Calcium in PDB 5yn2: Crystal Structure of Apo Pullulanase From Klebsiella Pneumoniae in Space Group P43212

The structure of Crystal Structure of Apo Pullulanase From Klebsiella Pneumoniae in Space Group P43212, PDB code: 5yn2 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)	43.80 / 2.30
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	89.038, 89.038, 301.843, 90.00, 90.00, 90.00
R / Rfree (%)	18.4 / 24.2

The structure of Crystal Structure of Apo Pullulanase From Klebsiella Pneumoniae in Space Group P43212 also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Calcium atom in the Crystal Structure of Apo Pullulanase From Klebsiella Pneumoniae in Space Group P43212 (pdb code 5yn2). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Apo Pullulanase From Klebsiella Pneumoniae in Space Group P43212, PDB code: 5yn2:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of Apo Pullulanase From Klebsiella Pneumoniae in Space Group P43212


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 Apo Pullulanase From Klebsiella Pneumoniae in Space Group P43212 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1101 b:37.2 occ:1.00 OD1 A:ASP893 2.3 38.3 1.0 O A:TYR555 2.4 35.0 1.0 O A:HOH1391 2.4 34.0 1.0 OD1 A:ASP553 2.4 37.6 1.0 O A:HOH1365 2.5 33.3 1.0 O A:HOH1555 2.5 36.4 1.0 O A:ALA550 2.5 36.7 1.0 CG A:ASP553 3.5 37.8 1.0 CG A:ASP893 3.5 39.2 1.0 C A:ALA550 3.5 39.4 1.0 C A:TYR555 3.5 32.4 1.0 CA A:ALA550 3.8 40.1 1.0 OD2 A:ASP553 3.9 39.8 1.0 N A:TYR555 4.1 36.6 1.0 OD2 A:ASP893 4.1 39.7 1.0 CA A:TYR555 4.2 35.6 1.0 CB A:ALA550 4.2 34.0 1.0 O A:HOH1308 4.3 41.9 1.0 CB A:TYR555 4.3 36.3 1.0 O A:ASP553 4.5 33.2 1.0 ND2 A:ASN556 4.6 33.8 1.0 N A:ASN556 4.6 32.8 1.0 CB A:ASP893 4.6 30.5 1.0 N A:ASP553 4.7 38.6 1.0 CA A:ASP893 4.7 38.8 1.0 N A:GLN551 4.7 42.8 1.0 O A:ASP893 4.7 37.9 1.0 C A:ASP553 4.8 38.0 1.0 CB A:ASP553 4.8 34.5 1.0 CB A:ASN556 4.9 31.8 1.0 CA A:ASN556 4.9 33.0 1.0 CA A:ASP553 5.0 38.4 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Apo Pullulanase From Klebsiella Pneumoniae in Space Group P43212


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 Apo Pullulanase From Klebsiella Pneumoniae in Space Group P43212 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1102 b:33.5 occ:1.00 OD1 A:ASP481 2.2 30.4 1.0 O A:HOH1289 2.4 31.4 1.0 OE2 A:GLU487 2.4 37.6 1.0 O A:LEU482 2.4 36.8 1.0 OE2 A:GLU568 2.4 35.8 1.0 O A:HOH1486 2.4 35.2 1.0 CD A:GLU568 3.3 35.2 1.0 CD A:GLU487 3.3 37.5 1.0 CG A:ASP481 3.4 32.8 1.0 OE1 A:GLU568 3.5 31.5 1.0 C A:LEU482 3.5 32.5 1.0 N A:LEU482 3.6 32.1 1.0 CG A:GLU487 4.0 36.7 1.0 OG A:SER388 4.0 32.2 1.0 C A:ASP481 4.1 31.2 1.0 OD2 A:ASP481 4.1 33.7 1.0 CA A:LEU482 4.1 33.2 1.0 OE1 A:GLU487 4.2 40.2 1.0 O A:HOH1321 4.2 32.7 1.0 CA A:ASP481 4.3 34.3 1.0 N A:GLY569 4.3 34.5 1.0 CB A:ASP481 4.4 29.3 1.0 CG A:LEU482 4.5 35.0 1.0 O A:HOH1241 4.5 38.2 1.0 O A:VAL485 4.6 40.8 1.0 N A:ALA483 4.6 35.3 1.0 CG A:GLU568 4.7 28.5 1.0 CB A:LEU482 4.8 34.5 1.0 CD1 A:LEU482 4.8 39.9 1.0 O A:ASP481 4.8 32.8 1.0 CA A:GLU568 4.9 31.5 1.0 CA A:ALA483 4.9 34.6 1.0 CD2 A:PHE562 5.0 34.9 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Apo Pullulanase From Klebsiella Pneumoniae in Space Group P43212


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 Apo Pullulanase From Klebsiella Pneumoniae in Space Group P43212 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1103 b:68.5 occ:1.00 O A:ASP162 2.2 56.0 1.0 OD2 A:ASP148 2.4 59.9 1.0 O A:THR150 2.6 59.1 1.0 OD1 A:ASP148 2.7 64.9 1.0 CG A:ASP148 2.9 59.3 1.0 OD1 A:ASP162 3.0 60.9 1.0 C A:ASP162 3.4 60.2 1.0 CG A:ASP162 3.5 61.6 1.0 C A:THR150 3.7 53.9 1.0 OD2 A:ASP162 3.9 59.6 1.0 CB A:THR150 3.9 55.5 1.0 O A:HOH1221 3.9 63.6 1.0 OE1 A:GLU45 4.0 51.2 1.0 NE2 A:GLN48 4.0 64.5 1.0 CA A:ASP162 4.1 58.9 1.0 CA A:THR150 4.2 52.6 1.0 CB A:ASP162 4.3 62.1 1.0 CG2 A:THR150 4.3 47.1 1.0 N A:THR150 4.4 59.2 1.0 CB A:ASP148 4.4 57.3 1.0 N A:SER163 4.5 55.9 1.0 O A:HOH1208 4.6 51.9 1.0 CA A:SER163 4.7 53.5 1.0 N A:VAL151 4.8 51.1 1.0 CB A:SER163 4.9 58.9 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Apo Pullulanase From Klebsiella Pneumoniae in Space Group P43212


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 Apo Pullulanase From Klebsiella Pneumoniae in Space Group P43212 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1104 b:62.1 occ:1.00 O A:ASP1003 2.2 49.9 1.0 OD2 A:ASP994 2.2 50.1 1.0 OE1 A:GLN1070 2.2 54.6 1.0 O A:HOH1210 2.3 51.6 1.0 O A:VAL1006 2.4 52.2 1.0 OG A:SER1001 2.4 48.3 1.0 CB A:SER1001 3.1 48.4 1.0 CG A:ASP994 3.2 50.1 1.0 CD A:GLN1070 3.3 61.2 1.0 C A:ASP1003 3.3 56.0 1.0 C A:VAL1006 3.5 50.1 1.0 CA A:SER1001 3.8 46.4 1.0 NE2 A:GLN1070 3.8 53.0 1.0 CB A:ASP994 3.8 47.9 1.0 N A:ASP1003 3.8 50.6 1.0 O A:ASP994 3.9 50.9 1.0 CA A:ASP1003 4.1 51.8 1.0 OD1 A:ASP994 4.2 51.0 1.0 C A:SER1001 4.2 52.3 1.0 N A:VAL1006 4.2 45.5 1.0 OD1 A:ASP1007 4.3 57.1 1.0 N A:SER1004 4.3 56.1 1.0 CB A:ASP1003 4.4 49.8 1.0 N A:LEU1002 4.4 53.7 1.0 N A:ASP1007 4.4 45.2 1.0 C A:SER1004 4.4 60.7 1.0 CA A:ASP1007 4.4 48.6 1.0 CA A:SER1004 4.5 57.5 1.0 O A:SER1004 4.5 57.4 1.0 CA A:VAL1006 4.5 51.4 1.0 CG A:GLN1070 4.6 53.5 1.0 N A:ARG1005 4.7 57.1 1.0 CB A:GLN1070 4.8 52.1 1.0 C A:ASP994 4.8 53.5 1.0 O A:SER1001 4.9 52.2 1.0 CA A:ASP994 5.0 45.8 1.0 C A:LEU1002 5.0 53.1 1.0

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