Zinc in PDB 7exw: GH127 Beta-L-Arabinofuranosidase HYPBA1 Covalently Complexed with Alpha-L-Arabinofuranosylamide

Enzymatic activity of GH127 Beta-L-Arabinofuranosidase HYPBA1 Covalently Complexed with Alpha-L-Arabinofuranosylamide

All present enzymatic activity of GH127 Beta-L-Arabinofuranosidase HYPBA1 Covalently Complexed with Alpha-L-Arabinofuranosylamide:
3.2.1.185;

Protein crystallography data

The structure of GH127 Beta-L-Arabinofuranosidase HYPBA1 Covalently Complexed with Alpha-L-Arabinofuranosylamide, PDB code: 7exw was solved by K.Sawano, T.Arakawa, C.Yamada, K.Fujita, S.Fushinobu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.20 / 2.20
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 74.757, 74.757, 252.046, 90, 90, 120
R / Rfree (%) 21.7 / 27

Zinc Binding Sites:

The binding sites of Zinc atom in the GH127 Beta-L-Arabinofuranosidase HYPBA1 Covalently Complexed with Alpha-L-Arabinofuranosylamide (pdb code 7exw). 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 Alpha-L-Arabinofuranosylamide, PDB code: 7exw:

Zinc binding site 1 out of 1 in 7exw

Go back to Zinc Binding Sites List in 7exw
Zinc binding site 1 out of 1 in the GH127 Beta-L-Arabinofuranosidase HYPBA1 Covalently Complexed with Alpha-L-Arabinofuranosylamide


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 Alpha-L-Arabinofuranosylamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn802

b:41.4
occ:1.00
 OE2 A:GLU338 2.1 37.5 1.0
SG A:CYS418 2.2 38.3 1.0
SG A:CYS340 2.3 43.0 1.0
SG A:CYS417 2.3 41.9 1.0
N A:CYS418 3.0 41.2 1.0
CD A:GLU338 3.0 40.0 1.0
CB A:CYS340 3.2 39.1 1.0
CG A:GLU338 3.2 38.7 1.0
CB A:CYS417 3.3 42.6 1.0
CA A:CYS418 3.3 41.2 1.0
CB A:CYS418 3.4 39.9 1.0
C A:CYS417 3.5 39.0 1.0
N A:CYS340 4.0 39.0 1.0
CA A:CYS417 4.0 42.0 1.0
CA A:CYS340 4.1 38.7 1.0
OE1 A:GLU338 4.2 37.9 1.0
O2 A:09X801 4.2 41.0 1.0
CD1 A:TYR386 4.3 49.2 1.0
O A:CYS417 4.3 42.7 1.0
C2 A:09X801 4.5 47.0 1.0
O A:HOH928 4.6 36.0 1.0
CB A:GLU338 4.7 38.1 1.0
CE1 A:TYR386 4.7 51.8 1.0
N A:CYS417 4.7 44.2 1.0
NAF A:09X801 4.8 52.4 1.0
C A:CYS418 4.9 43.5 1.0

Reference:

S.Maruyama, K.Sawano, S.Amaki, T.Suzuki, S.Narita, K.Kimura, T.Arakawa, C.Yamada, Y.Ito, N.Dohmae, K.Fujita, A.Ishiwata, S.Fushinobu. Substrate Complex Structure, Active Site Labeling and Catalytic Role of the Zinc Ion in Cysteine Glycosidase. Glycobiology 2021.
ISSN: ESSN 1460-2423
PubMed: 34735571
DOI: 10.1093/GLYCOB/CWAB103
Page generated: Thu Nov 25 10:56:23 2021

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