Calcium in PDB 2fgz: Crystal Structure Analysis of Apo Pullulanase From Klebsiella Pneumoniae

All present enzymatic activity of Crystal Structure Analysis of Apo Pullulanase From Klebsiella Pneumoniae:
3.2.1.41;

The structure of Crystal Structure Analysis of Apo Pullulanase From Klebsiella Pneumoniae, PDB code: 2fgz was solved by B.Mikami, H.Iwamoto, Y.Katsuya, H.-J.Yoon, E.Demirkan-Sarikaya, D.Malle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	14.94 / 1.75
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	148.984, 60.214, 132.791, 90.00, 112.61, 90.00
R / Rfree (%)	18.3 / 21.4

The binding sites of Calcium atom in the Crystal Structure Analysis of Apo Pullulanase From Klebsiella Pneumoniae (pdb code 2fgz). 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 Analysis of Apo Pullulanase From Klebsiella Pneumoniae, PDB code: 2fgz:
Jump to Calcium binding site number: 1; 2; 3; 4;

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure Analysis of Apo Pullulanase From Klebsiella Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1191 b:14.0 occ:1.00 O A:TYR555 2.3 13.1 1.0 OD2 A:ASP893 2.4 15.1 1.0 O A:HOH2094 2.4 13.2 1.0 O A:ALA550 2.4 14.1 1.0 OD1 A:ASP553 2.5 12.4 1.0 O A:HOH1393 2.5 16.4 1.0 O A:HOH1297 2.5 12.6 1.0 C A:TYR555 3.5 12.3 1.0 CG A:ASP553 3.5 15.2 1.0 C A:ALA550 3.5 15.0 1.0 CG A:ASP893 3.5 16.4 1.0 OD2 A:ASP553 3.8 13.0 1.0 CA A:ALA550 3.9 13.6 1.0 OD1 A:ASP893 4.1 17.6 1.0 CA A:TYR555 4.2 12.2 1.0 N A:TYR555 4.2 12.9 1.0 CB A:ALA550 4.2 13.3 1.0 CB A:TYR555 4.5 11.5 1.0 O A:ASP553 4.5 13.7 1.0 N A:ASN556 4.5 13.5 1.0 ND2 A:ASN556 4.6 15.2 1.0 O A:HOH1760 4.6 35.5 1.0 CB A:ASN556 4.6 14.5 1.0 N A:GLN551 4.7 14.1 1.0 N A:ASP553 4.7 13.2 1.0 O A:ASP893 4.7 13.9 1.0 CB A:ASP893 4.7 12.8 1.0 O A:THR484 4.8 18.7 1.0 CA A:ASP893 4.8 12.5 1.0 C A:ASP553 4.8 12.8 1.0 O A:HOH1511 4.8 19.6 1.0 CB A:ASP553 4.8 13.0 1.0 CA A:ASN556 4.9 13.0 1.0 CA A:ASP553 5.0 11.3 1.0

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure Analysis of Apo Pullulanase From Klebsiella Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1192 b:32.6 occ:1.00 O A:ASP1003 2.1 21.0 1.0 O A:HOH1644 2.1 18.0 1.0 OD2 A:ASP994 2.1 21.5 1.0 OE1 A:GLN1070 2.1 20.0 1.0 O A:VAL1006 2.2 20.2 1.0 OG A:SER1001 2.3 19.2 1.0 C A:ASP1003 3.2 21.5 1.0 CD A:GLN1070 3.2 21.7 1.0 CG A:ASP994 3.3 23.2 1.0 C A:VAL1006 3.3 20.4 1.0 CB A:SER1001 3.4 22.6 1.0 N A:ASP1003 3.8 21.2 1.0 NE2 A:GLN1070 3.9 20.7 1.0 CA A:ASP1003 4.0 21.5 1.0 CB A:ASP994 4.0 20.6 1.0 CA A:SER1001 4.1 21.9 1.0 O A:ASP994 4.1 20.4 1.0 N A:SER1004 4.1 20.8 1.0 OD1 A:ASP994 4.1 22.6 1.0 OD1 A:ASP1007 4.1 21.9 1.0 N A:ASP1007 4.2 19.0 1.0 N A:VAL1006 4.2 21.4 1.0 CA A:ASP1007 4.2 19.3 1.0 CB A:ASP1003 4.3 22.7 1.0 O A:HOH2149 4.3 27.4 1.0 CG A:GLN1070 4.3 21.4 1.0 CA A:SER1004 4.3 21.1 1.0 CA A:VAL1006 4.3 20.5 1.0 C A:SER1001 4.5 23.3 1.0 C A:SER1004 4.5 21.2 1.0 N A:LEU1002 4.5 21.2 1.0 CB A:GLN1070 4.6 22.1 1.0 N A:ARG1005 4.8 21.4 1.0 O A:SER1004 4.9 20.1 1.0 CG2 A:VAL1006 5.0 22.0 1.0 CG A:ASP1007 5.0 22.5 1.0 C A:ASP994 5.0 19.8 1.0

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure Analysis of Apo Pullulanase From Klebsiella Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1193 b:38.4 occ:1.00 O A:HOH1980 2.1 17.1 1.0 O A:HOH1306 2.1 25.1 1.0 O A:HOH1981 2.2 22.3 1.0 O A:HOH1305 2.2 21.2 1.0 O A:HOH2097 2.3 15.0 1.0 O A:HOH1569 2.3 23.4 1.0 OE1 A:GLU639 4.1 21.5 1.0 OE1 A:GLU633 4.1 24.3 1.0 NE A:ARG715 4.2 19.6 1.0 OD2 A:ASP714 4.2 22.4 1.0 OE1 A:GLN712 4.2 21.0 1.0 OD1 A:ASP714 4.2 21.5 1.0 NH2 A:ARG715 4.3 20.1 1.0 O A:HOH1567 4.4 21.6 1.0 OE2 A:GLU639 4.4 22.2 1.0 NE2 A:GLN712 4.5 19.3 1.0 O A:ASN711 4.5 27.5 1.0 O A:HOH2485 4.6 54.7 1.0 OE2 A:GLU633 4.6 23.0 1.0 CG A:ASP714 4.6 22.2 1.0 CD A:GLU639 4.6 21.0 1.0 CD A:GLN712 4.7 21.1 1.0 CZ A:ARG715 4.7 20.6 1.0 CD A:GLU633 4.8 23.8 1.0 ND2 A:ASN711 5.0 39.0 1.0

Calcium binding site 4 out of 4 in the Crystal Structure Analysis of Apo Pullulanase From Klebsiella Pneumoniae


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure Analysis of Apo Pullulanase From Klebsiella Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1194 b:16.3 occ:1.00 OD1 A:ASP481 2.2 10.0 1.0 O A:HOH1260 2.2 9.8 1.0 OE2 A:GLU568 2.2 13.0 1.0 OE2 A:GLU487 2.3 12.2 1.0 O A:LEU482 2.3 14.0 1.0 O A:HOH2093 2.3 11.7 1.0 CD A:GLU568 3.1 12.6 1.0 CD A:GLU487 3.2 12.4 1.0 OE1 A:GLU568 3.3 15.6 1.0 CG A:ASP481 3.4 13.2 1.0 C A:LEU482 3.4 13.9 1.0 N A:LEU482 3.7 13.4 1.0 CG A:GLU487 3.8 12.5 1.0 OG A:SER388 4.0 12.5 1.0 OD2 A:ASP481 4.1 13.3 1.0 C A:ASP481 4.1 11.9 1.0 OE1 A:GLU487 4.2 12.3 1.0 CA A:LEU482 4.2 12.9 1.0 O A:HOH1259 4.3 11.4 1.0 N A:GLY569 4.3 12.9 1.0 CA A:ASP481 4.3 12.3 1.0 CB A:ASP481 4.4 12.7 1.0 O A:HOH1286 4.4 14.3 1.0 CG A:LEU482 4.5 14.3 1.0 N A:ALA483 4.5 12.9 1.0 CG A:GLU568 4.5 11.5 1.0 O A:VAL485 4.6 14.6 1.0 CA A:ALA483 4.7 14.9 1.0 CA A:GLU568 4.8 12.0 1.0 O A:ASP481 4.9 12.7 1.0 CB A:LEU482 4.9 15.7 1.0 CD1 A:LEU482 4.9 17.3 1.0 CB A:GLU568 4.9 11.2 1.0

B.Mikami, H.Iwamoto, D.Malle, H.-J.Yoon, E.Demirkan-Sarikaya, Y.Mezaki, Y.Katsuya. Crystal Structure of Pullulanase: Evidence For Parallel Binding of Oligosaccharides in the Active Site J.Mol.Biol. V. 359 690 2006.
ISSN: ISSN 0022-2836
PubMed: 16650854
DOI: 10.1016/J.JMB.2006.03.058