Fluorine in PDB 2pis: Efforts Toward Expansion of the Genetic Alphabet: Structure and Replication of Unnatural Base Pairs

The structure of Efforts Toward Expansion of the Genetic Alphabet: Structure and Replication of Unnatural Base Pairs, PDB code: 2pis was solved by S.Matsuda, J.D.Fillo, A.A.Henry, S.J.Wilkins, P.Rai, T.J.Dwyer, B.H.Geierstanger, D.E.Wemmer, P.G.Schultz, G.Spraggon, F.E.Romesberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	100.00 / 2.80
Space group	I 41 2 2 1
Cell size a, b, c (Å), α, β, γ (°)	146.025, 146.025, 93.140, 90.00, 90.00, 90.00
R / Rfree (%)	22.4 / 30.3

The structure of Efforts Toward Expansion of the Genetic Alphabet: Structure and Replication of Unnatural Base Pairs also contains other interesting chemical elements:

Bromine	(Br)	12 atoms
Magnesium	(Mg)	6 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Fluorine atom in the Efforts Toward Expansion of the Genetic Alphabet: Structure and Replication of Unnatural Base Pairs (pdb code 2pis). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 12 binding sites of Fluorine where determined in the Efforts Toward Expansion of the Genetic Alphabet: Structure and Replication of Unnatural Base Pairs, PDB code: 2pis:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 12 in the Efforts Toward Expansion of the Genetic Alphabet: Structure and Replication of Unnatural Base Pairs


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Efforts Toward Expansion of the Genetic Alphabet: Structure and Replication of Unnatural Base Pairs within 5.0Å range: probe atom residue distance (Å) B Occ A:F7 b:59.5 occ:1.00 F A:FFD7 0.0 59.5 1.0 C1 A:FFD7 1.4 47.5 1.0 C A:FFD7 2.4 45.7 1.0 C3 A:FFD7 2.4 33.7 1.0 C8 A:DA6 3.6 25.7 1.0 C6 A:FFD7 3.6 46.7 1.0 C4 A:FFD7 3.6 43.7 1.0 N7 A:DA6 3.9 28.7 1.0 C2' A:DA6 4.1 51.2 1.0 N9 A:DA6 4.1 35.7 1.0 C5 A:FFD7 4.1 51.0 1.0 C5 A:DA6 4.5 26.2 1.0 O4 A:DT8 4.5 26.8 1.0 C7 A:DT8 4.6 18.3 1.0 C4 A:DA6 4.6 13.4 1.0 C1' A:DA6 4.7 40.0 1.0 C1' A:FFD7 4.9 32.3 1.0 O4' A:FFD7 5.0 36.2 1.0

Fluorine binding site 2 out of 12 in the Efforts Toward Expansion of the Genetic Alphabet: Structure and Replication of Unnatural Base Pairs


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Efforts Toward Expansion of the Genetic Alphabet: Structure and Replication of Unnatural Base Pairs within 5.0Å range: probe atom residue distance (Å) B Occ B:F20 b:69.7 occ:1.00 F B:FFD20 0.0 69.7 1.0 C1 B:FFD20 1.3 32.2 1.0 C B:FFD20 2.3 34.8 1.0 C3 B:FFD20 2.4 31.4 1.0 C8 B:DA19 3.1 21.2 1.0 N7 B:DA19 3.2 28.1 1.0 N9 B:DA19 3.5 38.7 1.0 C6 B:FFD20 3.6 39.3 1.0 C4 B:FFD20 3.6 43.4 1.0 C5 B:DA19 3.6 16.0 1.0 C2' B:DA19 3.8 69.2 1.0 C4 B:DA19 3.8 2.0 1.0 C5 B:FFD20 4.1 50.0 1.0 O4 B:DT21 4.2 32.4 1.0 C1' B:DA19 4.2 49.7 1.0 C6 B:DA19 4.5 3.7 1.0 N3 B:DA19 4.7 26.1 1.0 C7 B:DT21 4.8 4.2 1.0 C4 B:DT21 4.8 10.9 1.0 C1' B:FFD20 4.8 38.9 1.0 C3' B:DA19 4.9 69.0 1.0 N6 A:DA6 4.9 33.8 1.0

Fluorine binding site 3 out of 12 in the Efforts Toward Expansion of the Genetic Alphabet: Structure and Replication of Unnatural Base Pairs


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Efforts Toward Expansion of the Genetic Alphabet: Structure and Replication of Unnatural Base Pairs within 5.0Å range: probe atom residue distance (Å) B Occ C:F7 b:56.7 occ:1.00 F C:FFD7 0.0 56.7 1.0 C1 C:FFD7 1.3 28.5 1.0 C3 C:FFD7 2.4 27.3 1.0 C C:FFD7 2.4 25.1 1.0 C8 C:DA6 3.2 36.1 1.0 N7 C:DA6 3.3 32.4 1.0 C6 C:FFD7 3.6 27.5 1.0 C4 C:FFD7 3.6 30.5 1.0 N9 C:DA6 3.7 40.7 1.0 C5 C:DA6 3.8 24.9 1.0 O4 C:DT8 3.9 18.2 1.0 C4 C:DA6 4.0 36.6 1.0 C5 C:FFD7 4.1 33.8 1.0 C2' C:DA6 4.3 72.9 1.0 C1' C:DA6 4.4 49.6 1.0 C4 C:DT8 4.6 18.9 1.0 C6 C:DA6 4.7 39.2 1.0 C7 C:DT8 4.8 26.0 1.0 O4' C:FFD7 4.8 63.2 1.0 C1' C:FFD7 4.9 27.4 1.0 N3 C:DA6 5.0 29.9 1.0

Fluorine binding site 4 out of 12 in the Efforts Toward Expansion of the Genetic Alphabet: Structure and Replication of Unnatural Base Pairs


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Efforts Toward Expansion of the Genetic Alphabet: Structure and Replication of Unnatural Base Pairs within 5.0Å range: probe atom residue distance (Å) B Occ D:F20 b:57.5 occ:1.00 F D:FFD20 0.0 57.5 1.0 C1 D:FFD20 1.3 55.6 1.0 C D:FFD20 2.4 56.3 1.0 C3 D:FFD20 2.4 56.0 1.0 N3 D:DA19 3.2 40.2 1.0 C4 D:DA19 3.4 48.0 1.0 C2 D:DA19 3.5 41.2 1.0 C6 D:FFD20 3.6 58.3 1.0 C4 D:FFD20 3.6 62.7 1.0 N9 D:DA19 3.9 58.8 1.0 C5 D:DA19 3.9 41.9 1.0 N1 D:DA19 4.0 61.0 1.0 C2' D:DA19 4.1 68.6 1.0 C5 D:FFD20 4.1 53.1 1.0 C6 D:DA19 4.2 61.3 1.0 C1' D:DA19 4.4 56.2 1.0 O4 D:DT21 4.5 20.6 1.0 C8 D:DA19 4.6 61.2 1.0 N7 D:DA19 4.6 58.3 1.0 C7 D:DT21 4.8 33.8 1.0 O4' D:DA19 4.9 57.8 1.0 C1' D:FFD20 4.9 60.4 1.0 O4' D:FFD20 4.9 48.7 1.0

Fluorine binding site 5 out of 12 in the Efforts Toward Expansion of the Genetic Alphabet: Structure and Replication of Unnatural Base Pairs


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Efforts Toward Expansion of the Genetic Alphabet: Structure and Replication of Unnatural Base Pairs within 5.0Å range: probe atom residue distance (Å) B Occ E:F7 b:74.4 occ:1.00 F E:FFD7 0.0 74.4 1.0 C1 E:FFD7 1.3 38.1 1.0 C E:FFD7 2.3 32.8 1.0 C3 E:FFD7 2.4 32.9 1.0 C2' E:DA6 3.1 51.1 1.0 N9 E:DA6 3.2 33.9 1.0 C8 E:DA6 3.3 30.8 1.0 C6 E:FFD7 3.6 33.7 1.0 C4 E:DA6 3.6 29.2 1.0 C4 E:FFD7 3.6 35.0 1.0 N7 E:DA6 3.6 32.3 1.0 C1' E:DA6 3.7 40.5 1.0 C5 E:DA6 3.8 10.6 1.0 C5 E:FFD7 4.1 42.8 1.0 N3 E:DA6 4.3 35.1 1.0 O4 E:DT8 4.5 27.1 1.0 C3' E:DA6 4.5 62.7 1.0 C6 E:DA6 4.7 11.1 1.0 C1' E:FFD7 4.8 37.6 1.0 O4' E:DA6 4.9 33.0 1.0

Fluorine binding site 6 out of 12 in the Efforts Toward Expansion of the Genetic Alphabet: Structure and Replication of Unnatural Base Pairs


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Efforts Toward Expansion of the Genetic Alphabet: Structure and Replication of Unnatural Base Pairs within 5.0Å range: probe atom residue distance (Å) B Occ F:F20 b:68.8 occ:1.00 F F:FFD20 0.0 68.8 1.0 C1 F:FFD20 1.3 44.6 1.0 C F:FFD20 2.4 45.1 1.0 C3 F:FFD20 2.4 39.4 1.0 C2' F:DA19 3.3 76.5 1.0 C8 F:DA19 3.6 40.6 1.0 C6 F:FFD20 3.6 46.5 1.0 N9 F:DA19 3.6 50.3 1.0 C4 F:FFD20 3.6 47.4 1.0 C1' F:DA19 4.0 47.6 1.0 N7 F:DA19 4.0 42.3 1.0 C4 F:DA19 4.1 9.6 1.0 C5 F:FFD20 4.1 51.5 1.0 C5 F:DA19 4.3 12.8 1.0 C7 F:DT21 4.3 42.3 1.0 O4 F:DT21 4.5 54.9 1.0 C3' F:DA19 4.7 80.2 1.0 N3 F:DA19 4.8 24.0 1.0 C1' F:FFD20 4.9 51.1 1.0 O4' F:FFD20 5.0 68.7 1.0 C5 F:DT21 5.0 36.5 1.0

Fluorine binding site 7 out of 12 in the Efforts Toward Expansion of the Genetic Alphabet: Structure and Replication of Unnatural Base Pairs


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Efforts Toward Expansion of the Genetic Alphabet: Structure and Replication of Unnatural Base Pairs within 5.0Å range: probe atom residue distance (Å) B Occ G:F7 b:52.7 occ:1.00 F G:FFD7 0.0 52.7 1.0 C1 G:FFD7 1.3 37.8 1.0 C3 G:FFD7 2.3 35.8 1.0 C G:FFD7 2.3 41.9 1.0 C8 G:DA6 3.5 35.1 1.0 C6 G:FFD7 3.6 47.7 1.0 C4 G:FFD7 3.6 36.2 1.0 N7 G:DA6 3.7 14.6 1.0 N9 G:DA6 4.0 29.9 1.0 C5 G:FFD7 4.1 48.7 1.0 O4 G:DT8 4.1 27.1 1.0 C5 G:DA6 4.1 21.0 1.0 C2' G:DA6 4.3 68.5 1.0 C4 G:DA6 4.3 15.2 1.0 C1' G:DA6 4.7 37.3 1.0 O4' G:FFD7 4.8 58.7 1.0 N6 H:DA19 4.8 32.0 1.0 C1' G:FFD7 4.8 52.2 1.0 C4 G:DT8 4.9 20.7 1.0 C7 G:DT8 4.9 24.0 1.0 C6 G:DA6 5.0 19.6 1.0

Fluorine binding site 8 out of 12 in the Efforts Toward Expansion of the Genetic Alphabet: Structure and Replication of Unnatural Base Pairs


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Efforts Toward Expansion of the Genetic Alphabet: Structure and Replication of Unnatural Base Pairs within 5.0Å range: probe atom residue distance (Å) B Occ H:F20 b:52.9 occ:1.00 F H:FFD20 0.0 52.9 1.0 C1 H:FFD20 1.4 36.2 1.0 C3 H:FFD20 2.4 20.6 1.0 C H:FFD20 2.4 29.9 1.0 C8 H:DA19 2.5 27.5 1.0 N9 H:DA19 2.8 42.5 1.0 C2' H:DA19 2.9 63.0 1.0 N7 H:DA19 3.0 37.6 1.0 C4 H:DA19 3.4 19.4 1.0 C1' H:DA19 3.4 51.0 1.0 C5 H:DA19 3.4 19.1 1.0 C6 H:FFD20 3.6 27.4 1.0 C4 H:FFD20 3.6 37.5 1.0 C5 H:FFD20 4.1 47.5 1.0 C3' H:DA19 4.2 59.4 1.0 N3 H:DA19 4.3 36.6 1.0 O4' H:DA19 4.5 57.5 1.0 C6 H:DA19 4.5 32.0 1.0 O4 H:DT21 4.6 23.1 1.0 C1' H:FFD20 4.9 49.6 1.0

Fluorine binding site 9 out of 12 in the Efforts Toward Expansion of the Genetic Alphabet: Structure and Replication of Unnatural Base Pairs


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Efforts Toward Expansion of the Genetic Alphabet: Structure and Replication of Unnatural Base Pairs within 5.0Å range: probe atom residue distance (Å) B Occ I:F7 b:0.2 occ:1.00 F I:FFD7 0.0 0.2 1.0 C1 I:FFD7 1.3 0.1 1.0 C I:FFD7 2.4 0.6 1.0 C3 I:FFD7 2.4 99.6 1.0 C8 I:DA6 2.8 83.2 1.0 C2' I:DA6 3.1 87.8 1.0 N9 I:DA6 3.1 86.0 1.0 N7 I:DA6 3.3 93.6 1.0 C1' I:DA6 3.6 87.0 1.0 C6 I:FFD7 3.6 98.9 1.0 C4 I:FFD7 3.6 95.5 1.0 C4 I:DA6 3.7 81.9 1.0 C5 I:DA6 3.8 92.0 1.0 C7 I:DT8 3.8 93.8 1.0 C5 I:FFD7 4.1 98.6 1.0 C3' I:DA6 4.2 82.3 1.0 O4' I:DA6 4.3 83.7 1.0 C5 I:DT8 4.6 96.2 1.0 O2P I:FFD7 4.7 82.4 1.0 N3 I:DA6 4.7 79.1 1.0 O4 I:DT8 4.7 0.5 1.0 C1' I:FFD7 4.9 95.0 1.0 C6 I:DA6 4.9 89.6 1.0 C4' I:DA6 4.9 79.7 1.0 O4' I:FFD7 5.0 85.7 1.0 OP2 I:DA6 5.0 95.2 1.0 C4 I:DT8 5.0 0.2 1.0

Fluorine binding site 10 out of 12 in the Efforts Toward Expansion of the Genetic Alphabet: Structure and Replication of Unnatural Base Pairs


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Efforts Toward Expansion of the Genetic Alphabet: Structure and Replication of Unnatural Base Pairs within 5.0Å range: probe atom residue distance (Å) B Occ J:F20 b:92.7 occ:1.00 F J:FFD20 0.0 92.7 1.0 C1 J:FFD20 1.4 86.0 1.0 C J:FFD20 2.4 81.8 1.0 C3 J:FFD20 2.4 84.3 1.0 C6 J:FFD20 3.6 79.5 1.0 C4 J:FFD20 3.6 59.4 1.0 C8 J:DA19 3.8 71.7 1.0 N9 J:DA19 3.9 65.2 1.0 N7 J:DA19 4.0 89.3 1.0 C4 J:DA19 4.0 79.4 1.0 O4 J:DT21 4.1 74.2 1.0 C5 J:DA19 4.1 86.8 1.0 C5 J:FFD20 4.1 79.6 1.0 C2' J:DA19 4.3 78.8 1.0 C1' J:DA19 4.4 71.8 1.0 C7 J:DT21 4.6 48.6 1.0 N3 J:DA19 4.7 82.0 1.0 C4 J:DT21 4.7 60.5 1.0 N6 I:DA6 4.8 83.4 1.0 C6 J:DA19 4.9 78.6 1.0 C1' J:FFD20 4.9 81.5 1.0

S.Matsuda, J.D.Fillo, A.A.Henry, P.Rai, S.J.Wilkens, T.J.Dwyer, B.H.Geierstanger, D.E.Wemmer, P.G.Schultz, G.Spraggon, F.E.Romesberg. Efforts Toward Expansion of the Genetic Alphabet: Structure and Replication of Unnatural Base Pairs. J.Am.Chem.Soc. V. 129 10466 2007.
ISSN: ISSN 0002-7863
PubMed: 17685517
DOI: 10.1021/JA072276D