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Fluorine in PDB 3p4b: Alternatingly Modified 2'Fluoro Rna Octamer F/RA2U2-P3

Protein crystallography data

The structure of Alternatingly Modified 2'Fluoro Rna Octamer F/RA2U2-P3, PDB code: 3p4b was solved by P.S.Pallan, E.M.Greene, P.A.Jicman, R.K.Pandey, M.Manoharan, E.Rozners, M.Egli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 21.69 / 1.45
Space group P 3
Cell size a, b, c (Å), α, β, γ (°) 43.383, 43.383, 60.987, 90.00, 90.00, 120.00
R / Rfree (%) 19.7 / 25.1

Other elements in 3p4b:

The structure of Alternatingly Modified 2'Fluoro Rna Octamer F/RA2U2-P3 also contains other interesting chemical elements:

Barium (Ba) 2 atoms

Fluorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Fluorine atom in the Alternatingly Modified 2'Fluoro Rna Octamer F/RA2U2-P3 (pdb code 3p4b). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 24 binding sites of Fluorine where determined in the Alternatingly Modified 2'Fluoro Rna Octamer F/RA2U2-P3, PDB code: 3p4b:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 24 in 3p4b

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Fluorine binding site 1 out of 24 in the Alternatingly Modified 2'Fluoro Rna Octamer F/RA2U2-P3


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Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Alternatingly Modified 2'Fluoro Rna Octamer F/RA2U2-P3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F101

b:18.5
occ:1.00
F2' A:CFZ101 0.0 18.5 1.0
C2' A:CFZ101 1.4 14.7 1.0
C1' A:CFZ101 2.3 17.8 1.0
C3' A:CFZ101 2.4 19.7 1.0
O3' A:CFZ101 2.8 19.0 1.0
C4' A:CFZ101 2.8 21.0 1.0
O4' A:CFZ101 3.0 19.0 1.0
O A:HOH712 3.2 18.1 1.0
C5' A:G102 3.4 18.3 1.0
O5' A:G102 3.5 20.7 1.0
O4' A:G102 3.5 17.3 1.0
N1 A:CFZ101 3.6 15.4 1.0
O2 A:CFZ101 3.7 15.0 1.0
P A:G102 3.9 21.6 1.0
C4' A:G102 4.0 16.7 1.0
O E:HOH711 4.1 17.8 1.0
C2 A:CFZ101 4.1 13.7 1.0
C5' A:CFZ101 4.2 20.8 1.0
C2' E:G508 4.3 16.4 1.0
O2' E:G508 4.5 13.7 1.0
C8 A:G102 4.6 13.4 1.0
OP2 A:G102 4.7 20.7 1.0
C6 A:CFZ101 4.7 19.7 1.0
OP1 A:G102 4.8 21.7 1.0
C1' A:G102 4.8 16.7 1.0
O3' E:G508 4.9 17.4 1.0
O5' A:CFZ101 5.0 23.0 1.0

Fluorine binding site 2 out of 24 in 3p4b

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Fluorine binding site 2 out of 24 in the Alternatingly Modified 2'Fluoro Rna Octamer F/RA2U2-P3


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Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Alternatingly Modified 2'Fluoro Rna Octamer F/RA2U2-P3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F103

b:18.0
occ:1.00
F A:AF2103 0.0 18.0 1.0
C2' A:AF2103 1.4 16.7 1.0
C1' A:AF2103 2.3 17.1 1.0
C3' A:AF2103 2.4 15.4 1.0
O3' A:AF2103 2.8 17.9 1.0
C4' A:AF2103 2.8 15.6 1.0
O4' A:AF2103 3.0 18.9 1.0
O A:HOH840 3.3 46.1 1.0
O A:HOH841 3.3 26.9 1.0
O4' A:A104 3.3 14.8 1.0
C5' A:A104 3.5 15.9 1.0
N9 A:AF2103 3.6 14.8 1.0
O5' A:A104 3.7 17.0 1.0
P A:A104 4.0 17.2 1.0
C4' A:A104 4.0 14.4 1.0
C4 A:AF2103 4.3 14.2 1.0
C5' A:AF2103 4.3 17.5 1.0
N3 A:AF2103 4.3 15.4 1.0
C1' A:A104 4.6 15.9 1.0
C8 A:AF2103 4.7 16.3 1.0
C8 A:A104 4.7 11.8 1.0
OP2 A:A104 4.8 19.1 1.0
OP1 A:A104 4.8 19.7 1.0
O5' A:AF2103 4.9 17.6 1.0
N9 A:A104 4.9 12.3 1.0

Fluorine binding site 3 out of 24 in 3p4b

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Fluorine binding site 3 out of 24 in the Alternatingly Modified 2'Fluoro Rna Octamer F/RA2U2-P3


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Alternatingly Modified 2'Fluoro Rna Octamer F/RA2U2-P3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F105

b:20.7
occ:1.00
F2' A:UFT105 0.0 20.7 1.0
C2' A:UFT105 1.4 19.7 1.0
C1' A:UFT105 2.3 19.5 1.0
C3' A:UFT105 2.3 18.7 1.0
O3' A:UFT105 2.7 20.2 1.0
C4' A:UFT105 2.9 19.6 1.0
O4' A:UFT105 3.0 19.1 1.0
O5' A:U106 3.4 20.2 1.0
C5' A:U106 3.4 17.0 1.0
O4' A:U106 3.5 15.9 1.0
N1 A:UFT105 3.5 17.1 1.0
O A:HOH806 3.7 32.6 1.0
O2 A:UFT105 3.7 20.1 1.0
P A:U106 3.7 21.9 1.0
C4' A:U106 4.0 17.4 1.0
C2 A:UFT105 4.0 15.7 1.0
C6 A:U106 4.3 17.6 1.0
C5' A:UFT105 4.3 20.3 1.0
C6 A:UFT105 4.6 17.3 1.0
OP2 A:U106 4.6 21.8 1.0
C1' A:U106 4.7 15.8 1.0
OP1 A:U106 4.7 21.6 1.0
O A:HOH834 4.7 28.6 1.0
N1 A:U106 4.9 17.4 1.0
O5' A:UFT105 5.0 17.7 1.0

Fluorine binding site 4 out of 24 in 3p4b

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Fluorine binding site 4 out of 24 in the Alternatingly Modified 2'Fluoro Rna Octamer F/RA2U2-P3


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Alternatingly Modified 2'Fluoro Rna Octamer F/RA2U2-P3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F107

b:19.4
occ:1.00
F2' A:CFZ107 0.0 19.4 1.0
C2' A:CFZ107 1.4 16.9 1.0
C1' A:CFZ107 2.4 15.2 1.0
C3' A:CFZ107 2.4 19.1 1.0
O3' A:CFZ107 2.8 19.1 1.0
C4' A:CFZ107 2.8 16.1 1.0
O4' A:CFZ107 3.0 17.2 1.0
O A:HOH803 3.2 27.5 0.3
C5' A:G108 3.5 20.6 1.0
O4' A:G108 3.5 20.9 1.0
N1 A:CFZ107 3.6 17.2 1.0
O5' A:G108 3.8 20.2 1.0
O2 A:CFZ107 3.8 19.4 1.0
P A:G108 4.0 21.1 1.0
C4' A:G108 4.0 21.2 1.0
C2 A:CFZ107 4.2 13.8 1.0
C5' A:CFZ107 4.3 14.0 1.0
C6 A:CFZ107 4.6 14.6 1.0
OP1 A:G108 4.8 24.1 1.0
C1' A:G108 4.9 22.1 1.0
OP2 A:G108 4.9 19.6 1.0
O5' A:CFZ107 5.0 15.9 1.0

Fluorine binding site 5 out of 24 in 3p4b

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Fluorine binding site 5 out of 24 in the Alternatingly Modified 2'Fluoro Rna Octamer F/RA2U2-P3


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Alternatingly Modified 2'Fluoro Rna Octamer F/RA2U2-P3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F201

b:22.7
occ:1.00
F2' B:CFZ201 0.0 22.7 1.0
C2' B:CFZ201 1.4 21.0 1.0
C3' B:CFZ201 2.4 23.7 1.0
C1' B:CFZ201 2.4 24.1 1.0
O3' B:CFZ201 2.7 23.1 1.0
C4' B:CFZ201 2.9 22.7 1.0
O4' B:CFZ201 3.0 25.1 1.0
C5' B:G202 3.3 22.0 1.0
O5' B:G202 3.4 21.3 1.0
O B:HOH738 3.5 31.9 1.0
O4' B:G202 3.7 20.1 1.0
N1 B:CFZ201 3.7 20.8 1.0
P B:G202 3.7 23.6 1.0
O2 B:CFZ201 4.0 20.1 1.0
C4' B:G202 4.1 19.5 1.0
C2 B:CFZ201 4.3 17.2 1.0
C5' B:CFZ201 4.4 27.2 1.0
OP1 B:G202 4.6 24.7 1.0
OP2 B:G202 4.6 23.7 1.0
C8 B:G202 4.7 17.6 1.0
C6 B:CFZ201 4.7 19.2 1.0
O C:HOH790 4.8 32.1 1.0

Fluorine binding site 6 out of 24 in 3p4b

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Fluorine binding site 6 out of 24 in the Alternatingly Modified 2'Fluoro Rna Octamer F/RA2U2-P3


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Alternatingly Modified 2'Fluoro Rna Octamer F/RA2U2-P3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F203

b:19.6
occ:1.00
F B:AF2203 0.0 19.6 1.0
C2' B:AF2203 1.4 17.6 1.0
C3' B:AF2203 2.3 19.2 1.0
C1' B:AF2203 2.4 18.0 1.0
C4' B:AF2203 2.7 15.9 1.0
O3' B:AF2203 2.8 18.1 1.0
O4' B:AF2203 3.0 17.4 1.0
C5' B:A204 3.5 18.3 1.0
O4' B:A204 3.6 18.1 1.0
N9 B:AF2203 3.6 17.8 1.0
O5' B:A204 3.8 18.0 1.0
P B:A204 4.0 20.7 1.0
C4' B:A204 4.0 15.3 1.0
C5' B:AF2203 4.2 18.2 1.0
C4 B:AF2203 4.2 17.9 1.0
N3 B:AF2203 4.3 19.3 1.0
C8 B:AF2203 4.7 17.6 1.0
OP1 B:A204 4.9 24.3 1.0
C1' B:A204 4.9 18.2 1.0
OP2 B:A204 4.9 22.1 1.0
O5' B:AF2203 4.9 18.4 1.0

Fluorine binding site 7 out of 24 in 3p4b

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Fluorine binding site 7 out of 24 in the Alternatingly Modified 2'Fluoro Rna Octamer F/RA2U2-P3


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Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Alternatingly Modified 2'Fluoro Rna Octamer F/RA2U2-P3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F205

b:15.5
occ:1.00
F2' B:UFT205 0.0 15.5 1.0
C2' B:UFT205 1.4 12.4 1.0
C3' B:UFT205 2.3 11.4 1.0
C1' B:UFT205 2.3 12.1 1.0
O3' B:UFT205 2.7 12.4 1.0
C4' B:UFT205 2.8 12.9 1.0
O4' B:UFT205 3.0 13.5 1.0
O4' B:U206 3.2 14.6 1.0
C5' B:U206 3.3 14.8 1.0
O5' B:U206 3.6 13.3 1.0
N1 B:UFT205 3.6 12.1 1.0
C4' B:U206 3.8 16.2 1.0
O2 B:UFT205 3.8 15.6 1.0
P B:U206 3.8 13.1 1.0
C2 B:UFT205 4.2 13.2 1.0
C5' B:UFT205 4.3 12.7 1.0
C6 B:U206 4.5 12.4 1.0
C1' B:U206 4.6 15.6 1.0
C6 B:UFT205 4.7 14.6 1.0
OP2 B:U206 4.7 16.5 1.0
OP1 B:U206 4.7 15.5 1.0
N1 B:U206 4.9 12.7 1.0
O A:HOH834 4.9 28.6 1.0
O5' B:UFT205 5.0 12.9 1.0

Fluorine binding site 8 out of 24 in 3p4b

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Fluorine binding site 8 out of 24 in the Alternatingly Modified 2'Fluoro Rna Octamer F/RA2U2-P3


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Alternatingly Modified 2'Fluoro Rna Octamer F/RA2U2-P3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F207

b:17.2
occ:1.00
F2' B:CFZ207 0.0 17.2 1.0
C2' B:CFZ207 1.4 13.3 1.0
C1' B:CFZ207 2.3 13.9 1.0
C3' B:CFZ207 2.4 16.1 1.0
O3' B:CFZ207 2.8 15.8 1.0
C4' B:CFZ207 2.8 17.4 1.0
O4' B:CFZ207 3.0 15.8 1.0
C5' B:G208 3.3 13.7 1.0
O5' B:G208 3.6 15.3 1.0
O4' B:G208 3.6 9.7 1.0
N1 B:CFZ207 3.6 12.0 1.0
O2 B:CFZ207 3.8 12.2 1.0
P B:G208 3.9 20.3 1.0
C4' B:G208 4.0 11.1 1.0
C2 B:CFZ207 4.2 12.0 1.0
C5' B:CFZ207 4.3 21.7 1.0
C6 B:CFZ207 4.7 13.0 1.0
OP1 B:G208 4.8 23.3 1.0
OP2 B:G208 4.8 24.0 1.0
C1' B:G208 4.9 8.7 1.0

Fluorine binding site 9 out of 24 in 3p4b

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Fluorine binding site 9 out of 24 in the Alternatingly Modified 2'Fluoro Rna Octamer F/RA2U2-P3


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Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Alternatingly Modified 2'Fluoro Rna Octamer F/RA2U2-P3 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F301

b:22.8
occ:1.00
F2' C:CFZ301 0.0 22.8 1.0
C2' C:CFZ301 1.4 21.0 1.0
C1' C:CFZ301 2.4 22.4 1.0
C3' C:CFZ301 2.4 23.1 1.0
O3' C:CFZ301 2.7 23.7 1.0
C4' C:CFZ301 2.9 23.1 1.0
O4' C:CFZ301 3.0 24.0 1.0
O C:HOH790 3.3 32.1 1.0
C5' C:G302 3.3 20.1 1.0
O5' C:G302 3.4 21.2 1.0
O C:HOH819 3.5 37.8 1.0
O4' C:G302 3.6 18.6 1.0
N1 C:CFZ301 3.7 20.2 1.0
P C:G302 3.7 24.1 1.0
O2 C:CFZ301 3.9 19.6 1.0
C4' C:G302 4.1 16.8 1.0
C2 C:CFZ301 4.2 17.8 1.0
C5' C:CFZ301 4.4 25.3 1.0
OP2 C:G302 4.6 23.2 1.0
OP1 C:G302 4.6 24.8 1.0
C8 C:G302 4.7 18.1 1.0
C6 C:CFZ301 4.7 17.6 1.0
O B:HOH738 4.7 31.9 1.0
C1' C:G302 4.9 18.6 1.0

Fluorine binding site 10 out of 24 in 3p4b

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Fluorine binding site 10 out of 24 in the Alternatingly Modified 2'Fluoro Rna Octamer F/RA2U2-P3


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Alternatingly Modified 2'Fluoro Rna Octamer F/RA2U2-P3 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F303

b:20.0
occ:1.00
F C:AF2303 0.0 20.0 1.0
C2' C:AF2303 1.4 19.6 1.0
C3' C:AF2303 2.4 17.5 1.0
C1' C:AF2303 2.4 18.8 1.0
C4' C:AF2303 2.8 16.1 1.0
O3' C:AF2303 2.8 18.2 1.0
O4' C:AF2303 3.0 17.1 1.0
C5' C:A304 3.5 16.3 1.0
O4' C:A304 3.5 17.4 1.0
N9 C:AF2303 3.6 17.5 1.0
O5' C:A304 3.8 17.2 1.0
P C:A304 4.0 21.2 1.0
C4' C:A304 4.1 15.0 1.0
C5' C:AF2303 4.3 17.9 1.0
C4 C:AF2303 4.3 16.4 1.0
N3 C:AF2303 4.3 19.4 1.0
C8 C:AF2303 4.7 15.2 1.0
C1' C:A304 4.8 17.6 1.0
OP1 C:A304 4.9 23.9 1.0
OP2 C:A304 4.9 22.3 1.0
O5' C:AF2303 4.9 19.0 1.0

Reference:

P.S.Pallan, E.M.Greene, P.A.Jicman, R.K.Pandey, M.Manoharan, E.Rozners, M.Egli. Unexpected Origins of the Enhanced Pairing Affinity of 2'-Fluoro-Modified Rna. Nucleic Acids Res. V. 39 3482 2011.
ISSN: ISSN 0305-1048
PubMed: 21183463
DOI: 10.1093/NAR/GKQ1270
Page generated: Sun Dec 13 11:53:00 2020

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