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Zinc in PDB 7exv: GH127 Beta-L-Arabinofuranosidase HYPBA1 Covalently Complexed with P- Nitrophenyl Beta-L-Arabinofuranoylamide

Enzymatic activity of GH127 Beta-L-Arabinofuranosidase HYPBA1 Covalently Complexed with P- Nitrophenyl Beta-L-Arabinofuranoylamide

All present enzymatic activity of GH127 Beta-L-Arabinofuranosidase HYPBA1 Covalently Complexed with P- Nitrophenyl Beta-L-Arabinofuranoylamide:
3.2.1.185;

Protein crystallography data

The structure of GH127 Beta-L-Arabinofuranosidase HYPBA1 Covalently Complexed with P- Nitrophenyl Beta-L-Arabinofuranoylamide, PDB code: 7exv 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) 46.14 / 2.60
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 77.547, 77.547, 253.529, 90, 90, 120
R / Rfree (%) 25.1 / 31

Zinc Binding Sites:

The binding sites of Zinc atom in the GH127 Beta-L-Arabinofuranosidase HYPBA1 Covalently Complexed with P- Nitrophenyl Beta-L-Arabinofuranoylamide (pdb code 7exv). 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 P- Nitrophenyl Beta-L-Arabinofuranoylamide, PDB code: 7exv:

Zinc binding site 1 out of 1 in 7exv

Go back to Zinc Binding Sites List in 7exv
Zinc binding site 1 out of 1 in the GH127 Beta-L-Arabinofuranosidase HYPBA1 Covalently Complexed with P- Nitrophenyl Beta-L-Arabinofuranoylamide


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 P- Nitrophenyl Beta-L-Arabinofuranoylamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn901

b:62.8
occ:1.00
 SG A:CYS418 2.2 65.0 1.0
SG A:CYS340 2.3 61.4 1.0
SG A:CYS417 2.3 69.1 1.0
OE2 A:GLU338 2.7 49.5 1.0
CB A:CYS340 3.1 62.1 1.0
C7 A:08U902 3.3 108.8 1.0
CG A:GLU338 3.4 47.6 1.0
CD A:GLU338 3.4 56.0 1.0
CB A:CYS418 3.5 74.1 1.0
N A:CYS418 3.6 69.4 1.0
CB A:CYS417 3.6 68.3 1.0
CA A:CYS418 3.7 71.9 1.0
C A:CYS417 3.8 72.1 1.0
N A:CYS340 3.9 49.6 1.0
CA A:CYS340 4.1 54.2 1.0
CZ A:TYR386 4.2 56.2 1.0
O A:CYS417 4.2 70.0 1.0
C2 A:08U902 4.2 98.0 1.0
CA A:CYS417 4.3 76.4 1.0
O2 A:08U902 4.3 80.9 1.0
CE2 A:TYR386 4.4 60.7 1.0
OH A:TYR386 4.4 65.4 1.0
C6 A:08U902 4.5 103.8 1.0
CE1 A:TYR386 4.5 69.0 1.0
OE1 A:GLU338 4.7 74.8 1.0
C1 A:08U902 4.8 99.3 1.0
CD2 A:TYR386 4.8 62.8 1.0
N A:CYS417 4.9 74.7 1.0
CD1 A:TYR386 4.9 70.6 1.0
CB A:GLU338 4.9 55.7 1.0
CG A:TYR386 5.0 69.2 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: Tue Oct 29 20:04:07 2024

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