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Calcium in PDB 2ydp: Structure of the E242A Mutant of the Alpha-L-Arabinofuranosidase ARB93A From Fusarium Graminearum in Complex with An Iminosugar Inhibitor

Enzymatic activity of Structure of the E242A Mutant of the Alpha-L-Arabinofuranosidase ARB93A From Fusarium Graminearum in Complex with An Iminosugar Inhibitor

All present enzymatic activity of Structure of the E242A Mutant of the Alpha-L-Arabinofuranosidase ARB93A From Fusarium Graminearum in Complex with An Iminosugar Inhibitor:
3.2.1.55;

Protein crystallography data

The structure of Structure of the E242A Mutant of the Alpha-L-Arabinofuranosidase ARB93A From Fusarium Graminearum in Complex with An Iminosugar Inhibitor, PDB code: 2ydp was solved by E.D.Goddard-Borger, R.Carapito, J.M.Jeltsch, V.Phalip, R.V.Stick, A.Varrot, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.97 / 1.85
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 56.930, 57.800, 91.600, 90.14, 93.55, 114.50
R / Rfree (%) 17.1 / 22.6

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of the E242A Mutant of the Alpha-L-Arabinofuranosidase ARB93A From Fusarium Graminearum in Complex with An Iminosugar Inhibitor (pdb code 2ydp). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Structure of the E242A Mutant of the Alpha-L-Arabinofuranosidase ARB93A From Fusarium Graminearum in Complex with An Iminosugar Inhibitor, PDB code: 2ydp:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 2ydp

Go back to Calcium Binding Sites List in 2ydp
Calcium binding site 1 out of 3 in the Structure of the E242A Mutant of the Alpha-L-Arabinofuranosidase ARB93A From Fusarium Graminearum in Complex with An Iminosugar Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of the E242A Mutant of the Alpha-L-Arabinofuranosidase ARB93A From Fusarium Graminearum in Complex with An Iminosugar Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca502

b:31.9
occ:1.00
 O A:PRO33 2.3 20.0 1.0
O A:HOH2029 2.4 31.1 1.0
O A:HOH2025 2.4 33.8 1.0
OD1 A:ASP32 2.5 27.3 1.0
OD1 B:ASN248 2.5 25.7 1.0
O A:HOH2024 2.7 17.0 1.0
O A:HOH2392 3.2 49.8 1.0
C A:PRO33 3.5 20.8 1.0
CG A:ASP32 3.5 23.9 1.0
CG B:ASN248 3.6 22.6 1.0
N A:PRO33 3.9 20.6 1.0
ND2 B:ASN248 4.0 19.4 1.0
OD2 A:ASP32 4.1 27.8 1.0
CG A:PRO33 4.1 20.1 1.0
CD A:PRO33 4.1 19.8 1.0
O A:GLY364 4.1 19.4 1.0
C A:ASP32 4.2 20.4 1.0
CA A:PRO33 4.2 20.0 1.0
C A:PRO34 4.5 23.0 1.0
OE1 A:GLN41 4.5 18.1 1.0
N A:PRO34 4.5 21.0 1.0
O A:ASP32 4.6 20.7 1.0
CB A:ASP32 4.7 21.5 1.0
N A:THR35 4.7 24.0 1.0
CA A:PRO34 4.7 22.2 1.0
CB A:PRO33 4.7 20.4 1.0
O A:PRO34 4.7 22.4 1.0
CA A:ASP32 4.8 20.4 1.0
CB B:ASN248 4.9 20.5 1.0
O A:HOH2023 4.9 40.2 1.0
O A:ASN366 5.0 12.4 1.0

Calcium binding site 2 out of 3 in 2ydp

Go back to Calcium Binding Sites List in 2ydp
Calcium binding site 2 out of 3 in the Structure of the E242A Mutant of the Alpha-L-Arabinofuranosidase ARB93A From Fusarium Graminearum in Complex with An Iminosugar Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of the E242A Mutant of the Alpha-L-Arabinofuranosidase ARB93A From Fusarium Graminearum in Complex with An Iminosugar Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca502

b:41.0
occ:1.00
 OD1 B:ASP32 2.3 31.6 1.0
O B:HOH2006 2.3 34.5 1.0
O B:PRO33 2.4 28.7 1.0
CG B:ASP32 3.4 30.9 1.0
C B:PRO33 3.6 29.0 1.0
OD2 B:ASP32 3.9 33.0 1.0
O B:GLY364 4.0 29.3 1.0
N B:PRO33 4.0 28.8 1.0
CD B:PRO33 4.0 29.0 1.0
C B:ASP32 4.2 29.2 1.0
CG B:PRO33 4.2 28.4 1.0
CA B:PRO33 4.3 28.9 1.0
OE1 B:GLN41 4.5 27.1 1.0
CB B:ASP32 4.6 29.4 1.0
N B:PRO34 4.6 30.1 1.0
O B:ASP32 4.6 29.4 1.0
C B:PRO34 4.7 32.1 1.0
CA B:ASP32 4.7 28.7 1.0
N B:THR35 4.8 33.0 1.0
CB B:PRO33 4.8 27.9 1.0
CA B:PRO34 4.9 31.2 1.0
O B:ASN366 4.9 22.9 1.0
CG2 B:THR35 4.9 34.2 1.0

Calcium binding site 3 out of 3 in 2ydp

Go back to Calcium Binding Sites List in 2ydp
Calcium binding site 3 out of 3 in the Structure of the E242A Mutant of the Alpha-L-Arabinofuranosidase ARB93A From Fusarium Graminearum in Complex with An Iminosugar Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of the E242A Mutant of the Alpha-L-Arabinofuranosidase ARB93A From Fusarium Graminearum in Complex with An Iminosugar Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca502

b:24.1
occ:1.00
 O A:HOH2290 2.2 24.6 1.0
O C:PRO33 2.3 15.6 1.0
OD1 A:ASN248 2.4 18.3 1.0
OD1 C:ASP32 2.4 14.7 1.0
O C:HOH2009 2.6 38.9 1.0
O A:HOH2287 2.6 17.8 1.0
O A:HOH2289 2.8 32.6 1.0
CG A:ASN248 3.3 19.3 1.0
CG C:ASP32 3.5 16.9 1.0
C C:PRO33 3.5 16.4 1.0
ND2 A:ASN248 3.7 20.1 1.0
N C:PRO33 3.9 15.1 1.0
OD2 C:ASP32 4.0 20.1 1.0
O C:GLY364 4.0 18.3 1.0
C C:ASP32 4.1 15.8 1.0
CD C:PRO33 4.2 14.6 1.0
CG C:PRO33 4.2 14.6 1.0
CA C:PRO33 4.3 15.7 1.0
O C:ASP32 4.4 15.9 1.0
OE1 C:GLN41 4.4 18.8 1.0
O A:HOH2288 4.5 49.8 1.0
CB A:ASN248 4.5 16.1 1.0
C C:PRO34 4.5 17.7 1.0
N C:PRO34 4.6 17.3 1.0
CA A:ASN248 4.6 16.8 1.0
CB C:ASP32 4.7 16.5 1.0
O C:HOH2283 4.7 39.6 1.0
CA C:PRO34 4.7 17.1 1.0
CA C:ASP32 4.7 15.6 1.0
O C:PRO34 4.7 17.9 1.0
CB C:PRO33 4.8 15.3 1.0
N C:THR35 4.8 17.8 1.0
O C:ASN366 4.9 13.0 1.0
N A:ASN248 5.0 15.8 1.0

Reference:

E.D.Goddard-Borger, R.Carapito, J.Jeltsch, V.Phalip, R.V.Stick, A.Varrot. Alpha-L-Arabinofuranosylated Pyrrolidines As Arabinanase Inhibitors. Chem.Commun.(Camb.) V. 47 9684 2011.
ISSN: ISSN 1359-7345
PubMed: 21773614
DOI: 10.1039/C1CC13675E
Page generated: Tue Jul 8 09:37:51 2025

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