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Zinc in PDB 7exu: GH127 Beta-L-Arabinofuranosidase HYPBA1 E322Q Mutant Complexed with P- Nitrophenyl Beta-L-Arabinofuranoside

Enzymatic activity of GH127 Beta-L-Arabinofuranosidase HYPBA1 E322Q Mutant Complexed with P- Nitrophenyl Beta-L-Arabinofuranoside

All present enzymatic activity of GH127 Beta-L-Arabinofuranosidase HYPBA1 E322Q Mutant Complexed with P- Nitrophenyl Beta-L-Arabinofuranoside:
3.2.1.185;

Protein crystallography data

The structure of GH127 Beta-L-Arabinofuranosidase HYPBA1 E322Q Mutant Complexed with P- Nitrophenyl Beta-L-Arabinofuranoside, PDB code: 7exu was solved by S.Maruyama, 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) 46.31 / 2.30
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 78.182, 78.182, 253.502, 90, 90, 120
R / Rfree (%) 25.2 / 29

Zinc Binding Sites:

The binding sites of Zinc atom in the GH127 Beta-L-Arabinofuranosidase HYPBA1 E322Q Mutant Complexed with P- Nitrophenyl Beta-L-Arabinofuranoside (pdb code 7exu). 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 E322Q Mutant Complexed with P- Nitrophenyl Beta-L-Arabinofuranoside, PDB code: 7exu:

Zinc binding site 1 out of 1 in 7exu

Go back to Zinc Binding Sites List in 7exu
Zinc binding site 1 out of 1 in the GH127 Beta-L-Arabinofuranosidase HYPBA1 E322Q Mutant Complexed with P- Nitrophenyl Beta-L-Arabinofuranoside


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 E322Q Mutant Complexed with P- Nitrophenyl Beta-L-Arabinofuranoside within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn701

b:62.3
occ:1.00
 SG A:CYS418 2.0 58.1 1.0
SG A:CYS417 2.0 60.7 1.0
OE2 A:GLU338 2.2 58.2 1.0
SG A:CYS340 2.6 62.4 1.0
CD A:GLU338 3.2 55.0 1.0
CB A:CYS340 3.2 54.2 1.0
N A:CYS418 3.3 69.6 1.0
CB A:CYS417 3.3 71.5 1.0
CB A:CYS418 3.4 59.7 1.0
CG A:GLU338 3.5 55.4 1.0
CA A:CYS418 3.5 62.3 1.0
C A:CYS417 3.6 70.0 1.0
CE1 A:TYR386 3.9 71.4 1.0
CZ A:TYR386 4.0 76.8 1.0
CA A:CYS417 4.0 68.0 1.0
N A:CYS340 4.1 56.5 1.0
C2 A:07Y702 4.2 69.3 1.0
CA A:CYS340 4.2 56.4 1.0
O A:CYS417 4.3 81.4 1.0
CD1 A:TYR386 4.3 77.6 1.0
OH A:TYR386 4.3 74.6 1.0
OE1 A:GLU338 4.3 58.5 1.0
O2 A:07Y702 4.4 62.5 1.0
CE2 A:TYR386 4.5 81.5 1.0
N A:CYS417 4.6 70.5 1.0
C1 A:07Y702 4.7 69.9 1.0
CG A:TYR386 4.7 74.9 1.0
CD2 A:TYR386 4.8 79.6 1.0
CB A:GLU338 4.9 54.8 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 20:04:12 2024

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