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Fluorine in PDB 3p5s: Structural Insights Into the Catalytic Mechanism of CD38: Evidence For A Conformationally Flexible Covalent Enzyme-Substrate Complex

Enzymatic activity of Structural Insights Into the Catalytic Mechanism of CD38: Evidence For A Conformationally Flexible Covalent Enzyme-Substrate Complex

All present enzymatic activity of Structural Insights Into the Catalytic Mechanism of CD38: Evidence For A Conformationally Flexible Covalent Enzyme-Substrate Complex:
3.2.2.5;

Protein crystallography data

The structure of Structural Insights Into the Catalytic Mechanism of CD38: Evidence For A Conformationally Flexible Covalent Enzyme-Substrate Complex, PDB code: 3p5s was solved by P.F.Egea, H.Muller-Stauffler, I.Kohn, C.Cakou-Kefir, R.M.Stroud, E.Kellenberburger, F.Schuber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.01 / 1.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 46.205, 80.029, 157.725, 90.00, 90.00, 90.00
R / Rfree (%) 20.5 / 25.2

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structural Insights Into the Catalytic Mechanism of CD38: Evidence For A Conformationally Flexible Covalent Enzyme-Substrate Complex (pdb code 3p5s). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Structural Insights Into the Catalytic Mechanism of CD38: Evidence For A Conformationally Flexible Covalent Enzyme-Substrate Complex, PDB code: 3p5s:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 3p5s

Go back to Fluorine Binding Sites List in 3p5s
Fluorine binding site 1 out of 2 in the Structural Insights Into the Catalytic Mechanism of CD38: Evidence For A Conformationally Flexible Covalent Enzyme-Substrate Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structural Insights Into the Catalytic Mechanism of CD38: Evidence For A Conformationally Flexible Covalent Enzyme-Substrate Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F280

b:22.0
occ:1.00
 F2R A:AVU280 0.0 22.0 1.0
C2R A:AVU280 1.3 23.0 1.0
C3R A:AVU280 2.2 21.0 1.0
C1R A:AVU280 2.3 28.7 1.0
C4R A:AVU280 3.1 15.9 1.0
O4R A:AVU280 3.2 22.0 1.0
O3R A:AVU280 3.3 24.9 1.0
O A:HOH288 3.4 10.9 1.0
CB A:LEU137 3.4 14.1 1.0
CD2 A:LEU137 3.5 17.3 1.0
C5R A:AVU280 3.6 16.1 1.0
NE1 A:TRP118 3.7 15.0 1.0
CE2 A:TRP118 3.8 20.9 1.0
CZ2 A:TRP118 3.8 16.6 1.0
OE2 A:GLU218 3.8 23.8 1.0
OE2 A:GLU138 4.0 29.8 1.0
CG A:LEU137 4.1 15.5 1.0
N7 A:AVU280 4.2 30.8 1.0
OE1 A:GLU138 4.4 20.4 1.0
CD1 A:TRP118 4.5 17.1 1.0
OG A:SER185 4.5 20.3 1.0
C8 A:AVU280 4.6 29.1 1.0
O5R A:AVU280 4.6 24.8 1.0
CD2 A:TRP118 4.6 17.8 1.0
CH2 A:TRP118 4.7 14.3 1.0
CD A:GLU138 4.7 32.1 1.0
CD A:GLU218 4.7 26.0 1.0
CA A:LEU137 4.7 14.7 1.0
OE1 A:GLU218 4.7 18.1 1.0
N A:LEU137 4.8 13.4 1.0

Fluorine binding site 2 out of 2 in 3p5s

Go back to Fluorine Binding Sites List in 3p5s
Fluorine binding site 2 out of 2 in the Structural Insights Into the Catalytic Mechanism of CD38: Evidence For A Conformationally Flexible Covalent Enzyme-Substrate Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structural Insights Into the Catalytic Mechanism of CD38: Evidence For A Conformationally Flexible Covalent Enzyme-Substrate Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F280

b:41.8
occ:1.00
 F2R B:AVU280 0.0 41.8 1.0
C2R B:AVU280 1.3 29.9 1.0
C1R B:AVU280 2.3 40.5 1.0
C3R B:AVU280 2.3 40.8 1.0
O B:HOH300 3.0 23.9 1.0
CB B:LEU137 3.2 18.8 1.0
C4R B:AVU280 3.3 33.6 1.0
O4R B:AVU280 3.3 35.5 1.0
O3R B:AVU280 3.3 34.2 1.0
NE1 B:TRP118 3.5 31.5 1.0
CD2 B:LEU137 3.5 24.1 1.0
OE2 B:GLU138 3.6 40.0 1.0
CE2 B:TRP118 3.8 40.3 1.0
OE2 B:GLU218 3.9 35.1 1.0
C5R B:AVU280 3.9 29.5 1.0
CG B:LEU137 4.0 21.5 1.0
CZ2 B:TRP118 4.0 36.5 1.0
OE1 B:GLU138 4.2 28.5 1.0
CD1 B:TRP118 4.2 39.6 1.0
CD B:GLU138 4.3 42.1 1.0
CA B:LEU137 4.4 20.6 1.0
N B:LEU137 4.5 20.5 1.0
N7 B:AVU280 4.6 45.9 1.0
CD2 B:TRP118 4.6 36.2 1.0
OG B:SER185 4.7 26.1 1.0
CG B:TRP118 4.8 38.3 1.0
CD B:GLU218 4.9 38.0 1.0
CH2 B:TRP118 4.9 44.7 1.0
O5R B:AVU280 4.9 46.7 1.0

Reference:

P.F.Egea, H.Muller-Steffner, I.Kuhn, C.Cakir-Kiefer, N.J.Oppenheimer, R.M.Stroud, E.Kellenberger, F.Schuber. Insights Into the Mechanism of Bovine CD38/Nad+Glycohydrolase From the X-Ray Structures of Its Michaelis Complex and Covalently-Trapped Intermediates. Plos One V. 7 34918 2012.
ISSN: ESSN 1932-6203
PubMed: 22529956
DOI: 10.1371/JOURNAL.PONE.0034918
Page generated: Wed Jul 31 21:38:19 2024

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