Fluorine in PDB 8pqq: Nucleoside 2'Deoxyribosyltransferase From Chroococcidiopsis Thermalis Pcc 7203 E88Q Mutant Bound to Clofarabine

The structure of Nucleoside 2'Deoxyribosyltransferase From Chroococcidiopsis Thermalis Pcc 7203 E88Q Mutant Bound to Clofarabine, PDB code: 8pqq was solved by P.Tang, C.J.Harding, M.C.Czekster, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	58.93 / 2.23
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	136.1, 136.1, 87.44, 90, 90, 120
R / Rfree (%)	17.3 / 21.9

The structure of Nucleoside 2'Deoxyribosyltransferase From Chroococcidiopsis Thermalis Pcc 7203 E88Q Mutant Bound to Clofarabine also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Chlorine	(Cl)	4 atoms

The binding sites of Fluorine atom in the Nucleoside 2'Deoxyribosyltransferase From Chroococcidiopsis Thermalis Pcc 7203 E88Q Mutant Bound to Clofarabine (pdb code 8pqq). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Nucleoside 2'Deoxyribosyltransferase From Chroococcidiopsis Thermalis Pcc 7203 E88Q Mutant Bound to Clofarabine, PDB code: 8pqq:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Nucleoside 2'Deoxyribosyltransferase From Chroococcidiopsis Thermalis Pcc 7203 E88Q Mutant Bound to Clofarabine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Nucleoside 2'Deoxyribosyltransferase From Chroococcidiopsis Thermalis Pcc 7203 E88Q Mutant Bound to Clofarabine within 5.0Å range: probe atom residue distance (Å) B Occ A:F201 b:87.6 occ:1.00 F A:CFB201 0.0 87.6 1.0 C2' A:CFB201 1.3 88.7 1.0 C3' A:CFB201 2.3 84.8 1.0 N3 A:CFB201 2.3 91.3 1.0 C1' A:CFB201 2.3 95.6 1.0 C4 A:CFB201 2.6 92.6 1.0 N9 A:CFB201 2.6 92.3 1.0 C4' A:CFB201 3.2 91.7 1.0 O3' A:CFB201 3.3 68.3 1.0 O4' A:CFB201 3.3 97.3 1.0 C2 A:CFB201 3.4 96.1 1.0 CG A:PRO40 3.4 47.3 1.0 CB A:PRO40 3.6 47.6 1.0 C5' A:CFB201 3.6 80.1 1.0 CE2 A:PHE41 3.7 43.9 1.0 CZ A:PHE41 3.7 48.1 1.0 OD2 A:ASP62 3.8 53.6 1.0 C5 A:CFB201 3.9 94.9 1.0 C8 A:CFB201 3.9 91.5 1.0 CL A:CFB201 4.1 86.5 1.0 CD2 A:PHE41 4.2 43.3 1.0 CE1 A:PHE41 4.3 48.9 1.0 OE1 A:GLN88 4.3 67.7 1.0 N1 A:CFB201 4.4 105.9 1.0 O A:SER10 4.5 34.9 1.0 N7 A:CFB201 4.5 94.0 1.0 C6 A:CFB201 4.6 100.5 1.0 CG A:ASP62 4.7 52.2 1.0 OH A:TYR7 4.7 55.1 1.0 CG A:PHE41 4.8 42.5 1.0 CD1 A:PHE41 4.8 36.7 1.0 O5' A:CFB201 4.8 72.6 1.0 OD1 A:ASP62 4.9 50.9 1.0 CD A:PRO40 4.9 41.4 1.0 CA A:PRO40 4.9 45.6 1.0 NE2 A:GLN88 4.9 55.9 1.0 N A:PHE41 4.9 40.3 1.0

Fluorine binding site 2 out of 4 in the Nucleoside 2'Deoxyribosyltransferase From Chroococcidiopsis Thermalis Pcc 7203 E88Q Mutant Bound to Clofarabine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Nucleoside 2'Deoxyribosyltransferase From Chroococcidiopsis Thermalis Pcc 7203 E88Q Mutant Bound to Clofarabine within 5.0Å range: probe atom residue distance (Å) B Occ B:F201 b:130.7 occ:1.00 F B:CFB201 0.0 130.7 1.0 C2' B:CFB201 1.4 120.2 1.0 C3' B:CFB201 2.3 106.9 1.0 C1' B:CFB201 2.3 123.0 1.0 N3 B:CFB201 2.4 133.1 1.0 N9 B:CFB201 2.7 126.1 1.0 C4 B:CFB201 2.7 130.9 1.0 C4' B:CFB201 3.2 110.6 1.0 O4' B:CFB201 3.3 123.8 1.0 O3' B:CFB201 3.4 85.2 1.0 C2 B:CFB201 3.5 140.7 1.0 CE2 B:PHE41 3.5 40.3 1.0 CG B:PRO40 3.5 43.3 1.0 CB B:PRO40 3.5 41.4 1.0 CZ B:PHE41 3.5 47.2 1.0 C5' B:CFB201 3.6 93.2 1.0 C8 B:CFB201 4.0 123.6 1.0 CD2 B:PHE41 4.0 54.9 1.0 C5 B:CFB201 4.0 125.7 1.0 OD2 B:ASP62 4.0 66.7 1.0 CE1 B:PHE41 4.1 50.4 1.0 CL B:CFB201 4.2 165.5 1.0 CG B:PHE41 4.4 57.8 1.0 CD1 B:PHE41 4.5 50.3 1.0 N1 B:CFB201 4.6 133.2 1.0 N7 B:CFB201 4.6 122.6 1.0 OE1 B:GLN88 4.6 65.3 1.0 N B:PHE41 4.6 45.6 1.0 O B:SER10 4.7 52.2 1.0 OH B:TYR7 4.7 52.9 1.0 C B:PRO40 4.7 47.4 1.0 CA B:PRO40 4.7 44.2 1.0 C6 B:CFB201 4.8 123.7 1.0 O5' B:CFB201 4.8 83.5 1.0 CG B:ASP62 4.9 55.7 1.0

Fluorine binding site 3 out of 4 in the Nucleoside 2'Deoxyribosyltransferase From Chroococcidiopsis Thermalis Pcc 7203 E88Q Mutant Bound to Clofarabine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Nucleoside 2'Deoxyribosyltransferase From Chroococcidiopsis Thermalis Pcc 7203 E88Q Mutant Bound to Clofarabine within 5.0Å range: probe atom residue distance (Å) B Occ C:F201 b:89.3 occ:1.00 F C:CFB201 0.0 89.3 1.0 C2' C:CFB201 1.3 95.6 1.0 C3' C:CFB201 2.3 93.9 1.0 C1' C:CFB201 2.4 104.2 1.0 N3 C:CFB201 2.5 109.4 1.0 N9 C:CFB201 2.7 105.7 1.0 C4 C:CFB201 2.8 110.0 1.0 C4' C:CFB201 3.3 101.9 1.0 O4' C:CFB201 3.4 109.7 1.0 O3' C:CFB201 3.4 76.7 1.0 CG C:PRO40 3.4 48.4 1.0 C2 C:CFB201 3.5 114.3 1.0 CE2 C:PHE41 3.6 44.6 1.0 CZ C:PHE41 3.6 49.2 1.0 CB C:PRO40 3.6 51.6 1.0 C5' C:CFB201 3.6 86.5 1.0 C8 C:CFB201 3.9 109.0 1.0 C5 C:CFB201 4.0 113.5 1.0 OD2 C:ASP62 4.0 56.0 1.0 CD2 C:PHE41 4.1 52.9 1.0 CE1 C:PHE41 4.1 58.7 1.0 CL C:CFB201 4.3 112.7 1.0 O C:SER10 4.4 51.1 1.0 N7 C:CFB201 4.6 110.8 1.0 N1 C:CFB201 4.6 119.6 1.0 CD1 C:PHE41 4.6 54.4 1.0 CG C:PHE41 4.6 54.2 1.0 OE1 C:GLN88 4.6 70.3 1.0 OH C:TYR7 4.7 61.0 1.0 C6 C:CFB201 4.8 119.2 1.0 CG C:ASP62 4.8 61.4 1.0 N C:PHE41 4.8 71.9 1.0 O5' C:CFB201 4.9 72.5 1.0 CA C:PRO40 4.9 57.4 1.0 CD C:PRO40 4.9 49.0 1.0 C C:PRO40 5.0 68.4 1.0

Fluorine binding site 4 out of 4 in the Nucleoside 2'Deoxyribosyltransferase From Chroococcidiopsis Thermalis Pcc 7203 E88Q Mutant Bound to Clofarabine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Nucleoside 2'Deoxyribosyltransferase From Chroococcidiopsis Thermalis Pcc 7203 E88Q Mutant Bound to Clofarabine within 5.0Å range: probe atom residue distance (Å) B Occ D:F201 b:82.7 occ:1.00 F D:CFB201 0.0 82.7 1.0 C2' D:CFB201 1.3 90.1 1.0 N3 D:CFB201 2.1 111.0 1.0 C1' D:CFB201 2.3 101.7 1.0 C3' D:CFB201 2.3 87.8 1.0 C4 D:CFB201 2.4 112.6 1.0 N9 D:CFB201 2.5 108.9 1.0 C2 D:CFB201 3.2 113.9 1.0 C4' D:CFB201 3.3 86.9 1.0 O4' D:CFB201 3.3 97.2 1.0 O3' D:CFB201 3.4 85.5 1.0 CZ D:PHE41 3.5 70.2 1.0 CE1 D:PHE41 3.5 53.8 1.0 CG D:PRO40 3.6 53.0 1.0 OD2 D:ASP62 3.6 62.4 1.0 C5 D:CFB201 3.6 115.2 1.0 CB D:PRO40 3.7 55.5 1.0 C8 D:CFB201 3.7 110.7 1.0 C5' D:CFB201 3.8 77.2 1.0 CL D:CFB201 4.0 106.2 1.0 CE2 D:PHE41 4.1 76.3 1.0 CD1 D:PHE41 4.1 53.9 1.0 N1 D:CFB201 4.2 117.6 1.0 N7 D:CFB201 4.3 114.2 1.0 C6 D:CFB201 4.4 115.7 1.0 O D:SER10 4.6 54.3 1.0 CG D:ASP62 4.6 64.4 1.0 CD2 D:PHE41 4.6 69.0 1.0 CG D:PHE41 4.7 60.4 1.0 OH D:TYR7 4.8 68.7 1.0 OE1 D:GLN88 4.8 87.2 1.0 O5' D:CFB201 4.8 72.2 1.0 NE2 D:GLN88 4.8 105.9 1.0 N D:PHE41 5.0 60.6 1.0 CA D:PRO40 5.0 56.2 1.0 OD1 D:ASP62 5.0 69.4 1.0

P.Tang, C.J.Harding, A.L.Dickson, R.G.Da Silva, D.J.Harrison, C.M.Czekster. Snapshots of the Reaction Coordinate of A Thermophilic 2'-Deoxyribonucleoside/Ribonucleoside Transferase Acs Catalysis 3090 2024.
ISSN: ESSN 2155-5435
DOI: 10.1021/ACSCATAL.3C06260