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

Protein crystallography data

The structure of Crystal Structure of Pullulanase From Klebsiella Pneumoniae Complex at 10 Mm Alpha-Cyclodextrin, PDB code: 5yne 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) 49.75 / 2.20
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 89.210, 89.210, 299.647, 90.00, 90.00, 90.00
R / Rfree (%) 18.1 / 24.2

Calcium Binding Sites:

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

Calcium binding site 1 out of 5 in 5yne

Go back to Calcium Binding Sites List in 5yne
Calcium binding site 1 out of 5 in the Crystal Structure of Pullulanase From Klebsiella Pneumoniae Complex at 10 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 10 Mm Alpha-Cyclodextrin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1101

b:18.6
occ:1.00
 OD1 A:ASP893 2.3 24.2 1.0
O A:TYR555 2.4 17.6 1.0
O A:ALA550 2.4 21.2 1.0
O A:HOH1382 2.5 18.9 1.0
OD1 A:ASP553 2.5 17.0 1.0
O A:HOH1313 2.5 18.9 1.0
O A:HOH1539 2.6 17.1 1.0
C A:ALA550 3.5 24.3 1.0
CG A:ASP893 3.5 20.7 1.0
CG A:ASP553 3.5 19.3 1.0
C A:TYR555 3.6 16.1 1.0
CA A:ALA550 3.9 20.8 1.0
OD2 A:ASP553 3.9 17.6 1.0
OD2 A:ASP893 4.1 19.1 1.0
N A:TYR555 4.2 16.3 1.0
CA A:TYR555 4.3 14.7 1.0
CB A:ALA550 4.3 16.9 1.0
O A:HOH1483 4.4 25.8 1.0
O A:ASP553 4.4 15.9 1.0
CB A:TYR555 4.5 15.2 1.0
O A:ASP893 4.6 15.3 1.0
N A:ASN556 4.7 15.2 1.0
N A:GLN551 4.7 23.1 1.0
N A:ASP553 4.7 22.2 1.0
O A:HOH1630 4.7 25.6 1.0
CB A:ASP893 4.7 17.7 1.0
C A:ASP553 4.8 18.1 1.0
CA A:ASP893 4.8 17.9 1.0
ND2 A:ASN556 4.8 17.6 1.0
CB A:ASP553 4.8 18.9 1.0
CB A:ASN556 4.9 17.5 1.0
O A:THR484 4.9 25.1 1.0
O A:HOH1383 5.0 25.5 1.0
C A:ASP893 5.0 19.9 1.0

Calcium binding site 2 out of 5 in 5yne

Go back to Calcium Binding Sites List in 5yne
Calcium binding site 2 out of 5 in the Crystal Structure of Pullulanase From Klebsiella Pneumoniae Complex at 10 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 10 Mm Alpha-Cyclodextrin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1102

b:17.8
occ:1.00
 OE2 A:GLU487 2.3 12.2 1.0
OD1 A:ASP481 2.3 14.2 1.0
O A:LEU482 2.3 16.7 1.0
O A:HOH1290 2.3 12.4 1.0
OE2 A:GLU568 2.4 13.5 1.0
O A:HOH1426 2.5 14.3 1.0
CD A:GLU568 3.2 16.6 1.0
CD A:GLU487 3.3 18.3 1.0
OE1 A:GLU568 3.4 16.4 1.0
C A:LEU482 3.5 13.8 1.0
CG A:ASP481 3.5 14.5 1.0
N A:LEU482 3.7 13.7 1.0
CG A:GLU487 3.9 12.5 1.0
OG A:SER388 4.0 12.8 1.0
C A:ASP481 4.2 16.2 1.0
CA A:LEU482 4.2 15.0 1.0
OE1 A:GLU487 4.2 17.8 1.0
O A:HOH1346 4.2 12.1 1.0
OD2 A:ASP481 4.2 13.7 1.0
CA A:ASP481 4.3 10.7 1.0
N A:GLY569 4.4 12.5 1.0
O A:HOH1398 4.4 15.9 1.0
CB A:ASP481 4.5 12.1 1.0
CG A:LEU482 4.5 17.8 1.0
N A:ALA483 4.6 15.3 1.0
O A:VAL485 4.6 13.8 1.0
CG A:GLU568 4.7 11.6 1.0
CD1 A:LEU482 4.8 16.4 1.0
CA A:GLU568 4.8 15.1 1.0
CA A:ALA483 4.9 18.8 1.0
O A:ASP481 4.9 16.1 1.0
CB A:LEU482 4.9 11.6 1.0

Calcium binding site 3 out of 5 in 5yne

Go back to Calcium Binding Sites List in 5yne
Calcium binding site 3 out of 5 in the Crystal Structure of Pullulanase From Klebsiella Pneumoniae Complex at 10 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 10 Mm Alpha-Cyclodextrin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1103

b:46.9
occ:1.00
 O A:ASP162 2.3 47.0 1.0
OD1 A:ASP148 2.4 36.0 1.0
O A:THR150 2.4 40.8 1.0
O A:HOH1209 2.6 33.9 1.0
OD2 A:ASP148 2.6 42.4 1.0
OD1 A:ASP162 2.6 52.6 1.0
CG A:ASP148 2.9 38.1 1.0
CG A:ASP162 3.4 49.6 1.0
C A:ASP162 3.4 41.0 1.0
C A:THR150 3.5 37.2 1.0
CB A:THR150 3.9 33.9 1.0
CA A:ASP162 4.0 44.0 1.0
OD2 A:ASP162 4.0 58.7 1.0
O A:HOH1579 4.0 45.3 1.0
CA A:THR150 4.1 36.8 1.0
N A:THR150 4.2 28.5 1.0
CB A:ASP162 4.3 51.0 1.0
OE1 A:GLU45 4.3 39.5 1.0
CB A:ASP148 4.4 33.0 1.0
O A:HOH1267 4.5 31.6 1.0
N A:SER163 4.5 38.5 1.0
CG2 A:THR150 4.6 31.1 1.0
N A:VAL151 4.6 33.5 1.0
CA A:SER163 4.8 43.3 1.0
CA A:VAL151 4.9 26.9 1.0
OE1 A:GLN48 5.0 39.7 1.0
OG1 A:THR150 5.0 33.5 1.0

Calcium binding site 4 out of 5 in 5yne

Go back to Calcium Binding Sites List in 5yne
Calcium binding site 4 out of 5 in the Crystal Structure of Pullulanase From Klebsiella Pneumoniae Complex at 10 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 10 Mm Alpha-Cyclodextrin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1104

b:53.4
occ:1.00
 O A:HOH1201 2.2 29.3 1.0
O A:HOH1309 2.3 31.4 1.0
O A:HOH1322 2.4 28.4 1.0
O A:HOH1719 2.4 34.4 1.0
O A:HOH1239 2.4 31.1 1.0
O A:HOH1730 2.6 33.9 1.0
O A:ASN711 3.9 32.3 0.6
NE2 A:GLN712 4.1 27.6 1.0
OD2 A:ASP714 4.2 33.1 1.0
OD1 A:ASP714 4.2 29.8 1.0
OE2 A:GLU633 4.3 28.6 1.0
ND2 A:ASN711 4.3 41.3 0.4
O A:HOH1662 4.3 35.3 1.0
NE A:ARG715 4.3 25.3 1.0
OE1 A:GLU639 4.3 26.3 1.0
OE1 A:GLN712 4.4 33.0 1.0
O A:ASN711 4.5 30.6 0.4
OE2 A:GLU639 4.6 28.7 1.0
CD A:GLN712 4.6 34.0 1.0
CG A:ASP714 4.6 42.1 1.0
NH2 A:ARG715 4.7 26.4 1.0
ND2 A:ASN711 4.8 42.7 0.6
CD A:GLU639 4.9 30.1 1.0
CG A:ASN711 4.9 42.9 0.4
OE1 A:GLU633 5.0 30.3 1.0

Calcium binding site 5 out of 5 in 5yne

Go back to Calcium Binding Sites List in 5yne
Calcium binding site 5 out of 5 in the Crystal Structure of Pullulanase From Klebsiella Pneumoniae Complex at 10 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 10 Mm Alpha-Cyclodextrin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1105

b:58.3
occ:1.00
 OE1 A:GLN1070 2.2 42.3 1.0
OD2 A:ASP994 2.2 24.7 1.0
O A:ASP1003 2.3 41.9 1.0
OG A:SER1001 2.4 22.0 1.0
O A:VAL1006 2.4 37.8 1.0
CD A:GLN1070 3.0 45.6 1.0
CB A:SER1001 3.1 21.9 1.0
NE2 A:GLN1070 3.2 41.7 1.0
CG A:ASP994 3.2 29.1 1.0
O A:ASP994 3.5 39.7 1.0
C A:ASP1003 3.5 36.7 1.0
C A:VAL1006 3.6 35.8 1.0
CB A:ASP994 3.8 32.3 1.0
CA A:SER1001 3.9 22.7 1.0
N A:ASP1003 4.1 31.1 1.0
OD1 A:ASP1007 4.1 35.1 1.0
OD1 A:ASP994 4.2 26.2 1.0
CA A:ASP1003 4.2 31.4 1.0
CA A:ASP1007 4.3 28.2 1.0
CG A:GLN1070 4.3 43.2 1.0
C A:SER1001 4.3 34.1 1.0
N A:ASP1007 4.3 37.0 1.0
N A:VAL1006 4.4 35.8 1.0
C A:ASP994 4.5 42.2 1.0
N A:SER1004 4.5 38.0 0.9
CB A:ASP1003 4.5 36.2 1.0
CA A:SER1004 4.6 48.6 0.9
CA A:VAL1006 4.6 36.7 1.0
O A:SER1001 4.7 44.0 1.0
C A:SER1004 4.7 42.4 0.9
N A:LEU1002 4.7 31.5 1.0
CB A:GLN1070 4.8 44.4 1.0
CA A:ASP994 4.8 37.2 1.0
CG A:ASP1007 4.9 43.8 1.0
O A:SER1004 5.0 47.9 0.9

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 05:54:43 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy