Fluorine in PDB 7zeh: Human Cytosolic 5' Nucleotidase Iiib in Complex with 3,4-Dif- BN7GUANINE

Enzymatic activity of Human Cytosolic 5' Nucleotidase Iiib in Complex with 3,4-Dif- BN7GUANINE

All present enzymatic activity of Human Cytosolic 5' Nucleotidase Iiib in Complex with 3,4-Dif- BN7GUANINE:
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- BN7GUANINE, PDB code: 7zeh 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) 75.08 / 1.50
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 60.59, 80.89, 83.17, 82.22, 72.46, 68.2
R / Rfree (%) 18.8 / 22

Other elements in 7zeh:

The structure of Human Cytosolic 5' Nucleotidase Iiib in Complex with 3,4-Dif- BN7GUANINE also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Human Cytosolic 5' Nucleotidase Iiib in Complex with 3,4-Dif- BN7GUANINE (pdb code 7zeh). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the Human Cytosolic 5' Nucleotidase Iiib in Complex with 3,4-Dif- BN7GUANINE, PDB code: 7zeh:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 7zeh

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Fluorine binding site 1 out of 8 in the Human Cytosolic 5' Nucleotidase Iiib in Complex with 3,4-Dif- BN7GUANINE


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- BN7GUANINE within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:35.8
occ:1.00
 F1 A:IPQ401 0.0 35.8 1.0
C10 A:IPQ401 1.4 30.3 1.0
C11 A:IPQ401 2.4 28.3 1.0
C9 A:IPQ401 2.4 30.5 1.0
F2 A:IPQ401 2.7 41.6 1.0
O A:HOH738 3.1 48.6 1.0
C4 A:RBL402 3.4 36.3 1.0
C5 A:IPQ401 3.6 26.6 1.0
C12 A:IPQ401 3.6 24.6 1.0
C1 A:RBL402 3.6 33.6 1.0
C3 A:RBL402 3.7 28.6 1.0
O4 A:RBL402 3.7 41.9 1.0
CE2 A:TYR60 3.8 25.1 1.0
CD2 A:TYR60 4.0 25.7 1.0
C7 A:IPQ401 4.1 25.1 1.0
CZ A:TYR60 4.2 24.4 1.0
C2 A:RBL402 4.3 40.6 1.0
O A:HOH520 4.4 34.9 1.0
CG A:TYR60 4.6 24.1 1.0
CH2 A:TRP105 4.7 23.7 1.0
C5 A:RBL402 4.7 43.2 1.0
OH A:TYR60 4.7 23.8 1.0
O A:HOH740 4.8 42.1 1.0
O A:HOH586 4.8 30.3 1.0
CE1 A:TYR60 4.8 25.4 1.0
O4 A:PO4410 4.8 22.2 1.0
O1 A:RBL402 4.9 59.0 1.0
OE1 A:GLU88 4.9 27.3 1.0
OE2 A:GLU88 4.9 32.2 1.0
CD1 A:TYR60 5.0 24.8 1.0
CD1 A:LEU81 5.0 32.1 1.0

Fluorine binding site 2 out of 8 in 7zeh

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Fluorine binding site 2 out of 8 in the Human Cytosolic 5' Nucleotidase Iiib in Complex with 3,4-Dif- BN7GUANINE


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- BN7GUANINE within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:41.6
occ:1.00
 F2 A:IPQ401 0.0 41.6 1.0
C11 A:IPQ401 1.4 28.3 1.0
C10 A:IPQ401 2.3 30.3 1.0
C12 A:IPQ401 2.4 24.6 1.0
F1 A:IPQ401 2.7 35.8 1.0
O1 A:EDO403 2.7 60.9 1.0
C1 A:EDO403 3.2 59.0 1.0
C9 A:IPQ401 3.6 30.5 1.0
C7 A:IPQ401 3.6 25.1 1.0
O A:HOH520 3.8 34.9 1.0
C2 A:EDO403 3.8 48.3 1.0
CG A:TYR60 3.9 24.1 1.0
CB A:TYR60 4.1 25.9 1.0
C5 A:IPQ401 4.1 26.6 1.0
CD2 A:TYR60 4.1 25.7 1.0
O A:HOH738 4.2 48.6 1.0
CD1 A:LEU81 4.2 32.1 1.0
CD1 A:TYR60 4.4 24.8 1.0
O A:HOH638 4.5 49.3 1.0
CD2 A:LEU81 4.5 34.5 1.0
O6 A:IPQ401 4.6 26.4 1.0
CE2 A:TYR60 4.7 25.1 1.0
O2 A:EDO403 4.8 46.8 1.0
CZ2 A:TRP105 4.8 23.1 1.0
CG A:LEU81 4.9 32.5 1.0
C3 A:IPQ401 4.9 24.4 1.0
CE1 A:TYR60 4.9 25.4 1.0
O A:HOH740 4.9 42.1 1.0

Fluorine binding site 3 out of 8 in 7zeh

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Fluorine binding site 3 out of 8 in the Human Cytosolic 5' Nucleotidase Iiib in Complex with 3,4-Dif- BN7GUANINE


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- BN7GUANINE within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:40.4
occ:1.00
 F1 B:IPQ401 0.0 40.4 1.0
C10 B:IPQ401 1.3 33.2 1.0
C11 B:IPQ401 2.3 28.3 1.0
C9 B:IPQ401 2.4 27.7 1.0
F2 B:IPQ401 2.6 43.0 1.0
O1 B:RBL402 3.1 55.8 1.0
O B:HOH689 3.2 55.6 1.0
C4 B:RBL402 3.5 40.4 1.0
C12 B:IPQ401 3.6 23.9 1.0
C5 B:IPQ401 3.6 27.5 1.0
O4 B:RBL402 3.7 38.0 1.0
CE2 B:TYR60 3.8 24.6 1.0
C3 B:RBL402 3.9 35.1 1.0
CD2 B:TYR60 4.0 25.6 1.0
C7 B:IPQ401 4.1 26.0 1.0
CZ B:TYR60 4.2 25.4 1.0
C1 B:RBL402 4.4 51.2 1.0
O B:HOH519 4.4 34.2 1.0
CG B:TYR60 4.6 25.1 1.0
C2 B:RBL402 4.7 38.6 1.0
CH2 B:TRP105 4.7 23.6 1.0
OH B:TYR60 4.7 24.3 1.0
O B:HOH704 4.8 49.3 1.0
CE1 B:TYR60 4.8 24.1 1.0
C5 B:RBL402 4.8 40.6 1.0
O1 B:PO4409 4.8 25.6 1.0
CD1 B:LEU81 4.9 28.8 1.0
OE1 B:GLU88 4.9 26.1 1.0
CD1 B:TYR60 5.0 25.2 1.0
OE2 B:GLU88 5.0 30.8 1.0

Fluorine binding site 4 out of 8 in 7zeh

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Fluorine binding site 4 out of 8 in the Human Cytosolic 5' Nucleotidase Iiib in Complex with 3,4-Dif- BN7GUANINE


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- BN7GUANINE within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:43.0
occ:1.00
 F2 B:IPQ401 0.0 43.0 1.0
C11 B:IPQ401 1.4 28.3 1.0
C10 B:IPQ401 2.3 33.2 1.0
C12 B:IPQ401 2.4 23.9 1.0
F1 B:IPQ401 2.6 40.4 1.0
C9 B:IPQ401 3.6 27.7 1.0
C7 B:IPQ401 3.6 26.0 1.0
O B:HOH519 3.9 34.2 1.0
CG B:TYR60 3.9 25.1 1.0
CB B:TYR60 4.0 24.6 1.0
CD2 B:TYR60 4.0 25.6 1.0
C5 B:IPQ401 4.1 27.5 1.0
CD1 B:LEU81 4.2 28.8 1.0
O B:HOH689 4.3 55.6 1.0
CD1 B:TYR60 4.3 25.2 1.0
O B:HOH701 4.4 46.9 1.0
CD2 B:LEU81 4.4 32.6 1.0
O B:HOH676 4.4 46.4 1.0
O6 B:IPQ401 4.6 27.5 1.0
CE2 B:TYR60 4.6 24.6 1.0
CE1 B:TYR60 4.8 24.1 1.0
CZ2 B:TRP105 4.9 23.7 1.0
C3 B:IPQ401 4.9 25.5 1.0
CG B:LEU81 4.9 30.6 1.0
CZ B:TYR60 5.0 25.4 1.0
C1 B:IPQ401 5.0 25.4 1.0
O B:HOH704 5.0 49.3 1.0

Fluorine binding site 5 out of 8 in 7zeh

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Fluorine binding site 5 out of 8 in the Human Cytosolic 5' Nucleotidase Iiib in Complex with 3,4-Dif- BN7GUANINE


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Human Cytosolic 5' Nucleotidase Iiib in Complex with 3,4-Dif- BN7GUANINE within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F401

b:37.0
occ:1.00
 F1 C:IPQ401 0.0 37.0 1.0
C10 C:IPQ401 1.4 50.7 1.0
C11 C:IPQ401 2.3 42.1 1.0
C9 C:IPQ401 2.4 33.3 1.0
F2 C:IPQ401 2.7 47.0 1.0
O1 C:RBL402 3.0 63.6 1.0
C12 C:IPQ401 3.6 28.3 1.0
C5 C:IPQ401 3.6 23.7 1.0
C4 C:RBL402 3.7 52.3 1.0
O4 C:RBL402 3.8 55.1 1.0
C3 C:RBL402 4.1 38.2 1.0
C7 C:IPQ401 4.1 23.8 1.0
CE2 C:TYR60 4.1 22.7 1.0
C1 C:RBL402 4.2 57.4 1.0
CD2 C:TYR60 4.4 23.6 1.0
CZ C:TYR60 4.4 22.9 1.0
O C:HOH519 4.6 30.8 1.0
CH2 C:TRP105 4.6 22.9 1.0
C2 C:RBL402 4.8 45.9 1.0
OH C:TYR60 4.9 22.9 1.0
CG C:TYR60 4.9 22.9 1.0
CZ2 C:TRP105 4.9 21.8 1.0
CE1 C:TYR60 4.9 21.9 1.0

Fluorine binding site 6 out of 8 in 7zeh

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Fluorine binding site 6 out of 8 in the Human Cytosolic 5' Nucleotidase Iiib in Complex with 3,4-Dif- BN7GUANINE


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Human Cytosolic 5' Nucleotidase Iiib in Complex with 3,4-Dif- BN7GUANINE within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F401

b:47.0
occ:1.00
 F2 C:IPQ401 0.0 47.0 1.0
C11 C:IPQ401 1.3 42.1 1.0
C10 C:IPQ401 2.3 50.7 1.0
C12 C:IPQ401 2.3 28.3 1.0
F1 C:IPQ401 2.7 37.0 1.0
C9 C:IPQ401 3.6 33.3 1.0
C7 C:IPQ401 3.6 23.8 1.0
CD1 C:LEU81 3.7 34.1 1.0
O C:HOH519 3.9 30.8 1.0
C2 C:EDO406 4.0 51.0 1.0
C5 C:IPQ401 4.1 23.7 1.0
CG C:TYR60 4.1 22.9 1.0
CB C:TYR60 4.2 22.1 1.0
CD2 C:TYR60 4.3 23.6 1.0
CD1 C:TYR60 4.4 21.9 1.0
O6 C:IPQ401 4.6 24.6 1.0
O2 C:EDO406 4.7 48.0 1.0
CE2 C:TYR60 4.8 22.7 1.0
C3 C:IPQ401 4.9 24.6 1.0
CE1 C:TYR60 4.9 21.9 1.0
CZ2 C:TRP105 4.9 21.8 1.0
CG C:LEU81 4.9 32.7 1.0

Fluorine binding site 7 out of 8 in 7zeh

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Fluorine binding site 7 out of 8 in the Human Cytosolic 5' Nucleotidase Iiib in Complex with 3,4-Dif- BN7GUANINE


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Human Cytosolic 5' Nucleotidase Iiib in Complex with 3,4-Dif- BN7GUANINE within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F401

b:35.4
occ:1.00
 F1 D:IPQ401 0.0 35.4 1.0
C10 D:IPQ401 1.3 42.6 1.0
C11 D:IPQ401 2.3 36.3 1.0
C9 D:IPQ401 2.4 29.5 1.0
F2 D:IPQ401 2.7 39.8 1.0
O1 D:RBL402 2.7 57.4 1.0
O D:HOH2812 3.3 45.2 1.0
C4 D:RBL402 3.6 49.4 1.0
C12 D:IPQ401 3.6 23.6 1.0
C5 D:IPQ401 3.6 21.9 1.0
O4 D:RBL402 3.6 61.2 1.0
C3 D:RBL402 3.9 34.2 1.0
C1 D:RBL402 4.0 47.3 1.0
CE2 D:TYR60 4.1 22.7 1.0
C7 D:IPQ401 4.1 19.2 1.0
CD2 D:TYR60 4.3 23.6 1.0
CZ D:TYR60 4.4 22.9 1.0
CH2 D:TRP105 4.5 21.4 1.0
C2 D:RBL402 4.5 47.0 1.0
O D:HOH2617 4.6 31.1 1.0
OH D:TYR60 4.8 23.7 1.0
CZ2 D:TRP105 4.9 19.3 1.0
CG D:TYR60 4.9 22.6 1.0
CE1 D:TYR60 4.9 23.0 1.0
C5 D:RBL402 4.9 40.6 1.0
OE1 D:GLU88 5.0 29.4 1.0

Fluorine binding site 8 out of 8 in 7zeh

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Fluorine binding site 8 out of 8 in the Human Cytosolic 5' Nucleotidase Iiib in Complex with 3,4-Dif- BN7GUANINE


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Human Cytosolic 5' Nucleotidase Iiib in Complex with 3,4-Dif- BN7GUANINE within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F401

b:39.8
occ:1.00
 F2 D:IPQ401 0.0 39.8 1.0
C11 D:IPQ401 1.3 36.3 1.0
C10 D:IPQ401 2.3 42.6 1.0
C12 D:IPQ401 2.3 23.6 1.0
F1 D:IPQ401 2.7 35.4 1.0
C9 D:IPQ401 3.6 29.5 1.0
C7 D:IPQ401 3.6 19.2 1.0
O D:HOH2617 4.0 31.1 1.0
CG D:TYR60 4.0 22.6 1.0
C5 D:IPQ401 4.1 21.9 1.0
CD2 D:TYR60 4.2 23.6 1.0
CB D:TYR60 4.2 21.9 1.0
CD2 D:LEU81 4.3 34.6 1.0
CD1 D:TYR60 4.4 22.0 1.0
O D:HOH2812 4.4 45.2 1.0
CD1 D:LEU81 4.5 34.5 1.0
O6 D:IPQ401 4.6 24.5 1.0
CE2 D:TYR60 4.7 22.7 1.0
O1 D:RBL402 4.7 57.4 1.0
CZ2 D:TRP105 4.8 19.3 1.0
CE1 D:TYR60 4.8 23.0 1.0
C3 D:IPQ401 4.8 20.4 1.0
CZ D:TYR60 5.0 22.9 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 16:08:26 2024

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