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. 2015 May 4;43(10):4785–4799. doi: 10.1093/nar/gkv427

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© The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

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Figure 3. — Plots of nucleotide conformational angles in the TTA loops. (A) Backbone and glycosidic torsion angles. These are shown for all structures containing at least one type-1 TTA (or UUA) loop. For structures which contain more than one type-1 loop only the first TTA loop is represented. (B) Comparison of backbone and glycosidic torsions angles. These are shown of the three type-1 propeller loops of the native human telomeric unimolecular quadruplex (PDB ID 1KF1) (each loop coloured separately; red, green or blue). (C) Comparison of backbone and glycosidic torsions angles. These are for the three type-1 propeller loops of a naphthalene diimide telomeric quadruplex complex (PDB ID 3T5E) (each loop coloured separately; red, green or blue). (D) Comparison of the backbone and glycosidic torsions angles. These are for the three type-1 propeller loops of the mesoporphyrin complex with a human telomeric quadruplex (PDB ID 4FXM) (each loop coloured separately; red, green or blue). (E) Comparison of the backbone and glycosidic torsions angles. These are for the three type-1 propeller loops in the berberine complex with a human telomeric quadruplex (PDB ID 3R6R) (each loop coloured separately; red, green or blue). (F) Dihedral angle plots for each of the TTA residues of each of the 12 loop types (each trace represents a distinct loop type). The loop 1 of 1KF1 (solid black line) can be used as a common reference. Dihedral angles are derived from loops from PDB structures 1KF1 (1), 2HRI (2 and 3), 3CCO (4), 3CDM (5 and 6), 3CE5 (7), 3MIJ (8), 3QSC (9), 3SC8 (10 and 11) and 4DA3 (12). (G) Type-9 loop backbone and glycosidic dihedral angles. These are from bimolecular human quadruplexes (PDB IDs 3QSF and 3QSC) complexed with salphen ligands. (H) Comparison of backbone and glycosidic dihedral angles in the TTA loops of the naphthalene diimide (ND) complex structures. Type-1 TTA loops are shown as blue dashed lines. Non-type-1 loops are shown as grey dashed lines. Structures represented are: PDB IDs 3SC8, 3T5E, 3UYH, 4DA3 and 4DAQ. (I) Comparison of TTA loop backbone and glycosidic dihedrals of naphthalene diimide complex crystal structures, for type-1 loops only.

Figure 3. — Plots of nucleotide conformational angles in the TTA loops. (A) Backbone and glycosidic torsion angles. These are shown for all structures containing at least one type-1 TTA (or UUA) loop. For structures which contain more than one type-1 loop only the first TTA loop is represented. (B) Comparison of backbone and glycosidic torsions angles. These are shown of the three type-1 propeller loops of the native human telomeric unimolecular quadruplex (PDB ID 1KF1) (each loop coloured separately; red, green or blue). (C) Comparison of backbone and glycosidic torsions angles. These are for the three type-1 propeller loops of a naphthalene diimide telomeric quadruplex complex (PDB ID 3T5E) (each loop coloured separately; red, green or blue). (D) Comparison of the backbone and glycosidic torsions angles. These are for the three type-1 propeller loops of the mesoporphyrin complex with a human telomeric quadruplex (PDB ID 4FXM) (each loop coloured separately; red, green or blue). (E) Comparison of the backbone and glycosidic torsions angles. These are for the three type-1 propeller loops in the berberine complex with a human telomeric quadruplex (PDB ID 3R6R) (each loop coloured separately; red, green or blue). (F) Dihedral angle plots for each of the TTA residues of each of the 12 loop types (each trace represents a distinct loop type). The loop 1 of 1KF1 (solid black line) can be used as a common reference. Dihedral angles are derived from loops from PDB structures 1KF1 (1), 2HRI (2 and 3), 3CCO (4), 3CDM (5 and 6), 3CE5 (7), 3MIJ (8), 3QSC (9), 3SC8 (10 and 11) and 4DA3 (12). (G) Type-9 loop backbone and glycosidic dihedral angles. These are from bimolecular human quadruplexes (PDB IDs 3QSF and 3QSC) complexed with salphen ligands. (H) Comparison of backbone and glycosidic dihedral angles in the TTA loops of the naphthalene diimide (ND) complex structures. Type-1 TTA loops are shown as blue dashed lines. Non-type-1 loops are shown as grey dashed lines. Structures represented are: PDB IDs 3SC8, 3T5E, 3UYH, 4DA3 and 4DAQ. (I) Comparison of TTA loop backbone and glycosidic dihedrals of naphthalene diimide complex crystal structures, for type-1 loops only.