Zinc in PDB 7bzl: GH127 Beta-L-Arabinofuranosidase HYPBA1 Covalently Complexed with Beta-L-Arabinofuranose-Configured Cyclophellitol

Enzymatic activity of GH127 Beta-L-Arabinofuranosidase HYPBA1 Covalently Complexed with Beta-L-Arabinofuranose-Configured Cyclophellitol

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

Protein crystallography data

The structure of GH127 Beta-L-Arabinofuranosidase HYPBA1 Covalently Complexed with Beta-L-Arabinofuranose-Configured Cyclophellitol, PDB code: 7bzl 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) 46.03 / 2.30
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 77.401, 77.401, 252.864, 90, 90, 120
R / Rfree (%) 21.6 / 27.3

Zinc Binding Sites:

The binding sites of Zinc atom in the GH127 Beta-L-Arabinofuranosidase HYPBA1 Covalently Complexed with Beta-L-Arabinofuranose-Configured Cyclophellitol (pdb code 7bzl). 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, PDB code: 7bzl:

Zinc binding site 1 out of 1 in 7bzl

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn701

b:58.4
occ:1.00
 SG A:CYS418 2.2 58.2 1.0
SG A:CYS340 2.3 61.4 1.0
OE2 A:GLU338 2.4 44.4 1.0
SG A:CYS417 2.5 59.1 1.0
CB A:CYS340 3.0 49.4 1.0
N A:CYS418 3.2 67.0 1.0
CD A:GLU338 3.3 49.8 1.0
CB A:CYS418 3.4 66.1 1.0
CA A:CYS418 3.4 66.7 1.0
CG A:GLU338 3.5 48.8 1.0
CB A:CYS417 3.5 62.3 1.0
C A:CYS417 3.6 72.0 1.0
C5 A:FE0702 3.7 57.5 1.0
C4 A:FE0702 3.8 61.1 1.0
N A:CYS340 4.0 46.6 1.0
CA A:CYS417 4.1 69.0 1.0
CA A:CYS340 4.1 50.6 1.0
O A:CYS417 4.1 76.6 1.0
CZ A:TYR386 4.2 47.0 1.0
CE1 A:TYR386 4.2 41.5 1.0
O10 A:FE0702 4.3 59.6 1.0
CE2 A:TYR386 4.5 55.3 1.0
OH A:TYR386 4.5 52.8 1.0
OE1 A:GLU338 4.5 55.4 1.0
CD1 A:TYR386 4.6 44.6 1.0
N A:CYS417 4.6 68.0 1.0
CD2 A:TYR386 4.8 46.3 1.0
CG A:TYR386 4.8 49.2 1.0
CB A:GLU338 4.9 53.8 1.0
C A:CYS418 5.0 67.7 1.0
C6 A:FE0702 5.0 59.7 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: Wed Mar 3 16:20:01 2021

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