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Fluorine in PDB 2q1o: Crystal Structure Analysis of the Rna Dodecamer Cgc-NF2- Aauuggcg, with An Incorporated 2,4-Difluorotoluyl Residue (NF2)

Protein crystallography data

The structure of Crystal Structure Analysis of the Rna Dodecamer Cgc-NF2- Aauuggcg, with An Incorporated 2,4-Difluorotoluyl Residue (NF2), PDB code: 2q1o was solved by F.Li, P.S.Pallan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 1.10
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 22.900, 32.060, 42.930, 96.24, 83.87, 93.91
R / Rfree (%) 11 / 14.2

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure Analysis of the Rna Dodecamer Cgc-NF2- Aauuggcg, with An Incorporated 2,4-Difluorotoluyl Residue (NF2) (pdb code 2q1o). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the Crystal Structure Analysis of the Rna Dodecamer Cgc-NF2- Aauuggcg, with An Incorporated 2,4-Difluorotoluyl Residue (NF2), PDB code: 2q1o:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 2q1o

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Fluorine binding site 1 out of 8 in the Crystal Structure Analysis of the Rna Dodecamer Cgc-NF2- Aauuggcg, with An Incorporated 2,4-Difluorotoluyl Residue (NF2)


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 Rna Dodecamer Cgc-NF2- Aauuggcg, with An Incorporated 2,4-Difluorotoluyl Residue (NF2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F104

b:10.2
occ:1.00
 F2 A:NF2104 0.0 10.2 1.0
C2 A:NF2104 1.3 8.0 1.0
C3 A:NF2104 2.3 10.9 1.0
C1 A:NF2104 2.3 9.7 1.0
C1' A:NF2104 2.8 8.4 1.0
O A:HOH1065 3.0 13.1 1.0
N1 B:G109 3.1 8.9 1.0
C2 B:G110 3.2 7.1 1.0
N1 B:G110 3.3 6.7 1.0
N2 B:G110 3.3 8.4 1.0
C2' A:NF2104 3.3 8.8 1.0
O6 B:G109 3.5 9.7 1.0
C4 A:NF2104 3.6 9.3 1.0
C6 A:NF2104 3.6 9.3 1.0
N3 B:G110 3.7 6.8 1.0
C6 B:G109 3.7 8.4 1.0
N7 A:A105 3.8 8.1 1.0
O2' A:NF2104 3.9 11.3 1.0
C8 A:A105 4.0 8.8 1.0
C6 B:G110 4.0 6.9 1.0
N2 B:G109 4.0 10.2 1.0
C5 A:A105 4.0 7.6 1.0
C2 B:G109 4.0 9.0 1.0
C5 A:NF2104 4.1 9.2 1.0
O4' A:NF2104 4.1 8.9 1.0
C4 B:G110 4.2 6.2 1.0
N3 A:C103 4.2 7.0 1.0
C4 A:A105 4.3 8.0 1.0
N9 A:A105 4.3 7.5 1.0
C5 B:G110 4.4 6.2 1.0
O B:HOH1153 4.5 33.0 1.0
C6 A:A105 4.6 7.7 1.0
O6 B:G110 4.6 7.9 1.0
O2 A:C103 4.6 8.8 1.0
C3' A:NF2104 4.6 9.1 1.0
O B:HOH1066 4.6 17.2 1.0
F4 A:NF2104 4.7 11.0 1.0
C2 A:C103 4.7 7.8 1.0
N6 A:A105 4.9 9.0 1.0
C4 A:C103 4.9 7.1 1.0
O4' A:A105 4.9 8.2 1.0

Fluorine binding site 2 out of 8 in 2q1o

Go back to Fluorine Binding Sites List in 2q1o
Fluorine binding site 2 out of 8 in the Crystal Structure Analysis of the Rna Dodecamer Cgc-NF2- Aauuggcg, with An Incorporated 2,4-Difluorotoluyl Residue (NF2)


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 Rna Dodecamer Cgc-NF2- Aauuggcg, with An Incorporated 2,4-Difluorotoluyl Residue (NF2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F104

b:11.0
occ:1.00
 F4 A:NF2104 0.0 11.0 1.0
C4 A:NF2104 1.3 9.3 1.0
C3 A:NF2104 2.3 10.9 1.0
C5 A:NF2104 2.4 9.2 1.0
CM A:NF2104 2.8 11.4 1.0
O A:HOH1040 2.9 18.9 1.0
O B:HOH1265 3.0 40.4 1.0
O A:HOH1028 3.4 17.5 1.0
N4 A:C103 3.4 7.7 1.0
C4 A:C103 3.6 7.1 1.0
C2 A:NF2104 3.6 8.0 1.0
C6 A:NF2104 3.6 9.3 1.0
C5 A:C103 3.7 8.3 1.0
N6 A:A105 3.7 9.0 1.0
O A:HOH1043 3.8 14.9 1.0
O B:HOH1026 3.8 24.1 1.0
O B:HOH1060 4.0 24.4 1.0
C1 A:NF2104 4.1 9.7 1.0
N3 A:C103 4.3 7.0 1.0
O6 B:G109 4.4 9.7 1.0
O B:HOH1206 4.5 38.1 1.0
C6 A:C103 4.6 8.3 1.0
F2 A:NF2104 4.7 10.2 1.0
O A:HOH1061 4.7 19.3 1.0
N7 A:A105 4.7 8.1 1.0
C6 A:A105 4.7 7.7 1.0

Fluorine binding site 3 out of 8 in 2q1o

Go back to Fluorine Binding Sites List in 2q1o
Fluorine binding site 3 out of 8 in the Crystal Structure Analysis of the Rna Dodecamer Cgc-NF2- Aauuggcg, with An Incorporated 2,4-Difluorotoluyl Residue (NF2)


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 Rna Dodecamer Cgc-NF2- Aauuggcg, with An Incorporated 2,4-Difluorotoluyl Residue (NF2) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F104

b:7.5
occ:1.00
 F2 B:NF2104 0.0 7.5 1.0
C2 B:NF2104 1.4 5.9 1.0
C3 B:NF2104 2.4 8.2 1.0
C1 B:NF2104 2.4 7.2 1.0
C1' B:NF2104 2.8 6.5 1.0
N1 A:G109 3.0 6.4 1.0
O A:HOH1071 3.1 9.7 1.0
C2 A:G110 3.1 5.7 1.0
N2 A:G110 3.3 6.7 1.0
N1 A:G110 3.3 5.8 1.0
C2' B:NF2104 3.4 6.7 1.0
O6 A:G109 3.5 7.1 1.0
C4 B:NF2104 3.6 5.8 1.0
C6 B:NF2104 3.6 5.5 1.0
N3 A:G110 3.7 5.4 1.0
C6 A:G109 3.8 6.3 1.0
N7 B:A105 3.9 5.6 1.0
O2' B:NF2104 3.9 7.6 1.0
C5 B:A105 3.9 5.1 1.0
C2 A:G109 4.0 6.4 1.0
N2 A:G109 4.0 7.3 1.0
C6 A:G110 4.0 5.4 1.0
C8 B:A105 4.1 6.2 1.0
C5 B:NF2104 4.1 5.8 1.0
O4' B:NF2104 4.2 6.4 1.0
C4 B:A105 4.2 4.9 1.0
C4 A:G110 4.2 5.0 1.0
N9 B:A105 4.3 5.7 1.0
N3 B:C103 4.3 5.7 1.0
O A:HOH1074 4.3 12.7 1.0
C6 B:A105 4.3 5.3 1.0
C5 A:G110 4.4 5.5 1.0
O2 B:C103 4.6 6.3 1.0
O6 A:G110 4.7 6.4 1.0
C3' B:NF2104 4.7 7.2 1.0
F4 B:NF2104 4.7 7.5 1.0
C2 B:C103 4.7 5.7 1.0
N6 B:A105 4.7 6.2 1.0
N3 B:A105 4.9 6.0 1.0
N1 B:A105 5.0 5.6 1.0
O4' B:A105 5.0 7.3 1.0
C4 B:C103 5.0 5.8 1.0

Fluorine binding site 4 out of 8 in 2q1o

Go back to Fluorine Binding Sites List in 2q1o
Fluorine binding site 4 out of 8 in the Crystal Structure Analysis of the Rna Dodecamer Cgc-NF2- Aauuggcg, with An Incorporated 2,4-Difluorotoluyl Residue (NF2)


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 Rna Dodecamer Cgc-NF2- Aauuggcg, with An Incorporated 2,4-Difluorotoluyl Residue (NF2) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F104

b:7.5
occ:1.00
 F4 B:NF2104 0.0 7.5 1.0
C4 B:NF2104 1.3 5.8 1.0
C3 B:NF2104 2.3 8.2 1.0
C5 B:NF2104 2.4 5.8 1.0
CM B:NF2104 2.8 7.5 1.0
O B:HOH1018 3.1 17.9 1.0
O A:HOH1085 3.1 26.0 1.0
N4 B:C103 3.3 6.2 1.0
O A:HOH1009 3.3 14.1 1.0
C4 B:C103 3.6 5.8 1.0
C2 B:NF2104 3.6 5.9 1.0
O A:HOH1119 3.6 27.8 1.0
C6 B:NF2104 3.6 5.5 1.0
N6 B:A105 3.7 6.2 1.0
O B:HOH1017 3.7 0.3 1.0
O B:HOH1316 3.7 39.1 1.0
C5 B:C103 3.7 5.8 1.0
O B:HOH1014 3.9 10.5 1.0
O A:HOH1008 4.0 19.6 1.0
C1 B:NF2104 4.1 7.2 1.0
N3 B:C103 4.3 5.7 1.0
O A:HOH1195 4.3 25.2 1.0
O6 A:G109 4.4 7.1 1.0
C6 B:C103 4.6 6.0 1.0
C6 B:A105 4.7 5.3 1.0
F2 B:NF2104 4.7 7.5 1.0
N7 B:A105 4.8 5.6 1.0
O B:HOH1013 4.8 14.3 1.0
O4 A:U108 4.9 8.6 1.0

Fluorine binding site 5 out of 8 in 2q1o

Go back to Fluorine Binding Sites List in 2q1o
Fluorine binding site 5 out of 8 in the Crystal Structure Analysis of the Rna Dodecamer Cgc-NF2- Aauuggcg, with An Incorporated 2,4-Difluorotoluyl Residue (NF2)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure Analysis of the Rna Dodecamer Cgc-NF2- Aauuggcg, with An Incorporated 2,4-Difluorotoluyl Residue (NF2) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F104

b:8.1
occ:1.00
 F2 C:NF2104 0.0 8.1 1.0
C2 C:NF2104 1.4 6.5 1.0
C3 C:NF2104 2.3 8.6 1.0
C1 C:NF2104 2.4 7.7 1.0
C1' C:NF2104 2.8 6.2 1.0
C2' C:NF2104 3.3 6.2 1.0
N2 D:G110 3.4 6.9 1.0
O6 D:G109 3.4 15.0 1.0
N1 D:G109 3.4 14.3 1.0
C2 D:G110 3.5 5.7 1.0
C4 C:NF2104 3.6 6.9 1.0
C6 C:NF2104 3.6 7.0 1.0
N1 D:G110 3.6 5.8 1.0
C8 C:A105 3.7 7.6 1.0
N7 C:A105 3.8 7.5 1.0
C6 D:G109 3.8 12.9 1.0
N9 C:A105 3.9 7.3 1.0
C5 C:A105 4.0 6.9 1.0
O2' C:NF2104 4.0 6.7 1.0
C4 C:A105 4.0 7.7 1.0
N3 C:C103 4.1 7.2 1.0
C5 C:NF2104 4.1 7.9 1.0
O4' C:NF2104 4.2 6.1 1.0
O4' C:A105 4.3 8.6 1.0
O2 C:C103 4.3 7.2 1.0
N3 D:G110 4.3 5.9 1.0
C2 C:C103 4.4 6.4 1.0
C1' C:A105 4.5 8.2 1.0
C6 D:G110 4.5 5.7 1.0
C2 D:G109 4.5 13.7 1.0
N2 D:G109 4.6 20.2 1.0
C3' C:NF2104 4.6 6.3 1.0
F4 C:NF2104 4.7 9.0 1.0
C6 C:A105 4.7 7.5 1.0
N3 C:A105 4.8 8.5 1.0
C4 C:C103 4.8 7.1 1.0
C4 D:G110 5.0 5.5 1.0

Fluorine binding site 6 out of 8 in 2q1o

Go back to Fluorine Binding Sites List in 2q1o
Fluorine binding site 6 out of 8 in the Crystal Structure Analysis of the Rna Dodecamer Cgc-NF2- Aauuggcg, with An Incorporated 2,4-Difluorotoluyl Residue (NF2)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure Analysis of the Rna Dodecamer Cgc-NF2- Aauuggcg, with An Incorporated 2,4-Difluorotoluyl Residue (NF2) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F104

b:9.0
occ:1.00
 F4 C:NF2104 0.0 9.0 1.0
C4 C:NF2104 1.3 6.9 1.0
C3 C:NF2104 2.3 8.6 1.0
C5 C:NF2104 2.4 7.9 1.0
CM C:NF2104 2.9 9.9 1.0
O D:HOH1322 3.1 42.1 1.0
O C:HOH1116 3.2 21.9 1.0
N4 C:C103 3.3 7.8 1.0
O C:HOH1111 3.4 16.1 1.0
C4 C:C103 3.4 7.1 1.0
N6 C:A105 3.5 8.3 1.0
C5 C:C103 3.5 8.3 1.0
C2 C:NF2104 3.6 6.5 1.0
C6 C:NF2104 3.6 7.0 1.0
O C:HOH1117 3.6 13.2 1.0
C1 C:NF2104 4.1 7.7 1.0
N3 C:C103 4.2 7.2 1.0
N7 C:A105 4.2 7.5 1.0
C6 C:A105 4.3 7.5 1.0
O C:HOH1110 4.3 14.6 1.0
O D:HOH1112 4.3 24.7 1.0
C6 C:C103 4.4 7.8 1.0
C5 C:A105 4.5 6.9 1.0
O6 D:G109 4.6 15.0 1.0
F2 C:NF2104 4.7 8.1 1.0
O D:HOH1286 4.9 41.4 1.0
C2 C:C103 4.9 6.4 1.0

Fluorine binding site 7 out of 8 in 2q1o

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Fluorine binding site 7 out of 8 in the Crystal Structure Analysis of the Rna Dodecamer Cgc-NF2- Aauuggcg, with An Incorporated 2,4-Difluorotoluyl Residue (NF2)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Crystal Structure Analysis of the Rna Dodecamer Cgc-NF2- Aauuggcg, with An Incorporated 2,4-Difluorotoluyl Residue (NF2) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F104

b:11.7
occ:1.00
 F2 D:NF2104 0.0 11.7 1.0
C2 D:NF2104 1.3 11.4 1.0
C3 D:NF2104 2.3 13.2 1.0
C1 D:NF2104 2.4 11.6 1.0
C1' D:NF2104 2.8 10.8 1.0
N1 C:G109 3.0 9.2 1.0
O C:HOH1168 3.1 13.8 1.0
C2 C:G110 3.3 8.5 1.0
C2' D:NF2104 3.3 10.8 1.0
N2 C:G110 3.3 10.5 1.0
N1 C:G110 3.4 9.2 1.0
O6 C:G109 3.5 10.9 1.0
C4 D:NF2104 3.6 12.1 1.0
C6 D:NF2104 3.6 11.1 1.0
N7 D:A105 3.7 9.0 1.0
C6 C:G109 3.7 8.9 1.0
N3 C:G110 3.8 8.0 1.0
C5 D:A105 3.8 8.1 1.0
C8 D:A105 3.9 8.7 1.0
O2' D:NF2104 3.9 12.6 1.0
N2 C:G109 4.0 9.4 1.0
C2 C:G109 4.0 9.3 1.0
C5 D:NF2104 4.1 12.3 1.0
C6 C:G110 4.1 8.8 1.0
O4' D:NF2104 4.1 11.8 1.0
C4 D:A105 4.2 7.9 1.0
N3 D:C103 4.2 10.4 1.0
N9 D:A105 4.2 8.1 1.0
C6 D:A105 4.4 8.2 1.0
C4 C:G110 4.4 8.4 1.0
O2 D:C103 4.6 11.0 1.0
C5 C:G110 4.6 7.9 1.0
C3' D:NF2104 4.6 11.1 1.0
C2 D:C103 4.6 10.0 1.0
F4 D:NF2104 4.6 15.1 1.0
O6 C:G110 4.7 9.2 1.0
N6 D:A105 4.7 8.6 1.0
C4 D:C103 4.8 9.7 1.0
O4' D:A105 4.9 8.5 1.0
N3 D:A105 5.0 8.5 1.0

Fluorine binding site 8 out of 8 in 2q1o

Go back to Fluorine Binding Sites List in 2q1o
Fluorine binding site 8 out of 8 in the Crystal Structure Analysis of the Rna Dodecamer Cgc-NF2- Aauuggcg, with An Incorporated 2,4-Difluorotoluyl Residue (NF2)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Crystal Structure Analysis of the Rna Dodecamer Cgc-NF2- Aauuggcg, with An Incorporated 2,4-Difluorotoluyl Residue (NF2) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F104

b:15.1
occ:1.00
 F4 D:NF2104 0.0 15.1 1.0
C4 D:NF2104 1.3 12.1 1.0
C3 D:NF2104 2.3 13.2 1.0
C5 D:NF2104 2.4 12.3 1.0
CM D:NF2104 2.9 16.2 1.0
O C:HOH1174 3.0 32.0 1.0
O D:HOH1166 3.1 33.9 1.0
O D:HOH1167 3.3 30.7 1.0
N4 D:C103 3.3 10.8 1.0
O D:HOH1164 3.4 21.6 1.0
C4 D:C103 3.5 9.7 1.0
C2 D:NF2104 3.6 11.4 1.0
C6 D:NF2104 3.6 11.1 1.0
C5 D:C103 3.7 11.2 1.0
O D:HOH1170 3.8 19.6 1.0
O C:HOH1171 3.8 27.3 1.0
N6 D:A105 3.9 8.6 1.0
C1 D:NF2104 4.1 11.6 1.0
O C:HOH1135 4.3 23.9 1.0
N3 D:C103 4.3 10.4 1.0
O6 C:G109 4.5 10.9 1.0
C6 D:C103 4.6 11.2 1.0
F2 D:NF2104 4.6 11.7 1.0
O D:HOH1165 4.7 17.9 1.0
N7 D:A105 4.8 9.0 1.0
C6 D:A105 4.8 8.2 1.0

Reference:

F.Li, P.S.Pallan, M.A.Maier, K.G.Rajeev, S.L.Mathieu, C.Kreutz, Y.Fan, J.Sanghvi, R.Micura, E.Rozners, M.Manoharan, M.Egli. Crystal Structure, Stability and in Vitro Rnai Activity of Oligoribonucleotides Containing the Ribo-Difluorotoluyl Nucleotide: Insights Into Substrate Requirements By the Human Risc AGO2 Enzyme. Nucleic Acids Res. V. 35 6424 2007.
ISSN: ISSN 0305-1048
PubMed: 17881374
DOI: 10.1093/NAR/GKM664
Page generated: Wed Jul 31 15:40:02 2024

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