Fluorine in PDB 2fil: Crystal Structure Analysis of the A-Dna Decamer Gcgt-2'Omea-Fat-Acgc, with Incorporated 2'-O-Methylated-Adenosine (2'Omea) and 2'- Fluoroarabino-Thymidine (Fat)

The structure of Crystal Structure Analysis of the A-Dna Decamer Gcgt-2'Omea-Fat-Acgc, with Incorporated 2'-O-Methylated-Adenosine (2'Omea) and 2'- Fluoroarabino-Thymidine (Fat), PDB code: 2fil was solved by M.Egli, F.Li, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.69
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	32.733, 69.180, 32.831, 90.00, 92.21, 90.00
R / Rfree (%)	20.3 / 21.5

The structure of Crystal Structure Analysis of the A-Dna Decamer Gcgt-2'Omea-Fat-Acgc, with Incorporated 2'-O-Methylated-Adenosine (2'Omea) and 2'- Fluoroarabino-Thymidine (Fat) also contains other interesting chemical elements:

Cobalt

(Co)

7 atoms

The binding sites of Fluorine atom in the Crystal Structure Analysis of the A-Dna Decamer Gcgt-2'Omea-Fat-Acgc, with Incorporated 2'-O-Methylated-Adenosine (2'Omea) and 2'- Fluoroarabino-Thymidine (Fat) (pdb code 2fil). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Crystal Structure Analysis of the A-Dna Decamer Gcgt-2'Omea-Fat-Acgc, with Incorporated 2'-O-Methylated-Adenosine (2'Omea) and 2'- Fluoroarabino-Thymidine (Fat), PDB code: 2fil:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Crystal Structure Analysis of the A-Dna Decamer Gcgt-2'Omea-Fat-Acgc, with Incorporated 2'-O-Methylated-Adenosine (2'Omea) and 2'- Fluoroarabino-Thymidine (Fat)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure Analysis of the A-Dna Decamer Gcgt-2'Omea-Fat-Acgc, with Incorporated 2'-O-Methylated-Adenosine (2'Omea) and 2'- Fluoroarabino-Thymidine (Fat) within 5.0Å range: probe atom residue distance (Å) B Occ A:F106 b:72.8 occ:1.00 F2' A:TAF106 0.0 72.8 1.0 C2' A:TAF106 1.4 66.6 1.0 C1' A:TAF106 2.3 59.3 1.0 C3' A:TAF106 2.3 68.2 1.0 N1 A:TAF106 2.5 54.3 1.0 C8 A:DA107 2.6 52.5 1.0 O5' A:DA107 2.8 68.3 1.0 C2 A:TAF106 2.9 53.0 1.0 N7 A:DA107 3.1 53.0 1.0 N9 A:DA107 3.1 52.4 1.0 O2 A:TAF106 3.1 53.7 1.0 C5' A:DA107 3.2 67.0 1.0 O3' A:TAF106 3.2 73.7 1.0 C6 A:TAF106 3.3 49.6 1.0 O4' A:TAF106 3.4 62.4 1.0 O4' A:DA107 3.4 64.1 1.0 C4' A:TAF106 3.5 68.2 1.0 P A:DA107 3.7 78.1 1.0 C1' A:DA107 3.7 57.5 1.0 C5 A:DA107 3.8 49.0 1.0 C4 A:DA107 3.8 53.8 1.0 N3 A:TAF106 3.8 53.5 1.0 C4' A:DA107 3.9 65.5 1.0 C2' A:DA107 4.0 61.1 1.0 C5 A:TAF106 4.2 44.7 1.0 OP1 A:DA107 4.2 72.3 1.0 C4 A:TAF106 4.4 51.4 1.0 C3' A:DA107 4.6 66.4 1.0 C5' A:TAF106 4.7 68.9 1.0 O5' A:TAF106 4.8 65.5 1.0 O A:HOH1298 4.9 68.0 1.0 C6 A:DA107 4.9 51.3 1.0 OP2 A:DA107 4.9 72.2 1.0 N3 A:DA107 4.9 49.9 1.0

Fluorine binding site 2 out of 4 in the Crystal Structure Analysis of the A-Dna Decamer Gcgt-2'Omea-Fat-Acgc, with Incorporated 2'-O-Methylated-Adenosine (2'Omea) and 2'- Fluoroarabino-Thymidine (Fat)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure Analysis of the A-Dna Decamer Gcgt-2'Omea-Fat-Acgc, with Incorporated 2'-O-Methylated-Adenosine (2'Omea) and 2'- Fluoroarabino-Thymidine (Fat) within 5.0Å range: probe atom residue distance (Å) B Occ B:F206 b:66.3 occ:1.00 F2' B:TAF206 0.0 66.3 1.0 C2' B:TAF206 1.4 62.7 1.0 C3' B:TAF206 2.3 59.9 1.0 C1' B:TAF206 2.4 60.8 1.0 N1 B:TAF206 2.7 56.5 1.0 O4' B:DA207 3.0 66.7 1.0 O3' B:TAF206 3.0 62.9 1.0 C2 B:TAF206 3.1 58.8 1.0 O2 B:TAF206 3.3 58.9 1.0 C8 B:DA207 3.4 58.8 1.0 C6 B:TAF206 3.4 57.3 1.0 N9 B:DA207 3.4 60.8 1.0 O4' B:TAF206 3.5 59.9 1.0 C4' B:TAF206 3.5 56.5 1.0 C5' B:DA207 3.7 73.2 1.0 C1' B:DA207 3.7 62.6 1.0 O5' B:DA207 3.8 75.9 1.0 O B:HOH1197 3.8 50.9 1.0 P B:DA207 3.9 72.2 1.0 C4' B:DA207 3.9 70.1 1.0 N7 B:DA207 4.0 61.4 1.0 C4 B:DA207 4.0 62.8 1.0 N3 B:TAF206 4.1 56.7 1.0 O B:HOH1150 4.1 59.4 1.0 C5 B:DA207 4.3 61.0 1.0 C5 B:TAF206 4.3 52.9 1.0 C2' B:DA207 4.4 66.8 1.0 OP2 B:DA207 4.5 73.5 1.0 O B:HOH1103 4.6 66.8 1.0 C4 B:TAF206 4.7 56.3 1.0 C5' B:TAF206 4.7 55.8 1.0 N3 B:DA207 4.8 61.2 1.0 O5' B:TAF206 4.8 55.7 1.0 C3' B:DA207 4.9 68.8 1.0

Fluorine binding site 3 out of 4 in the Crystal Structure Analysis of the A-Dna Decamer Gcgt-2'Omea-Fat-Acgc, with Incorporated 2'-O-Methylated-Adenosine (2'Omea) and 2'- Fluoroarabino-Thymidine (Fat)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure Analysis of the A-Dna Decamer Gcgt-2'Omea-Fat-Acgc, with Incorporated 2'-O-Methylated-Adenosine (2'Omea) and 2'- Fluoroarabino-Thymidine (Fat) within 5.0Å range: probe atom residue distance (Å) B Occ C:F306 b:62.6 occ:1.00 F2' C:TAF306 0.0 62.6 1.0 C2' C:TAF306 1.4 57.9 1.0 C1' C:TAF306 2.3 52.5 1.0 C3' C:TAF306 2.4 58.9 1.0 N1 C:TAF306 2.6 53.8 1.0 O5' C:DA307 2.8 69.2 1.0 C8 C:DA307 3.0 41.1 1.0 C2 C:TAF306 3.0 48.9 1.0 O4' C:DA307 3.1 55.2 1.0 O2 C:TAF306 3.1 53.1 1.0 O3' C:TAF306 3.2 64.1 1.0 N9 C:DA307 3.3 46.3 1.0 O4' C:TAF306 3.4 54.6 1.0 C6 C:TAF306 3.5 50.0 1.0 C4' C:TAF306 3.5 56.6 1.0 P C:DA307 3.6 71.0 1.0 N7 C:DA307 3.6 48.5 1.0 OP2 C:DA307 3.6 67.3 1.0 C1' C:DA307 3.6 48.9 1.0 C5' C:DA307 3.8 65.8 1.0 C4' C:DA307 4.0 61.2 1.0 N3 C:TAF306 4.0 51.1 1.0 C2' C:DA307 4.0 56.2 1.0 C4 C:DA307 4.1 43.8 1.0 C5 C:DA307 4.2 40.9 1.0 C5 C:TAF306 4.4 44.3 1.0 C4 C:TAF306 4.7 42.5 1.0 C3' C:DA307 4.8 60.1 1.0 O C:HOH1127 4.9 46.8 0.5 C5' C:TAF306 4.9 53.0 1.0 OP1 C:DA307 4.9 67.5 1.0

Fluorine binding site 4 out of 4 in the Crystal Structure Analysis of the A-Dna Decamer Gcgt-2'Omea-Fat-Acgc, with Incorporated 2'-O-Methylated-Adenosine (2'Omea) and 2'- Fluoroarabino-Thymidine (Fat)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure Analysis of the A-Dna Decamer Gcgt-2'Omea-Fat-Acgc, with Incorporated 2'-O-Methylated-Adenosine (2'Omea) and 2'- Fluoroarabino-Thymidine (Fat) within 5.0Å range: probe atom residue distance (Å) B Occ D:F406 b:58.2 occ:1.00 F2' D:TAF406 0.0 58.2 1.0 C2' D:TAF406 1.4 53.6 1.0 C3' D:TAF406 2.3 51.6 1.0 C1' D:TAF406 2.3 49.0 1.0 N1 D:TAF406 2.5 47.9 1.0 C8 D:DA407 2.8 41.3 1.0 O D:HOH1066 2.8 58.4 1.0 C2 D:TAF406 2.9 51.0 1.0 O5' D:DA407 3.1 61.6 1.0 O3' D:TAF406 3.1 54.7 1.0 C6 D:TAF406 3.2 44.7 1.0 O2 D:TAF406 3.2 52.0 1.0 N7 D:DA407 3.2 41.6 1.0 O4' D:TAF406 3.3 52.3 1.0 N9 D:DA407 3.4 48.2 1.0 C4' D:TAF406 3.5 47.8 1.0 O4' D:DA407 3.5 52.8 1.0 P D:DA407 3.6 61.5 1.0 C5' D:DA407 3.7 55.0 1.0 N3 D:TAF406 3.9 45.0 1.0 C5 D:DA407 3.9 40.5 1.0 C1' D:DA407 4.0 46.2 1.0 C4 D:DA407 4.0 45.2 1.0 C5 D:TAF406 4.1 40.6 1.0 O D:HOH1106 4.1 48.9 1.0 C4' D:DA407 4.2 54.0 1.0 C4 D:TAF406 4.4 47.3 1.0 O5' D:TAF406 4.6 42.8 1.0 C5' D:TAF406 4.6 45.2 1.0 C2' D:DA407 4.7 54.0 1.0 O D:HOH1022 4.8 38.2 0.5

F.Li, S.Sarkhel, C.J.Wilds, Z.Wawrzak, T.P.Prakash, M.Manoharan, M.Egli. 2'-Fluoroarabino- and Arabinonucleic Acid Show Different Conformations, Resulting in Deviating Rna Affinities and Processing of Their Heteroduplexes with Rna By Rnase H. Biochemistry V. 45 4141 2006.
ISSN: ISSN 0006-2960
PubMed: 16566588
DOI: 10.1021/BI052322R