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Fluorine in PDB 2wbk: Structure of the Michaelis Complex of Beta-Mannosidase, MAN2A, Provides Insight Into the Conformational Itinerary of Mannoside Hydrolysis

Enzymatic activity of Structure of the Michaelis Complex of Beta-Mannosidase, MAN2A, Provides Insight Into the Conformational Itinerary of Mannoside Hydrolysis

All present enzymatic activity of Structure of the Michaelis Complex of Beta-Mannosidase, MAN2A, Provides Insight Into the Conformational Itinerary of Mannoside Hydrolysis:
3.2.1.25;

Protein crystallography data

The structure of Structure of the Michaelis Complex of Beta-Mannosidase, MAN2A, Provides Insight Into the Conformational Itinerary of Mannoside Hydrolysis, PDB code: 2wbk was solved by W.A.Offen, D.L.Zechel, S.G.Withers, H.J.Gilbert, G.J.Davies, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.84 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 91.447, 115.504, 97.705, 90.00, 115.99, 90.00
R / Rfree (%) 16.9 / 23.2

Other elements in 2wbk:

The structure of Structure of the Michaelis Complex of Beta-Mannosidase, MAN2A, Provides Insight Into the Conformational Itinerary of Mannoside Hydrolysis also contains other interesting chemical elements:

Bromine (Br) 12 atoms
Chlorine (Cl) 7 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structure of the Michaelis Complex of Beta-Mannosidase, MAN2A, Provides Insight Into the Conformational Itinerary of Mannoside Hydrolysis (pdb code 2wbk). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Structure of the Michaelis Complex of Beta-Mannosidase, MAN2A, Provides Insight Into the Conformational Itinerary of Mannoside Hydrolysis, PDB code: 2wbk:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 2wbk

Go back to Fluorine Binding Sites List in 2wbk
Fluorine binding site 1 out of 2 in the Structure of the Michaelis Complex of Beta-Mannosidase, MAN2A, Provides Insight Into the Conformational Itinerary of Mannoside Hydrolysis


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of the Michaelis Complex of Beta-Mannosidase, MAN2A, Provides Insight Into the Conformational Itinerary of Mannoside Hydrolysis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1869

b:14.5
occ:1.00
F2 A:M2F1869 0.0 14.5 1.0
C2 A:M2F1869 1.4 16.6 1.0
C1 A:M2F1869 2.3 14.9 1.0
C3 A:M2F1869 2.4 18.3 1.0
O3 A:M2F1869 2.7 19.1 1.0
ND2 A:ASN461 2.7 12.1 1.0
O1 A:M2F1869 2.8 18.4 1.0
NE2 A:GLN555 3.1 14.0 1.0
NE1 A:TRP395 3.2 11.1 1.0
CG A:ASN461 3.4 13.4 1.0
OD1 A:ASN461 3.5 12.7 1.0
OE1 A:GLN555 3.5 14.7 1.0
O5 A:M2F1869 3.6 13.7 1.0
C4 A:M2F1869 3.7 14.5 1.0
CD A:GLN555 3.7 14.3 1.0
CD1 A:TRP395 3.8 10.3 1.0
OE2 A:GLU462 3.9 9.9 1.0
OE1 A:GLU462 3.9 15.8 1.0
CD A:GLU462 3.9 12.0 1.0
C5B A:M2F1869 4.1 21.9 1.0
C5 A:M2F1869 4.1 16.9 1.0
CE2 A:TRP395 4.2 11.9 1.0
SG A:CYS424 4.2 14.6 1.0
CZ3 A:TRP645 4.3 11.5 1.0
CH2 A:TRP645 4.5 12.8 1.0
O1B A:M2F1869 4.5 27.9 1.0
CE3 A:TRP645 4.6 12.3 1.0
CG A:GLU462 4.6 12.8 1.0
CZ2 A:TRP395 4.7 12.0 1.0
C4B A:M2F1869 4.8 22.3 1.0
CB A:ASN461 4.8 9.5 1.0
O4 A:M2F1869 4.8 17.1 1.0
CZ2 A:TRP645 4.9 12.5 1.0
CG A:TRP395 4.9 12.4 1.0

Fluorine binding site 2 out of 2 in 2wbk

Go back to Fluorine Binding Sites List in 2wbk
Fluorine binding site 2 out of 2 in the Structure of the Michaelis Complex of Beta-Mannosidase, MAN2A, Provides Insight Into the Conformational Itinerary of Mannoside Hydrolysis


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of the Michaelis Complex of Beta-Mannosidase, MAN2A, Provides Insight Into the Conformational Itinerary of Mannoside Hydrolysis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1868

b:13.2
occ:1.00
F2 B:M2F1868 0.0 13.2 1.0
C2 B:M2F1868 1.4 16.8 1.0
C1 B:M2F1868 2.4 17.9 1.0
C3 B:M2F1868 2.5 14.7 1.0
ND2 B:ASN461 2.6 12.3 1.0
O3 B:M2F1868 2.6 14.0 1.0
O1 B:M2F1868 2.9 20.4 1.0
NE1 B:TRP395 3.2 11.1 1.0
NE2 B:GLN555 3.3 16.5 1.0
CG B:ASN461 3.4 13.9 1.0
OE1 B:GLN555 3.4 12.8 1.0
OE1 B:GLU462 3.6 15.8 1.0
OD1 B:ASN461 3.6 16.6 1.0
O5 B:M2F1868 3.7 18.0 1.0
CD1 B:TRP395 3.8 12.6 1.0
CD B:GLN555 3.8 11.3 1.0
C4 B:M2F1868 3.8 13.9 1.0
CD B:GLU462 3.9 14.3 1.0
OE2 B:GLU462 3.9 12.1 1.0
C5B B:M2F1868 4.1 22.6 1.0
C5 B:M2F1868 4.2 15.2 1.0
SG B:CYS424 4.2 21.5 1.0
CZ3 B:TRP645 4.3 12.0 1.0
CE2 B:TRP395 4.3 11.6 1.0
CH2 B:TRP645 4.4 12.8 1.0
CE3 B:TRP645 4.5 13.0 1.0
O1B B:M2F1868 4.6 27.0 1.0
C4B B:M2F1868 4.7 26.5 1.0
CB B:ASN461 4.7 10.8 1.0
CG B:GLU462 4.8 13.7 1.0
CZ2 B:TRP645 4.9 14.2 1.0
O4 B:M2F1868 4.9 11.8 1.0
CZ2 B:TRP395 4.9 8.4 1.0
CD2 B:TRP645 5.0 13.3 1.0
CG B:TRP395 5.0 12.7 1.0

Reference:

W.A.Offen, D.L.Zechel, S.G.Withers, H.J.Gilbert, G.J.Davies. Structure of the Michaelis Complex of Beta- Mannosidase, MAN2A, Provides Insight Into the Conformational Itinerary of Mannoside Hydrolysis. Cell(Cambridge,Mass.) V. 18 2484 2009.
ISSN: ISSN 0092-8674
PubMed: 19532864
DOI: 10.1039/B902240F
Page generated: Wed Jul 31 16:23:25 2024

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