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Calcium in PDB 6idy: Crystal Structure of Aspergillus Fumigatus Lipase B

Protein crystallography data

The structure of Crystal Structure of Aspergillus Fumigatus Lipase B, PDB code: 6idy was solved by Y.H.Wang, D.M.Lan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.48 / 2.15
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 152.190, 152.190, 134.290, 90.00, 90.00, 90.00
R / Rfree (%) 17.3 / 19.7

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Aspergillus Fumigatus Lipase B (pdb code 6idy). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of Aspergillus Fumigatus Lipase B, PDB code: 6idy:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 6idy

Go back to Calcium Binding Sites List in 6idy
Calcium binding site 1 out of 3 in the Crystal Structure of Aspergillus Fumigatus Lipase B


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 Aspergillus Fumigatus Lipase B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca501

b:25.9
occ:1.00
 O A:ALA377 2.2 25.3 1.0
O A:HIS380 2.3 29.8 1.0
O A:HOH658 2.4 27.6 1.0
O A:GLY382 2.4 25.0 1.0
O A:HOH635 2.4 26.2 1.0
OD1 A:ASP255 2.4 26.1 1.0
OD2 A:ASP255 2.5 29.5 1.0
CG A:ASP255 2.8 27.3 1.0
C A:ALA377 3.4 26.2 1.0
C A:HIS380 3.5 32.4 1.0
C A:GLY382 3.5 26.2 1.0
N A:GLY382 3.7 23.9 1.0
C A:ASP381 4.0 29.5 1.0
CA A:ALA377 4.2 22.1 1.0
CA A:ASP381 4.2 28.3 1.0
CA A:GLY382 4.2 22.7 1.0
O A:ASP254 4.3 24.5 1.0
N A:ASP381 4.3 29.5 1.0
CB A:ASP255 4.3 22.1 1.0
N A:LEU378 4.4 23.5 1.0
N A:HIS380 4.5 29.1 1.0
O A:HOH795 4.5 38.0 1.0
CA A:HIS380 4.6 29.1 1.0
CA A:LEU378 4.6 23.9 1.0
O A:ASP381 4.6 29.1 1.0
N A:PRO383 4.6 22.1 1.0
CB A:ALA377 4.7 21.9 1.0
O A:HOH654 4.7 27.4 1.0
C A:LEU378 4.8 29.6 1.0
CA A:PRO383 4.8 21.1 1.0
O A:HOH628 4.9 19.8 1.0

Calcium binding site 2 out of 3 in 6idy

Go back to Calcium Binding Sites List in 6idy
Calcium binding site 2 out of 3 in the Crystal Structure of Aspergillus Fumigatus Lipase B


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 Aspergillus Fumigatus Lipase B within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca501

b:25.8
occ:1.00
 O B:ALA377 2.2 24.0 1.0
O B:HIS380 2.3 28.9 1.0
O B:GLY382 2.4 23.4 1.0
O B:HOH711 2.4 24.9 1.0
O B:HOH726 2.4 27.5 1.0
OD1 B:ASP255 2.4 26.9 1.0
OD2 B:ASP255 2.5 25.3 1.0
CG B:ASP255 2.8 26.2 1.0
C B:ALA377 3.4 24.1 1.0
C B:HIS380 3.5 30.4 1.0
C B:GLY382 3.5 25.6 1.0
N B:GLY382 3.7 25.8 1.0
C B:ASP381 4.0 30.5 1.0
CA B:ALA377 4.1 20.2 1.0
CA B:GLY382 4.2 24.5 1.0
CA B:ASP381 4.2 28.1 1.0
O B:ASP254 4.3 26.0 1.0
N B:ASP381 4.3 28.3 1.0
CB B:ASP255 4.3 20.6 1.0
N B:LEU378 4.4 21.7 1.0
O B:HOH821 4.4 37.2 1.0
N B:HIS380 4.5 25.4 1.0
CA B:HIS380 4.6 25.6 1.0
CA B:LEU378 4.6 22.9 1.0
N B:PRO383 4.6 21.3 1.0
CB B:ALA377 4.6 20.1 1.0
O B:HOH638 4.7 27.4 1.0
O B:ASP381 4.7 30.1 1.0
C B:LEU378 4.8 28.1 1.0
CA B:PRO383 4.8 19.9 1.0
O B:HOH624 4.9 17.1 1.0
C B:ASP254 5.0 25.0 1.0
O B:HOH813 5.0 44.2 1.0

Calcium binding site 3 out of 3 in 6idy

Go back to Calcium Binding Sites List in 6idy
Calcium binding site 3 out of 3 in the Crystal Structure of Aspergillus Fumigatus Lipase B


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 Aspergillus Fumigatus Lipase B within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca501

b:37.7
occ:1.00
 O C:ALA377 2.1 38.8 1.0
O C:HOH639 2.3 37.7 1.0
OD2 C:ASP255 2.4 39.5 1.0
OD1 C:ASP255 2.4 34.6 1.0
O C:HIS380 2.4 42.8 1.0
O C:GLY382 2.5 37.9 1.0
O C:HOH703 2.6 34.0 1.0
CG C:ASP255 2.7 36.2 1.0
C C:ALA377 3.3 39.5 1.0
C C:GLY382 3.6 38.1 1.0
N C:GLY382 3.7 37.7 1.0
C C:HIS380 3.7 44.2 1.0
C C:ASP381 4.0 42.7 1.0
CA C:ALA377 4.1 34.8 1.0
CA C:GLY382 4.2 35.8 1.0
CA C:ASP381 4.2 40.5 1.0
CB C:ASP255 4.2 30.0 1.0
O C:ASP254 4.3 35.1 1.0
N C:LEU378 4.3 36.6 1.0
N C:ASP381 4.4 41.4 1.0
CA C:LEU378 4.5 37.8 1.0
N C:HIS380 4.7 40.4 1.0
CB C:ALA377 4.7 34.2 1.0
N C:PRO383 4.7 33.2 1.0
O C:ASP381 4.7 42.4 1.0
CA C:HIS380 4.8 40.6 1.0
C C:LEU378 4.8 44.1 1.0
CA C:PRO383 4.9 31.3 1.0
C C:ASP254 4.9 35.2 1.0
O C:HOH612 5.0 28.5 1.0

Reference:

Y.H.Wang, D.M.Lan. Crystal Structure of Aspergillus Fumigatus Lipase B To Be Published.
Page generated: Wed Jul 9 14:50:30 2025

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