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Zinc in PDB 3wkx: Crystal Structure of GH127 Beta-L-Arabinofuranosidase HYPBA1 From Bifidobacterium Longum Arabinose Complex Form

Enzymatic activity of Crystal Structure of GH127 Beta-L-Arabinofuranosidase HYPBA1 From Bifidobacterium Longum Arabinose Complex Form

All present enzymatic activity of Crystal Structure of GH127 Beta-L-Arabinofuranosidase HYPBA1 From Bifidobacterium Longum Arabinose Complex Form:
3.2.1.185;

Protein crystallography data

The structure of Crystal Structure of GH127 Beta-L-Arabinofuranosidase HYPBA1 From Bifidobacterium Longum Arabinose Complex Form, PDB code: 3wkx was solved by T.Ito, K.Saikawa, T.Arakawa, T.Wakagi, K.Fujita, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.70 / 2.00
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 77.726, 77.726, 252.668, 90.00, 90.00, 120.00
R / Rfree (%) 22.6 / 27.9

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of GH127 Beta-L-Arabinofuranosidase HYPBA1 From Bifidobacterium Longum Arabinose Complex Form (pdb code 3wkx). 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 Crystal Structure of GH127 Beta-L-Arabinofuranosidase HYPBA1 From Bifidobacterium Longum Arabinose Complex Form, PDB code: 3wkx:

Zinc binding site 1 out of 1 in 3wkx

Go back to Zinc Binding Sites List in 3wkx
Zinc binding site 1 out of 1 in the Crystal Structure of GH127 Beta-L-Arabinofuranosidase HYPBA1 From Bifidobacterium Longum Arabinose Complex Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of GH127 Beta-L-Arabinofuranosidase HYPBA1 From Bifidobacterium Longum Arabinose Complex Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn702

b:30.7
occ:0.60
 SG A:CYS418 2.1 36.7 1.0
SG A:CYS340 2.1 36.8 1.0
OE2 A:GLU338 2.2 29.4 1.0
SG A:CYS417 2.4 36.6 1.0
CB A:CYS340 3.1 30.7 1.0
CD A:GLU338 3.2 32.6 1.0
N A:CYS418 3.3 35.6 1.0
CB A:CYS418 3.3 35.3 1.0
CB A:CYS417 3.5 35.9 1.0
CA A:CYS418 3.5 36.2 1.0
CG A:GLU338 3.5 31.1 1.0
C A:CYS417 3.6 36.5 1.0
N A:CYS340 3.9 27.4 1.0
CA A:CYS417 4.1 31.8 1.0
CA A:CYS340 4.1 26.1 1.0
O A:CYS417 4.2 39.7 1.0
C2' A:FUB701 4.2 34.5 1.0
O A:HOH1028 4.3 33.5 1.0
CZ A:TYR386 4.3 32.2 1.0
OE1 A:GLU338 4.4 32.9 1.0
CE2 A:TYR386 4.4 28.8 1.0
CE1 A:TYR386 4.4 32.3 1.0
O2' A:FUB701 4.5 37.2 1.0
N A:CYS417 4.6 34.8 1.0
OH A:TYR386 4.7 27.2 1.0
CD2 A:TYR386 4.7 32.4 1.0
CD1 A:TYR386 4.7 30.8 1.0
CG A:TYR386 4.9 32.5 1.0
CB A:GLU338 5.0 28.8 1.0

Reference:

T.Ito, K.Saikawa, S.Kim, K.Fujita, A.Ishiwata, S.Kaeothip, T.Arakawa, T.Wakagi, G.T.Beckham, Y.Ito, S.Fushinobu. Crystal Structure of Glycoside Hydrolase Family 127 Beta-L-Arabinofuranosidase From Bifidobacterium Longum Biochem.Biophys.Res.Commun. 2014.
ISSN: ESSN 1090-2104
PubMed: 24680821
DOI: 10.1016/J.BBRC.2014.03.096
Page generated: Sat Oct 26 18:07:16 2024

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