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Fluorine in PDB 3vzn: Crystal Structure of the Bacillus Circulans Endo-Beta-(1,4)-Xylanase (Bcx) N35E Mutant with GLU78 Covalently Bonded to 2-Deoxy-2-Fluoro- Xylobiose

Enzymatic activity of Crystal Structure of the Bacillus Circulans Endo-Beta-(1,4)-Xylanase (Bcx) N35E Mutant with GLU78 Covalently Bonded to 2-Deoxy-2-Fluoro- Xylobiose

All present enzymatic activity of Crystal Structure of the Bacillus Circulans Endo-Beta-(1,4)-Xylanase (Bcx) N35E Mutant with GLU78 Covalently Bonded to 2-Deoxy-2-Fluoro- Xylobiose:
3.2.1.8;

Protein crystallography data

The structure of Crystal Structure of the Bacillus Circulans Endo-Beta-(1,4)-Xylanase (Bcx) N35E Mutant with GLU78 Covalently Bonded to 2-Deoxy-2-Fluoro- Xylobiose, PDB code: 3vzn was solved by M.L.Ludwiczek, I.D'angelo, G.N.Yalloway, M.Okon, J.E.Nielsen, N.C.Strynadka, S.G.Withers, L.P.Mcintosh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.28 / 1.67
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 39.395, 63.038, 64.360, 90.00, 104.89, 90.00
R / Rfree (%) 18.8 / 23.6

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of the Bacillus Circulans Endo-Beta-(1,4)-Xylanase (Bcx) N35E Mutant with GLU78 Covalently Bonded to 2-Deoxy-2-Fluoro- Xylobiose (pdb code 3vzn). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Crystal Structure of the Bacillus Circulans Endo-Beta-(1,4)-Xylanase (Bcx) N35E Mutant with GLU78 Covalently Bonded to 2-Deoxy-2-Fluoro- Xylobiose, PDB code: 3vzn:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 3vzn

Go back to Fluorine Binding Sites List in 3vzn
Fluorine binding site 1 out of 2 in the Crystal Structure of the Bacillus Circulans Endo-Beta-(1,4)-Xylanase (Bcx) N35E Mutant with GLU78 Covalently Bonded to 2-Deoxy-2-Fluoro- Xylobiose


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of the Bacillus Circulans Endo-Beta-(1,4)-Xylanase (Bcx) N35E Mutant with GLU78 Covalently Bonded to 2-Deoxy-2-Fluoro- Xylobiose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F201

b:27.0
occ:1.00
 F2 A:DFX201 0.0 27.0 1.0
C2 A:DFX201 1.4 29.4 1.0
C1 A:DFX201 2.4 27.8 1.0
C3 A:DFX201 2.4 28.4 1.0
OE1 A:GLU78 2.9 23.2 1.0
OE2 A:GLU78 2.9 19.7 1.0
O3 A:DFX201 2.9 30.6 1.0
CZ A:PHE125 3.2 19.9 1.0
CD A:GLU78 3.2 20.2 1.0
NH1 A:ARG112 3.3 37.0 1.0
NE2 A:GLN127 3.4 21.9 1.0
CE2 A:PHE125 3.4 23.7 1.0
O5 A:DFX201 3.6 27.3 1.0
C4 A:DFX201 3.7 29.5 1.0
CG A:ARG112 3.8 26.9 1.0
C5 A:DFX201 3.9 27.9 1.0
CZ A:ARG112 4.1 35.2 1.0
CD A:ARG112 4.3 31.3 1.0
OE2 A:GLU35 4.3 45.5 1.0
CE1 A:PHE125 4.4 21.3 1.0
NE A:ARG112 4.4 35.7 1.0
O4 A:DFX201 4.4 26.5 1.0
CD A:GLN127 4.5 22.5 1.0
CB A:ARG112 4.6 24.2 1.0
CG A:GLU78 4.6 21.2 1.0
O A:PRO116 4.6 23.0 1.0
OH A:TYR80 4.8 23.8 1.0
CD2 A:PHE125 4.8 22.7 1.0
CB A:ALA115 4.9 21.5 1.0
NH2 A:ARG112 4.9 39.3 1.0
CG A:GLN127 4.9 21.7 1.0
OE1 A:GLU35 5.0 41.2 1.0

Fluorine binding site 2 out of 2 in 3vzn

Go back to Fluorine Binding Sites List in 3vzn
Fluorine binding site 2 out of 2 in the Crystal Structure of the Bacillus Circulans Endo-Beta-(1,4)-Xylanase (Bcx) N35E Mutant with GLU78 Covalently Bonded to 2-Deoxy-2-Fluoro- Xylobiose


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of the Bacillus Circulans Endo-Beta-(1,4)-Xylanase (Bcx) N35E Mutant with GLU78 Covalently Bonded to 2-Deoxy-2-Fluoro- Xylobiose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F201

b:36.7
occ:1.00
 F2 B:DFX201 0.0 36.7 1.0
C2 B:DFX201 1.4 37.4 1.0
C3 B:DFX201 2.4 36.2 1.0
C1 B:DFX201 2.5 36.1 1.0
OE1 B:GLU78 2.7 28.9 1.0
O3 B:DFX201 2.9 36.5 1.0
OE2 B:GLU78 3.0 21.5 1.0
CD B:GLU78 3.2 23.6 1.0
NE2 B:GLN127 3.2 25.2 1.0
NH1 B:ARG112 3.5 34.0 1.0
CZ B:PHE125 3.6 26.8 1.0
O5 B:DFX201 3.8 39.0 1.0
C4 B:DFX201 3.8 39.1 1.0
CE2 B:PHE125 3.8 21.9 1.0
CG B:ARG112 3.9 31.6 1.0
C5 B:DFX201 4.2 39.8 1.0
CD B:GLN127 4.3 28.1 1.0
CB B:ALA115 4.4 31.6 1.0
CD B:ARG112 4.4 37.9 1.0
CZ B:ARG112 4.4 38.5 1.0
O B:PRO116 4.5 32.7 1.0
O4 B:DFX201 4.6 40.1 1.0
CG B:GLU78 4.6 23.1 1.0
OE2 B:GLU35 4.8 43.1 1.0
CG B:GLN127 4.8 24.6 1.0
NE B:ARG112 4.8 39.7 1.0
CB B:ARG112 4.9 31.5 1.0
CE1 B:PHE125 4.9 30.0 1.0
OH B:TYR80 4.9 25.9 1.0
CH2 B:TRP71 5.0 23.9 1.0

Reference:

M.L.Ludwiczek, I.D'angelo, G.N.Yalloway, J.A.Brockerman, M.Okon, J.E.Nielsen, N.C.Strynadka, S.G.Withers, L.P.Mcintosh. Strategies For Modulating the pH-Dependent Activity of A Family 11 Glycoside Hydrolase Biochemistry V. 52 3138 2013.
ISSN: ISSN 0006-2960
PubMed: 23578322
DOI: 10.1021/BI400034M
Page generated: Mon Jul 14 19:57:59 2025

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