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Zinc in PDB 7dif: GH127 Beta-L-Arabinofuranosidase HYPBA1 Covalently Complexed with Beta-L-Arabinofuranose-Configured Cyclophellitol at 1.75-Angstrom Resolution

Enzymatic activity of GH127 Beta-L-Arabinofuranosidase HYPBA1 Covalently Complexed with Beta-L-Arabinofuranose-Configured Cyclophellitol at 1.75-Angstrom Resolution

All present enzymatic activity of GH127 Beta-L-Arabinofuranosidase HYPBA1 Covalently Complexed with Beta-L-Arabinofuranose-Configured Cyclophellitol at 1.75-Angstrom Resolution:
3.2.1.185;

Protein crystallography data

The structure of GH127 Beta-L-Arabinofuranosidase HYPBA1 Covalently Complexed with Beta-L-Arabinofuranose-Configured Cyclophellitol at 1.75-Angstrom Resolution, PDB code: 7dif was solved by S.Amaki, N.G.S.Mcgregor, T.Arakawa, C.Yamada, V.Borlandelli, H.S.Overkleeft, G.J.Davies, S.Fushinobu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.05 / 1.75
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 77.714, 77.714, 252.094, 90, 90, 120
R / Rfree (%) 21.6 / 24.3

Other elements in 7dif:

The structure of GH127 Beta-L-Arabinofuranosidase HYPBA1 Covalently Complexed with Beta-L-Arabinofuranose-Configured Cyclophellitol at 1.75-Angstrom Resolution also contains other interesting chemical elements:

Potassium (K) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the GH127 Beta-L-Arabinofuranosidase HYPBA1 Covalently Complexed with Beta-L-Arabinofuranose-Configured Cyclophellitol at 1.75-Angstrom Resolution (pdb code 7dif). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the GH127 Beta-L-Arabinofuranosidase HYPBA1 Covalently Complexed with Beta-L-Arabinofuranose-Configured Cyclophellitol at 1.75-Angstrom Resolution, PDB code: 7dif:

Zinc binding site 1 out of 1 in 7dif

Go back to Zinc Binding Sites List in 7dif
Zinc binding site 1 out of 1 in the GH127 Beta-L-Arabinofuranosidase HYPBA1 Covalently Complexed with Beta-L-Arabinofuranose-Configured Cyclophellitol at 1.75-Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of GH127 Beta-L-Arabinofuranosidase HYPBA1 Covalently Complexed with Beta-L-Arabinofuranose-Configured Cyclophellitol at 1.75-Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn701

b:36.9
occ:1.00
 OE2 A:GLU338 2.2 36.8 1.0
SG A:CYS418 2.2 35.7 1.0
SG A:CYS340 2.3 37.8 1.0
SG A:CYS417 2.4 38.8 1.0
CB A:CYS340 3.1 32.0 1.0
CD A:GLU338 3.1 38.5 1.0
N A:CYS418 3.1 36.2 1.0
CB A:CYS418 3.3 36.6 1.0
CA A:CYS418 3.4 33.8 1.0
CG A:GLU338 3.4 37.0 1.0
CB A:CYS417 3.4 40.1 1.0
C5 A:FE0702 3.6 37.7 1.0
C A:CYS417 3.6 37.6 1.0
C4 A:FE0702 3.7 40.4 1.0
O A:HOH968 3.9 34.4 1.0
N A:CYS340 4.0 28.8 1.0
CA A:CYS417 4.0 34.5 1.0
CA A:CYS340 4.1 29.7 1.0
O10 A:FE0702 4.2 39.4 1.0
O A:CYS417 4.2 39.6 1.0
OE1 A:GLU338 4.3 37.6 1.0
CE1 A:TYR386 4.3 32.3 1.0
CZ A:TYR386 4.4 34.0 1.0
N A:CYS417 4.6 38.0 1.0
CE2 A:TYR386 4.6 35.2 1.0
CD1 A:TYR386 4.6 37.4 1.0
OH A:TYR386 4.7 36.2 1.0
O A:HOH900 4.8 40.6 1.0
CD2 A:TYR386 4.8 33.3 1.0
CG A:TYR386 4.8 32.0 1.0
CB A:GLU338 4.9 36.2 1.0
C A:CYS418 4.9 40.1 1.0
C6 A:FE0702 4.9 39.0 1.0

Reference:

N.G.S.Mcgregor, J.Coines, V.Borlandelli, S.Amaki, M.Artola, A.Nin-Hill, D.Linzel, C.Yamada, T.Arakawa, A.Ishiwata, Y.Ito, G.A.Van Der Marel, J.D.C.Code, S.Fushinobu, H.S.Overkleeft, C.Rovira, G.J.Davies. Cysteine Nucleophiles in Glycosidase Catalysis: Application of A Covalent Beta-L-Arabinofuranosidase Inhibitor Angew.Chem.Int.Ed.Engl. 2021.
ISSN: ESSN 1521-3773
DOI: 10.1002/ANIE.202013920
Page generated: Tue Oct 29 19:02:19 2024

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