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Manganese in PDB 2ydt: Structure of the Alpha-L-Arabinofuranosidase ARB93A From Fusarium Graminearum in Complexe with An Iminosugar Inhibitor

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

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

Protein crystallography data

The structure of Structure of the Alpha-L-Arabinofuranosidase ARB93A From Fusarium Graminearum in Complexe with An Iminosugar Inhibitor, PDB code: 2ydt 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) 44.69 / 1.60
Space group I 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 105.435, 105.435, 140.038, 90.00, 90.00, 90.00
R / Rfree (%) 14.2 / 17

Manganese Binding Sites:

The binding sites of Manganese atom in the Structure of the Alpha-L-Arabinofuranosidase ARB93A From Fusarium Graminearum in Complexe with An Iminosugar Inhibitor (pdb code 2ydt). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 5 binding sites of Manganese where determined in the Structure of the Alpha-L-Arabinofuranosidase ARB93A From Fusarium Graminearum in Complexe with An Iminosugar Inhibitor, PDB code: 2ydt:
Jump to Manganese binding site number: 1; 2; 3; 4; 5;

Manganese binding site 1 out of 5 in 2ydt

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Manganese binding site 1 out of 5 in the Structure of the Alpha-L-Arabinofuranosidase ARB93A From Fusarium Graminearum in Complexe with An Iminosugar Inhibitor


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Structure of the Alpha-L-Arabinofuranosidase ARB93A From Fusarium Graminearum in Complexe with An Iminosugar Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1507

b:11.4
occ:1.00
 OD1 A:ASP32 2.1 8.7 1.0
O A:HOH2024 2.2 11.0 1.0
O A:HOH2026 2.2 8.7 1.0
O A:HOH2499 2.2 9.2 1.0
O A:HOH2027 2.2 9.0 1.0
O A:HOH2025 2.3 10.3 1.0
CG A:ASP32 3.1 11.3 1.0
OD2 A:ASP32 3.3 14.0 1.0
O A:GLY364 4.0 10.2 1.0
O A:HOH2033 4.1 31.1 1.0
CG2 A:THR367 4.2 9.7 1.0
O A:HOH2070 4.2 9.8 1.0
O A:HOH2515 4.3 15.2 1.0
O3 A:SO41504 4.4 18.4 0.8
CD A:PRO33 4.4 8.1 1.0
O A:PRO33 4.4 8.9 1.0
O A:HOH2500 4.4 14.2 1.0
O A:HOH2016 4.4 17.0 1.0
CB A:ASP32 4.5 9.8 1.0
O A:ASN366 4.7 9.2 1.0
CG A:PRO33 4.9 9.2 1.0
N A:PRO33 4.9 8.1 1.0
CA A:ASP32 4.9 9.7 1.0
O A:HOH2030 4.9 19.2 1.0

Manganese binding site 2 out of 5 in 2ydt

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Manganese binding site 2 out of 5 in the Structure of the Alpha-L-Arabinofuranosidase ARB93A From Fusarium Graminearum in Complexe with An Iminosugar Inhibitor


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Structure of the Alpha-L-Arabinofuranosidase ARB93A From Fusarium Graminearum in Complexe with An Iminosugar Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1508

b:22.1
occ:0.50
 O A:HOH2521 1.9 35.6 1.0
O A:HOH2089 2.2 25.7 1.0
O A:HOH2088 2.2 20.1 1.0
OE1 A:GLN345 2.4 30.7 1.0
CD A:GLN345 3.5 31.3 1.0
CB A:GLN345 4.0 18.2 1.0
CG A:GLN345 4.3 23.9 1.0
CA A:SER51 4.3 14.2 1.0
OE1 A:GLU49 4.4 13.8 1.0
OE1 A:GLU106 4.4 13.4 1.0
O A:GLU49 4.4 11.7 1.0
O A:LEU50 4.4 12.6 1.0
O A:HOH2090 4.6 17.1 1.0
NE2 A:GLN345 4.6 33.8 1.0
N A:SER51 4.6 13.5 1.0
C A:LEU50 4.6 12.9 1.0
O A:HOH2206 4.7 30.6 1.0
O A:HOH2097 4.7 36.5 1.0
CB A:SER51 4.9 14.7 1.0

Manganese binding site 3 out of 5 in 2ydt

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Manganese binding site 3 out of 5 in the Structure of the Alpha-L-Arabinofuranosidase ARB93A From Fusarium Graminearum in Complexe with An Iminosugar Inhibitor


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Structure of the Alpha-L-Arabinofuranosidase ARB93A From Fusarium Graminearum in Complexe with An Iminosugar Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1509

b:28.6
occ:0.50
 OE2 A:GLU377 2.0 24.9 1.0
O A:HOH2512 2.1 19.1 0.5
O A:HOH2005 2.4 23.9 1.0
O A:HOH2511 2.7 28.6 0.5
CD A:GLU377 3.0 23.7 1.0
OE1 A:GLU377 3.4 24.0 1.0
O2 A:SO41502 3.8 19.0 0.9
O A:HOH2510 4.2 43.5 1.0
CG A:GLU377 4.4 20.1 1.0
O3 A:SO41502 4.8 24.1 0.9
S A:SO41502 4.8 20.9 0.9
CD A:ARG374 4.9 16.9 1.0

Manganese binding site 4 out of 5 in 2ydt

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Manganese binding site 4 out of 5 in the Structure of the Alpha-L-Arabinofuranosidase ARB93A From Fusarium Graminearum in Complexe with An Iminosugar Inhibitor


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Structure of the Alpha-L-Arabinofuranosidase ARB93A From Fusarium Graminearum in Complexe with An Iminosugar Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1510

b:21.7
occ:0.50
 O A:HOH2522 2.2 40.4 1.0
OD2 A:ASP32 2.2 14.0 1.0
O A:HOH2018 2.2 30.7 1.0
O A:HOH2028 2.3 34.4 1.0
CG A:ASP32 3.3 11.3 1.0
CB A:ASP32 3.8 9.8 1.0
O A:HOH2025 3.9 10.3 1.0
O A:HOH2016 4.2 17.0 1.0
OE1 A:GLU29 4.4 15.8 1.0
O A:HOH2030 4.4 19.2 1.0
OD1 A:ASP32 4.4 8.7 1.0
O A:HOH2022 4.5 37.1 1.0
O A:HOH2034 4.8 21.3 1.0

Manganese binding site 5 out of 5 in 2ydt

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Manganese binding site 5 out of 5 in the Structure of the Alpha-L-Arabinofuranosidase ARB93A From Fusarium Graminearum in Complexe with An Iminosugar Inhibitor


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Structure of the Alpha-L-Arabinofuranosidase ARB93A From Fusarium Graminearum in Complexe with An Iminosugar Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1511

b:23.4
occ:0.60
 O A:HOH2460 1.7 19.6 0.4
OD1 A:ASP330 2.2 20.2 1.0
OE2 A:GLU313 2.3 23.0 1.0
CG A:ASP330 3.2 18.3 1.0
CD A:GLU313 3.3 18.1 1.0
OD2 A:ASP330 3.4 25.0 1.0
CG A:GLU313 3.5 14.3 1.0
O A:HOH2456 4.4 15.8 1.0
OE1 A:GLU313 4.4 15.7 1.0
CB A:ASP330 4.5 14.4 1.0
NZ A:LYS328 4.9 27.9 1.0
CA A:ASP330 5.0 13.7 1.0
NH2 A:ARG311 5.0 30.2 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: Sat Oct 5 15:30:58 2024

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