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Fluorine in PDB 7bmi: Aspartyl/Asparaginyl Beta-Hydroxylase (Asph) Oxygenase and Tpr Domains in Complex with Manganese, 3-Fluoropyridine-2,4-Dicarboxylic Acid, and Factor X Substrate Peptide Fragment (39MER-4SER)

Enzymatic activity of Aspartyl/Asparaginyl Beta-Hydroxylase (Asph) Oxygenase and Tpr Domains in Complex with Manganese, 3-Fluoropyridine-2,4-Dicarboxylic Acid, and Factor X Substrate Peptide Fragment (39MER-4SER)

All present enzymatic activity of Aspartyl/Asparaginyl Beta-Hydroxylase (Asph) Oxygenase and Tpr Domains in Complex with Manganese, 3-Fluoropyridine-2,4-Dicarboxylic Acid, and Factor X Substrate Peptide Fragment (39MER-4SER):
1.14.11.16; 3.4.21.6;

Protein crystallography data

The structure of Aspartyl/Asparaginyl Beta-Hydroxylase (Asph) Oxygenase and Tpr Domains in Complex with Manganese, 3-Fluoropyridine-2,4-Dicarboxylic Acid, and Factor X Substrate Peptide Fragment (39MER-4SER), PDB code: 7bmi was solved by Y.Nakashima, L.Brewitz, C.J.Schofield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.06 / 1.66
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 49.702, 91.274, 122.629, 90, 90, 90
R / Rfree (%) 18.9 / 22

Other elements in 7bmi:

The structure of Aspartyl/Asparaginyl Beta-Hydroxylase (Asph) Oxygenase and Tpr Domains in Complex with Manganese, 3-Fluoropyridine-2,4-Dicarboxylic Acid, and Factor X Substrate Peptide Fragment (39MER-4SER) also contains other interesting chemical elements:

Manganese (Mn) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Aspartyl/Asparaginyl Beta-Hydroxylase (Asph) Oxygenase and Tpr Domains in Complex with Manganese, 3-Fluoropyridine-2,4-Dicarboxylic Acid, and Factor X Substrate Peptide Fragment (39MER-4SER) (pdb code 7bmi). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total only one binding site of Fluorine was determined in the Aspartyl/Asparaginyl Beta-Hydroxylase (Asph) Oxygenase and Tpr Domains in Complex with Manganese, 3-Fluoropyridine-2,4-Dicarboxylic Acid, and Factor X Substrate Peptide Fragment (39MER-4SER), PDB code: 7bmi:

Fluorine binding site 1 out of 1 in 7bmi

Go back to Fluorine Binding Sites List in 7bmi
Fluorine binding site 1 out of 1 in the Aspartyl/Asparaginyl Beta-Hydroxylase (Asph) Oxygenase and Tpr Domains in Complex with Manganese, 3-Fluoropyridine-2,4-Dicarboxylic Acid, and Factor X Substrate Peptide Fragment (39MER-4SER)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Aspartyl/Asparaginyl Beta-Hydroxylase (Asph) Oxygenase and Tpr Domains in Complex with Manganese, 3-Fluoropyridine-2,4-Dicarboxylic Acid, and Factor X Substrate Peptide Fragment (39MER-4SER) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F802

b:32.4
occ:1.00
F13 A:U4B802 0.0 32.4 1.0
C12 A:U4B802 1.3 31.4 1.0
C04 A:U4B802 2.3 30.5 1.0
C08 A:U4B802 2.4 30.8 1.0
HD13 A:ILE739 2.6 34.5 1.0
HE2 A:HIS690 2.6 37.2 1.0
O10 A:U4B802 2.7 31.2 1.0
HD11 A:ILE739 2.7 34.5 1.0
HE1 A:HIS690 2.7 37.2 1.0
C02 A:U4B802 2.8 32.0 1.0
HD11 A:ILE737 2.8 35.3 1.0
C09 A:U4B802 2.9 31.0 1.0
O01 A:U4B802 2.9 32.1 1.0
NE2 A:HIS690 3.0 30.9 1.0
CE1 A:HIS690 3.0 30.8 1.0
CD1 A:ILE739 3.1 28.6 1.0
O B:HOH202 3.4 38.7 1.0
C05 A:U4B802 3.6 30.9 1.0
N07 A:U4B802 3.6 31.9 1.0
O03 A:U4B802 3.7 32.6 1.0
CD1 A:ILE737 3.7 29.3 1.0
HG12 A:ILE739 3.7 34.2 1.0
HD12 A:ILE739 3.8 34.5 1.0
HD12 A:ILE737 3.9 35.3 1.0
HG A:SER668 4.0 35.6 1.0
CG1 A:ILE739 4.0 28.3 1.0
C06 A:U4B802 4.1 31.9 1.0
HD13 A:ILE737 4.1 35.3 1.0
O11 A:U4B802 4.1 32.5 1.0
CD2 A:HIS690 4.1 30.8 1.0
ND1 A:HIS690 4.2 31.6 1.0
HZ2 A:TRP625 4.2 38.1 1.0
HZ A:PHE719 4.4 44.5 1.0
H051 A:U4B802 4.5 37.3 1.0
HG21 A:ILE739 4.5 38.4 1.0
HB3 A:SER668 4.6 33.0 1.0
HG13 A:ILE739 4.6 34.2 1.0
HE21 A:GLN627 4.6 62.0 1.0
HB2 A:SER668 4.7 33.0 1.0
HD2 A:HIS690 4.7 37.1 1.0
CG A:HIS690 4.7 30.3 1.0
HH22 A:ARG735 4.7 33.3 1.0
OG A:SER668 4.8 29.5 1.0
HZ2 A:TRP711 4.8 36.6 1.0
HG13 A:ILE737 4.9 33.4 1.0
HH12 A:ARG735 4.9 35.5 1.0
HG23 A:ILE739 4.9 38.4 1.0
HG21 A:VAL727 4.9 39.3 1.0
CB A:SER668 4.9 27.4 1.0
CZ2 A:TRP625 4.9 31.6 1.0
CG1 A:ILE737 4.9 27.7 1.0
HE1 A:TRP625 4.9 35.1 1.0
HE22 A:GLN627 5.0 62.0 1.0
HE1 A:PHE719 5.0 45.0 1.0
HD3 A:ARG688 5.0 40.0 1.0

Reference:

L.Brewitz, Y.Nakashima, A.Tumber, E.Salah, C.J.Schofield. Fluorinated Derivatives of Pyridine-2,4-Dicarboxylate Are Potent Inhibitors of Human 2-Oxoglutarate Dependent Oxygenases J Fluor Chem V. 247 09804 2021.
DOI: 10.1016/J.JFLUCHEM.2021.109804
Page generated: Tue Jul 15 18:48:59 2025

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