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Fluorine in PDB 3kou: 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: 3kou was solved by P.F.Egea, H.Muller-Steffner, R.M.Stroud, N.J.Oppenheimer, E.Kellenberger, F.Schuber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.64 / 1.78
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 46.721, 81.287, 150.909, 90.00, 90.00, 90.00
R / Rfree (%) 20 / 24.3

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 3kou). 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: 3kou:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 3kou

Go back to Fluorine Binding Sites List in 3kou
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:F503

b:12.5
occ:1.00
F2D A:2NF503 0.0 12.5 1.0
C2D A:2NF503 1.3 9.9 1.0
C1D A:2NF503 2.4 12.3 1.0
C3D A:2NF503 2.5 11.3 1.0
OE2 A:GLU218 2.7 11.9 1.0
O3D A:2NF503 2.7 12.8 1.0
O A:HOH609 2.9 8.2 1.0
CE2 A:PHE188 3.2 9.4 1.0
CD A:GLU218 3.3 11.4 1.0
CD2 A:PHE188 3.4 9.7 1.0
OE1 A:GLU218 3.4 9.8 1.0
O4D A:2NF503 3.5 14.8 1.0
CB A:LEU137 3.6 9.1 1.0
C4D A:2NF503 3.6 8.9 1.0
CD1 A:PHE117 3.8 11.6 1.0
CD2 A:LEU137 4.0 12.6 1.0
CG A:LEU137 4.3 10.9 1.0
O A:HOH727 4.3 20.1 1.0
CZ A:PHE188 4.3 9.2 1.0
CE1 A:PHE117 4.4 10.2 1.0
CG A:GLU218 4.5 8.7 1.0
N A:LEU137 4.5 8.3 1.0
CG A:PHE188 4.6 10.1 1.0
CA A:LEU137 4.6 8.6 1.0
CA A:PHE117 4.7 10.3 1.0
OG A:SER185 4.7 8.9 1.0
CG A:PHE117 4.8 11.1 1.0
C5D A:2NF503 4.9 19.3 1.0
CD1 A:LEU137 4.9 8.9 1.0
O A:VAL116 4.9 11.9 1.0
CB A:PHE117 5.0 7.3 1.0
NE1 A:TRP118 5.0 15.6 1.0

Fluorine binding site 2 out of 2 in 3kou

Go back to Fluorine Binding Sites List in 3kou
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:F502

b:19.7
occ:1.00
F2D B:2NF502 0.0 19.7 1.0
C2D B:2NF502 1.3 22.9 1.0
C1D B:2NF502 2.3 17.2 1.0
C3D B:2NF502 2.4 18.4 1.0
O3D B:2NF502 2.5 17.9 1.0
OE2 B:GLU218 2.7 20.2 1.0
O B:HOH601 2.8 13.3 1.0
CD B:GLU218 3.3 18.7 1.0
O4D B:2NF502 3.4 23.4 1.0
OE1 B:GLU218 3.5 20.8 1.0
C4D B:2NF502 3.5 15.1 1.0
CD1 B:PHE117 3.7 18.4 1.0
CB B:LEU137 3.7 12.7 1.0
CD2 B:PHE188 3.7 18.0 1.0
CE2 B:PHE188 3.8 17.7 1.0
CD2 B:LEU137 3.9 17.4 1.0
O B:HOH679 4.2 26.1 1.0
CE1 B:PHE117 4.2 17.3 1.0
CG B:LEU137 4.4 15.1 1.0
CG B:GLU218 4.5 21.1 1.0
OG B:SER185 4.6 16.9 1.0
C5D B:2NF502 4.7 18.3 1.0
CG B:PHE117 4.7 24.8 1.0
CA B:PHE117 4.7 16.0 1.0
N B:LEU137 4.7 17.2 1.0
CA B:LEU137 4.8 15.4 1.0
CG B:PHE188 4.9 16.0 1.0
CB B:PHE117 4.9 17.9 1.0
NE1 B:TRP118 5.0 21.2 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: Mon Jul 14 17:20:35 2025

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