3.4 45.9 1.0
OD1 A:ASP1007 3.4 45.0 1.0
CB A:ASP994 3.7 37.4 1.0
C A:VAL1006 3.7 39.7 1.0
CA A:ASP1007 3.8 35.2 1.0
CA A:SER1001 3.8 36.7 1.0
C A:ASP994 4.1 47.5 1.0
N A:ASP1007 4.1 42.4 1.0
C A:ASP1003 4.2 44.9 1.0
CG A:ASP1007 4.2 50.8 1.0
OD1 A:ASP994 4.3 37.4 1.0
CG A:GLN1070 4.3 53.2 1.0
CB A:ASP1007 4.5 47.9 1.0
C A:SER1001 4.5 43.8 1.0
CA A:ASP994 4.5 42.4 1.0
N A:ASP1003 4.7 37.3 1.0
C A:ASP1007 4.7 33.6 1.0
CA A:GLN1074 4.8 45.5 1.0
CG A:GLN1074 4.8 44.1 1.0
CB A:GLN1074 4.8 42.7 1.0
CA A:ASP1003 4.9 40.2 1.0
N A:VAL1006 4.9 47.3 1.0
O A:SER1001 5.0 49.4 1.0
CA A:VAL1006 5.0 45.0 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: Sat Dec 12 05:54:44 2020

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