Fluorine in PDB 1s2d: Purine 2'-Deoxyribosyl Complex with Arabinoside: Ribosylated Intermediate (Araa)

All present enzymatic activity of Purine 2'-Deoxyribosyl Complex with Arabinoside: Ribosylated Intermediate (Araa):
2.4.2.6;

The structure of Purine 2'-Deoxyribosyl Complex with Arabinoside: Ribosylated Intermediate (Araa), PDB code: 1s2d was solved by R.Anand, P.A.Kaminski, S.E.Ealick, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.74 / 2.10
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	79.587, 79.587, 184.973, 90.00, 90.00, 90.00
R / Rfree (%)	22.9 / 25.3

The binding sites of Fluorine atom in the Purine 2'-Deoxyribosyl Complex with Arabinoside: Ribosylated Intermediate (Araa) (pdb code 1s2d). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Purine 2'-Deoxyribosyl Complex with Arabinoside: Ribosylated Intermediate (Araa), PDB code: 1s2d:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Purine 2'-Deoxyribosyl Complex with Arabinoside: Ribosylated Intermediate (Araa)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Purine 2'-Deoxyribosyl Complex with Arabinoside: Ribosylated Intermediate (Araa) within 5.0Å range: probe atom residue distance (Å) B Occ A:F101 b:35.2 occ:1.00 F2' A:AR4101 0.0 35.2 1.0 C2' A:AR4101 1.4 0.6 1.0 C1' A:AR4101 2.4 32.0 1.0 C3' A:AR4101 2.4 31.9 1.0 CB A:PRO44 3.1 34.0 1.0 CG A:PRO44 3.2 34.0 1.0 N1 A:ADE1245 3.3 29.1 1.0 O3' A:AR4101 3.3 31.3 1.0 OD2 A:ASP75 3.3 28.9 1.0 OE2 A:AR4101 3.3 26.6 1.0 C4' A:AR4101 3.4 31.5 1.0 CG A:ASP75 3.4 28.9 1.0 O4' A:AR4101 3.4 31.9 1.0 OD1 A:ASP75 3.4 28.9 1.0 OH A:TYR11 3.9 24.6 1.0 C5' A:AR4101 3.9 31.1 1.0 C2 A:ADE1245 3.9 28.8 1.0 CD A:AR4101 4.2 26.6 1.0 C6 A:ADE1245 4.2 30.2 1.0 N6 A:ADE1245 4.3 30.4 1.0 CB A:ASP75 4.3 28.9 1.0 OE1 A:AR4101 4.3 26.6 1.0 CE1 A:PHE45 4.3 33.7 1.0 CZ A:PHE45 4.6 33.7 1.0 CA A:PRO44 4.6 29.3 1.0 CD A:PRO44 4.6 34.0 1.0 CZ A:TYR11 4.9 24.6 1.0 CD1 A:PHE45 4.9 33.7 1.0

Fluorine binding site 2 out of 3 in the Purine 2'-Deoxyribosyl Complex with Arabinoside: Ribosylated Intermediate (Araa)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Purine 2'-Deoxyribosyl Complex with Arabinoside: Ribosylated Intermediate (Araa) within 5.0Å range: probe atom residue distance (Å) B Occ B:F101 b:35.2 occ:1.00 F2' B:AR4101 0.0 35.2 1.0 C2' B:AR4101 1.4 22.6 1.0 C3' B:AR4101 2.4 0.8 1.0 C1' B:AR4101 2.4 23.0 1.0 CB B:PRO44 3.1 40.8 1.0 O3' B:AR4101 3.3 0.3 1.0 N1 B:ADE1246 3.3 29.1 1.0 CG B:PRO44 3.3 40.8 1.0 OE2 B:AR4101 3.4 20.4 1.0 C4' B:AR4101 3.4 22.5 1.0 OD1 B:ASP75 3.4 32.4 1.0 OD2 B:ASP75 3.4 32.4 1.0 O4' B:AR4101 3.4 22.9 1.0 CG B:ASP75 3.5 32.4 1.0 C5' B:AR4101 3.9 22.1 1.0 OH B:TYR11 4.0 20.7 1.0 C2 B:ADE1246 4.1 28.8 1.0 C6 B:ADE1246 4.1 30.2 1.0 N6 B:ADE1246 4.1 30.4 1.0 CD B:AR4101 4.1 20.4 1.0 OE1 B:AR4101 4.3 20.4 1.0 CE2 B:PHE45 4.3 33.1 1.0 CB B:ASP75 4.4 32.4 1.0 CA B:PRO44 4.5 29.0 1.0 CZ B:PHE45 4.5 33.1 1.0 CD B:PRO44 4.7 40.8 1.0 CD2 B:PHE45 4.9 33.1 1.0

Fluorine binding site 3 out of 3 in the Purine 2'-Deoxyribosyl Complex with Arabinoside: Ribosylated Intermediate (Araa)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Purine 2'-Deoxyribosyl Complex with Arabinoside: Ribosylated Intermediate (Araa) within 5.0Å range: probe atom residue distance (Å) B Occ C:F101 b:35.2 occ:1.00 F2' C:AR4101 0.0 35.2 1.0 C2' C:AR4101 1.4 22.6 1.0 C3' C:AR4101 2.4 0.9 1.0 C1' C:AR4101 2.4 32.0 1.0 N1 C:ADE1247 3.1 29.1 1.0 OD2 C:ASP75 3.1 29.1 1.0 CG C:ASP75 3.2 29.1 1.0 CB C:PRO44 3.2 34.8 1.0 O3' C:AR4101 3.3 0.3 1.0 OE2 C:AR4101 3.3 22.1 1.0 C4' C:AR4101 3.4 31.5 1.0 OD1 C:ASP75 3.4 29.1 1.0 O4' C:AR4101 3.4 31.9 1.0 CG C:PRO44 3.5 34.8 1.0 C2 C:ADE1247 3.6 28.8 1.0 C5' C:AR4101 3.8 31.1 1.0 C6 C:ADE1247 4.0 30.2 1.0 CB C:ASP75 4.1 29.1 1.0 OH C:TYR11 4.1 25.3 1.0 CD C:AR4101 4.2 22.1 1.0 N6 C:ADE1247 4.2 30.4 1.0 OE1 C:AR4101 4.3 22.1 1.0 CE1 C:PHE45 4.4 29.1 1.0 CZ C:PHE45 4.6 29.1 1.0 CA C:PRO44 4.7 37.8 1.0 N3 C:ADE1247 4.8 29.4 1.0 CD C:PRO44 4.9 34.8 1.0 CD1 C:PHE45 5.0 29.1 1.0

R.Anand, P.A.Kaminski, S.E.Ealick. Structures of Purine 2'-Deoxyribosyltransferase, Substrate Complexes, and the Ribosylated Enzyme Intermediate at 2.0 A Resolution. Biochemistry V. 43 2384 2004.
ISSN: ISSN 0006-2960
PubMed: 14992575
DOI: 10.1021/BI035723K