Fluorine in PDB 7zeg: Human Cytosolic 5' Nucleotidase Iiib in Complex with 3,4-Dif-BN7GMP

Enzymatic activity of Human Cytosolic 5' Nucleotidase Iiib in Complex with 3,4-Dif-BN7GMP

All present enzymatic activity of Human Cytosolic 5' Nucleotidase Iiib in Complex with 3,4-Dif-BN7GMP:
3.1.3.5; 3.1.3.91;

Protein crystallography data

The structure of Human Cytosolic 5' Nucleotidase Iiib in Complex with 3,4-Dif-BN7GMP, PDB code: 7zeg was solved by D.Kubacka, M.Kozarski, M.R.Baranowski, R.Wojcik, J.Jemielity, J.Kowalska, J.Basquin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.69 / 1.56
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 40.755, 79.135, 94.388, 90, 93.23, 90
R / Rfree (%) 24 / 27.3

Other elements in 7zeg:

The structure of Human Cytosolic 5' Nucleotidase Iiib in Complex with 3,4-Dif-BN7GMP also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Human Cytosolic 5' Nucleotidase Iiib in Complex with 3,4-Dif-BN7GMP (pdb code 7zeg). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Human Cytosolic 5' Nucleotidase Iiib in Complex with 3,4-Dif-BN7GMP, PDB code: 7zeg:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 7zeg

Go back to Fluorine Binding Sites List in 7zeg
Fluorine binding site 1 out of 4 in the Human Cytosolic 5' Nucleotidase Iiib in Complex with 3,4-Dif-BN7GMP


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Human Cytosolic 5' Nucleotidase Iiib in Complex with 3,4-Dif-BN7GMP within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:30.9
occ:1.00
 F1 A:IOO401 0.0 30.9 1.0
C15 A:IOO401 1.4 30.9 1.0
C13 A:IOO401 2.4 26.3 1.0
C17 A:IOO401 2.4 32.8 1.0
F2 A:IOO401 2.8 35.8 1.0
O A:HOH565 2.9 31.1 1.0
CD2 A:HIS110 3.0 23.7 1.0
NE2 A:HIS110 3.2 24.0 1.0
CD1 A:ILE159 3.4 29.1 1.0
C14 A:IOO401 3.7 26.1 1.0
C16 A:IOO401 3.7 24.1 1.0
CD1 A:LEU113 3.8 39.5 1.0
CG1 A:ILE159 4.0 31.3 1.0
C12 A:IOO401 4.2 27.0 1.0
CG A:HIS110 4.3 20.8 1.0
CE1 A:HIS110 4.5 23.7 1.0
CB A:ALA109 4.6 26.3 1.0
CD2 A:LEU63 4.7 44.4 1.0
N A:HIS110 4.8 20.5 1.0
C A:ALA109 4.9 23.2 1.0
CG A:LEU113 5.0 30.4 1.0
CA A:HIS110 5.0 20.8 1.0

Fluorine binding site 2 out of 4 in 7zeg

Go back to Fluorine Binding Sites List in 7zeg
Fluorine binding site 2 out of 4 in the Human Cytosolic 5' Nucleotidase Iiib in Complex with 3,4-Dif-BN7GMP


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Human Cytosolic 5' Nucleotidase Iiib in Complex with 3,4-Dif-BN7GMP within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:35.8
occ:1.00
 F2 A:IOO401 0.0 35.8 1.0
C17 A:IOO401 1.4 32.8 1.0
C16 A:IOO401 2.4 24.1 1.0
C15 A:IOO401 2.4 30.9 1.0
F1 A:IOO401 2.8 30.9 1.0
CD2 A:LEU63 3.3 44.4 1.0
C13 A:IOO401 3.7 26.3 1.0
C12 A:IOO401 3.7 27.0 1.0
CD1 A:LEU113 3.9 39.5 1.0
C14 A:IOO401 4.2 26.1 1.0
CD2 A:LEU77 4.3 35.5 1.0
CB A:ALA109 4.3 26.3 1.0
OD2 A:ASP64 4.4 56.8 1.0
CD1 A:TYR60 4.6 25.7 1.0
OP1 A:IOO401 4.6 30.5 1.0
CG A:LEU113 4.7 30.4 1.0
CG A:LEU63 4.7 49.6 1.0
CD1 A:LEU77 4.8 45.8 1.0
C11 A:IOO401 4.8 23.2 1.0

Fluorine binding site 3 out of 4 in 7zeg

Go back to Fluorine Binding Sites List in 7zeg
Fluorine binding site 3 out of 4 in the Human Cytosolic 5' Nucleotidase Iiib in Complex with 3,4-Dif-BN7GMP


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Human Cytosolic 5' Nucleotidase Iiib in Complex with 3,4-Dif-BN7GMP within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:39.6
occ:1.00
 F1 B:IOO401 0.0 39.6 1.0
C15 B:IOO401 1.4 39.1 1.0
C13 B:IOO401 2.4 33.9 1.0
C17 B:IOO401 2.4 38.2 1.0
F2 B:IOO401 2.8 40.4 1.0
O B:HOH562 3.2 35.5 1.0
CD2 B:HIS110 3.2 31.6 1.0
CD1 B:LEU113 3.5 36.0 1.0
NE2 B:HIS110 3.5 37.1 1.0
C14 B:IOO401 3.7 35.6 1.0
C16 B:IOO401 3.7 31.5 1.0
CG1 B:ILE159 4.1 37.5 1.0
CD1 B:ILE159 4.2 39.2 1.0
C12 B:IOO401 4.2 32.7 1.0
O B:HOH582 4.4 50.1 1.0
CB B:ALA109 4.5 35.1 1.0
CG B:HIS110 4.6 30.2 1.0
CG B:LEU113 4.7 36.0 1.0
C B:ALA109 4.8 31.8 1.0
N B:HIS110 4.8 35.0 1.0
CE1 B:HIS110 4.9 34.9 1.0
O B:ALA109 4.9 34.2 1.0
CZ B:PHE195 4.9 27.9 1.0

Fluorine binding site 4 out of 4 in 7zeg

Go back to Fluorine Binding Sites List in 7zeg
Fluorine binding site 4 out of 4 in the Human Cytosolic 5' Nucleotidase Iiib in Complex with 3,4-Dif-BN7GMP


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Human Cytosolic 5' Nucleotidase Iiib in Complex with 3,4-Dif-BN7GMP within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:40.4
occ:1.00
 F2 B:IOO401 0.0 40.4 1.0
C17 B:IOO401 1.4 38.2 1.0
C16 B:IOO401 2.4 31.5 1.0
C15 B:IOO401 2.4 39.1 1.0
O B:HOH582 2.7 50.1 1.0
F1 B:IOO401 2.8 39.6 1.0
C12 B:IOO401 3.7 32.7 1.0
C13 B:IOO401 3.7 33.9 1.0
CD1 B:LEU113 3.9 36.0 1.0
CD2 B:LEU77 4.1 50.7 1.0
C14 B:IOO401 4.1 35.6 1.0
OD2 B:ASP64 4.2 60.9 1.0
CB B:ALA109 4.2 35.1 1.0
CG B:LEU113 4.5 36.0 1.0
CD1 B:TYR60 4.5 34.0 1.0
OP1 B:IOO401 4.5 35.3 1.0
CD2 B:LEU63 4.6 48.8 1.0
CD1 B:LEU77 4.7 41.3 1.0
CD2 B:LEU113 4.7 35.8 1.0
C11 B:IOO401 4.8 29.5 1.0
OD1 B:ASP64 4.9 57.8 1.0

Reference:

D.Kubacka, M.Kozarski, M.R.Baranowski, R.Wojcik, J.Panecka-Hofman, D.Strzelecka, J.Basquin, J.Jemielity, J.Kowalska. Substrate-Based Design of Cytosolic Nucleotidase Iiib Inhibitors and Structural Insights Into Inhibition Mechanism. Pharmaceuticals V. 15 2022.
ISSN: ESSN 1424-8247
PubMed: 35631380
DOI: 10.3390/PH15050554
Page generated: Fri Aug 2 16:08:11 2024

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