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Calcium in PDB 2fhb: Crystal Structure Analysis of Klebsiella Pneumoniae Pullulanase Complexed with Maltose

Enzymatic activity of Crystal Structure Analysis of Klebsiella Pneumoniae Pullulanase Complexed with Maltose

All present enzymatic activity of Crystal Structure Analysis of Klebsiella Pneumoniae Pullulanase Complexed with Maltose:
3.2.1.41;

Protein crystallography data

The structure of Crystal Structure Analysis of Klebsiella Pneumoniae Pullulanase Complexed with Maltose, PDB code: 2fhb 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) 14.96 / 1.80
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 150.258, 60.601, 135.104, 90.00, 114.43, 90.00
R / Rfree (%) 17.2 / 20.5

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure Analysis of Klebsiella Pneumoniae Pullulanase Complexed with Maltose (pdb code 2fhb). 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 Analysis of Klebsiella Pneumoniae Pullulanase Complexed with Maltose, PDB code: 2fhb:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 2fhb

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Calcium binding site 1 out of 5 in the Crystal Structure Analysis of Klebsiella Pneumoniae Pullulanase Complexed with Maltose


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 Klebsiella Pneumoniae Pullulanase Complexed with Maltose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2401

b:22.3
occ:1.00
 O A:TYR555 2.3 21.1 1.0
OD2 A:ASP893 2.3 20.9 1.0
O A:ALA550 2.4 23.0 1.0
O A:HOH1495 2.5 21.4 1.0
O A:HOH1494 2.5 21.0 1.0
OD1 A:ASP553 2.5 20.8 1.0
O A:HOH1272 2.6 17.9 1.0
C A:TYR555 3.5 21.4 1.0
C A:ALA550 3.5 23.1 1.0
CG A:ASP553 3.5 23.5 1.0
CG A:ASP893 3.5 22.9 1.0
OD2 A:ASP553 3.9 22.5 1.0
CA A:ALA550 4.0 22.8 1.0
OD1 A:ASP893 4.1 24.5 1.0
CA A:TYR555 4.2 21.5 1.0
N A:TYR555 4.2 21.0 1.0
O A:HOH1621 4.3 36.3 1.0
CB A:ALA550 4.3 21.7 1.0
O A:ASP553 4.6 19.9 1.0
CB A:TYR555 4.6 21.7 1.0
N A:ASN556 4.6 21.4 1.0
ND2 A:ASN556 4.6 22.5 1.0
CB A:ASN556 4.6 19.1 1.0
O A:ASP893 4.7 22.6 1.0
N A:GLN551 4.7 21.2 1.0
CB A:ASP893 4.7 20.5 1.0
CA A:ASP893 4.8 21.1 1.0
N A:ASP553 4.8 21.2 1.0
O A:THR484 4.8 27.9 1.0
C A:ASP553 4.8 19.5 1.0
CB A:ASP553 4.8 21.3 1.0
CA A:ASN556 4.9 20.9 1.0
O A:HOH1597 4.9 30.5 1.0

Calcium binding site 2 out of 5 in 2fhb

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Calcium binding site 2 out of 5 in the Crystal Structure Analysis of Klebsiella Pneumoniae Pullulanase Complexed with Maltose


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 Klebsiella Pneumoniae Pullulanase Complexed with Maltose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2402

b:48.3
occ:1.00
 OE1 A:GLN1070 2.0 43.8 1.0
OD2 A:ASP994 2.1 31.3 1.0
O A:HOH1525 2.1 31.9 1.0
O A:ASP1003 2.2 35.3 1.0
O A:VAL1006 2.3 35.2 1.0
OG A:SER1001 2.3 38.8 1.0
CD A:GLN1070 3.2 45.3 1.0
CG A:ASP994 3.2 31.4 1.0
C A:ASP1003 3.3 37.7 1.0
C A:VAL1006 3.4 35.0 1.0
CB A:SER1001 3.4 42.1 1.0
O A:ASP994 3.8 32.4 1.0
NE2 A:GLN1070 3.8 46.0 1.0
CB A:ASP994 3.9 30.0 1.0
N A:ASP1003 4.0 37.9 1.0
CA A:SER1001 4.1 41.5 1.0
O A:HOH2063 4.1 58.1 1.0
CA A:ASP1007 4.1 35.0 1.0
OD1 A:ASP1007 4.2 40.5 1.0
N A:ASP1007 4.2 34.6 1.0
CA A:ASP1003 4.2 38.1 1.0
OD1 A:ASP994 4.2 29.9 1.0
N A:SER1004 4.3 37.9 1.0
N A:VAL1006 4.3 38.0 1.0
CG A:GLN1070 4.4 43.5 1.0
CA A:VAL1006 4.4 36.3 1.0
C A:SER1001 4.5 41.2 1.0
CA A:SER1004 4.5 40.0 1.0
CB A:ASP1003 4.5 38.4 1.0
N A:LEU1002 4.6 40.2 1.0
C A:ASP994 4.7 32.2 1.0
CB A:GLN1070 4.7 43.5 1.0
C A:SER1004 4.8 40.3 1.0
CG A:ASP1007 4.9 39.5 1.0
CA A:ASP994 4.9 31.3 1.0

Calcium binding site 3 out of 5 in 2fhb

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Calcium binding site 3 out of 5 in the Crystal Structure Analysis of Klebsiella Pneumoniae Pullulanase Complexed with Maltose


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 Klebsiella Pneumoniae Pullulanase Complexed with Maltose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2403

b:43.8
occ:1.00
 O A:HOH1425 2.2 29.1 1.0
O A:HOH1247 2.2 33.6 1.0
O A:HOH1253 2.2 27.0 1.0
O A:HOH1746 2.2 21.7 1.0
O A:HOH1747 2.2 27.0 1.0
O A:HOH1748 2.3 26.7 1.0
NE A:ARG715 4.0 24.9 1.0
OE1 A:GLU639 4.1 33.2 1.0
OE1 A:GLU633 4.1 30.4 1.0
OD2 A:ASP714 4.2 29.4 1.0
O A:HOH1530 4.2 28.9 1.0
OE1 A:GLN712 4.3 25.0 1.0
NH2 A:ARG715 4.3 26.4 1.0
OE2 A:GLU639 4.3 34.5 1.0
OD1 A:ASP714 4.3 28.6 1.0
NE2 A:GLN712 4.5 24.2 1.0
OE2 A:GLU633 4.5 31.2 1.0
CZ A:ARG715 4.6 27.0 1.0
CD A:GLU639 4.6 31.5 1.0
CG A:ASP714 4.7 27.6 1.0
O A:ASN711 4.7 30.1 1.0
CD A:GLU633 4.7 29.0 1.0
CD A:GLN712 4.8 24.8 1.0
O A:HOH1934 4.9 64.1 1.0
O A:HOH1820 5.0 56.0 1.0

Calcium binding site 4 out of 5 in 2fhb

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Calcium binding site 4 out of 5 in the Crystal Structure Analysis of Klebsiella Pneumoniae Pullulanase Complexed with Maltose


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 Klebsiella Pneumoniae Pullulanase Complexed with Maltose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2404

b:23.9
occ:1.00
 OD1 A:ASP481 2.2 20.1 1.0
O A:LEU482 2.3 20.6 1.0
O A:HOH1254 2.3 22.2 1.0
O A:HOH1496 2.4 23.3 1.0
OE2 A:GLU487 2.4 18.8 1.0
OE2 A:GLU568 2.5 22.0 1.0
CD A:GLU568 3.3 18.2 1.0
CD A:GLU487 3.3 23.1 1.0
CG A:ASP481 3.4 20.6 1.0
C A:LEU482 3.5 23.1 1.0
OE1 A:GLU568 3.5 22.3 1.0
N A:LEU482 3.7 22.0 1.0
CG A:GLU487 3.9 22.6 1.0
OG A:SER388 4.1 20.5 1.0
OD2 A:ASP481 4.1 19.8 1.0
C A:ASP481 4.2 21.2 1.0
CA A:LEU482 4.2 23.1 1.0
O A:HOH1352 4.3 18.5 1.0
OE1 A:GLU487 4.3 20.8 1.0
N A:GLY569 4.3 23.4 1.0
CA A:ASP481 4.4 20.2 1.0
CB A:ASP481 4.5 19.6 1.0
N A:ALA483 4.5 21.7 1.0
CG A:LEU482 4.5 25.8 1.0
O A:HOH1129 4.5 23.9 1.0
O A:VAL485 4.6 23.0 1.0
CA A:ALA483 4.7 24.6 1.0
CG A:GLU568 4.7 21.4 1.0
CA A:GLU568 4.9 21.7 1.0
O A:ASP481 4.9 20.4 1.0
CB A:LEU482 4.9 23.6 1.0

Calcium binding site 5 out of 5 in 2fhb

Go back to Calcium Binding Sites List in 2fhb
Calcium binding site 5 out of 5 in the Crystal Structure Analysis of Klebsiella Pneumoniae Pullulanase Complexed with Maltose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure Analysis of Klebsiella Pneumoniae Pullulanase Complexed with Maltose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2408

b:97.3
occ:1.00
 O A:THR150 2.4 74.5 0.8
O A:ASP162 2.4 73.6 0.8
OD1 A:ASP148 2.5 81.9 0.8
OD1 A:ASP162 2.7 77.5 0.8
CG A:ASP148 2.8 81.8 0.8
OD2 A:ASP148 2.8 82.6 0.8
C A:THR150 3.4 74.4 0.8
CG A:ASP162 3.4 76.3 0.8
CB A:THR150 3.6 74.6 0.8
C A:ASP162 3.6 73.9 0.8
OD2 A:ASP162 3.9 76.9 0.8
CA A:THR150 3.9 74.9 0.8
CB A:ASP148 4.0 81.2 0.8
N A:THR150 4.1 76.0 0.8
CG2 A:THR150 4.2 74.1 0.8
CA A:ASP162 4.3 74.5 0.8
CB A:ASP162 4.4 75.5 0.8
OE1 A:GLU45 4.5 61.2 0.8
NE2 A:GLN48 4.5 68.5 0.8
N A:VAL151 4.6 73.7 0.8
OG1 A:THR150 4.6 73.8 0.8
N A:SER163 4.6 73.5 1.0
CA A:SER163 4.9 72.7 1.0
CA A:VAL151 5.0 73.4 0.8

Reference:

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
Page generated: Fri Jul 12 10:28:31 2024

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