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PDB ID Mentions in PubMed Central Article count: 8

Citations in PubMed

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PDB ID Mentions in PubMed Central

Data mentions are occurrences of PDB IDs in the full text articles from the PubMedCentral Open Access Subset of currently about 1 million articles. For each article, the sentences containing the PDB ID are listed. Article titles can be filtered by keywords and sorted by year.

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Predictive modelling of topology and loop variations in dimeric DNA quadruplex structures.

(2006) Nucleic Acids Res 34

PubMed: 16641317 | PubMedCentral: PMC1449907 | DOI: 10.1093/nar/gkl182

MATERIALS AND METHODS The Oxytricha nova d(G 4 T 4 G 4 ) 2 crystal structure ( 9 ) was used as a template for diagonal loop quadruplexes (PDB code 1JPQ).

Publication Year: 2006

Quadruplex DNA: sequence, topology and structure.

(2006) Nucleic Acids Res 34

PubMed: 17012276 | PubMedCentral: PMC1636468 | DOI: 10.1093/nar/gkl655

Figure 3 The crystal structure ( 28 ) of the bimolecular quadruplex formed by the O.nova telomeric sequence d(G 4 T 4 G 4 ) (PDB entry 1JPQ).

Publication Year: 2006

Sequence occurrence and structural uniqueness of a G-quadruplex in the human c-kit promoter.

(2007) Nucleic Acids Res 35

PubMed: 17720713 | PubMedCentral: PMC2034477 | DOI: 10.1093/nar/gkm609

The G17–G18 stacking in the loop is similar to that found in the T4-T5 stacking adopted in the loop region of the crystal structure of the Oxytricha telomeric sequence G 4 T 4 G 4 (40: PDB id ... JPQ).

Publication Year: 2007

DNA conformations and their sequence preferences.

(2008) Nucleic Acids Res 36

PubMed: 18477633 | PubMedCentral: PMC2441783 | DOI: 10.1093/nar/gkn260

The PDB codes of the structures used in the analysis Structure Type PDB Codes Noncomplexed A-DNA ( 46 ) 118d, 137d, 138d, 160d, 1d78, 1d79, 1dnz, 1kgk, 1m77, 1ma8, 1mlx, 1nzg, 1vj4, 1xjx, 1z7i, 1zex, ... zey, 1zf1, 1zf6, 1zf8, 1zf9, 1zfa, 213d, 243d, 260d, 295d, 2d94, 317d, 338d, 344d, 345d, 348d, 349d, 368d, 369d, 370d, 371d, 395d, 396d, 399d, 414d, 440d, 9dna, dh010, adh012, adh034 Noncomplexed B-DNA ( 72 ) 122d, 123d, 158d, 183d, 196d, 1bd1, 1bna, 1cw9, 1d23, 1d3r, 1d49, 1d56, 1d61, 1d8g, 1d8x, 1dou, 1dpn, 1edr, 1ehv, 1en3, 1en8, 1en9, 1ene, 1enn, 1fq2, 1g75, 1i3t, 1ikk, 1j8l, 1jgr, 1l4j, 1l6b, 1m6g, 1n1o, 1nvn, 1nvy, 1p4y, 1p54, 1s23, 1s2r, 1sgs, 1sk5, 1ub8, 1ve8, 1zf0, 1zf3, 1zf4, 1zf5, 1zf7, 1zfb, 1zff, 1zfg, 232d, 251d, 2d25, 307d, 355d, 3dnb, 403d, 423d, 428d, 431d, 436d, 454d, 455d, 456d, 460d, 463d, 476d, 477d, 5dnb, 9bna DNA/drug and DNA/ protein complexes, Z-DNA, quadruplexes (329) 110d, 115d, 131d, 145d, 151d, 152d, 159d, 181d, 182d, 184d, 190d, 191d, 1a1g, 1a1h, 1a1i, 1a1k, 1a2e, 1a73, 1aay, 1ais, 1azp, 1b94, 1b97, 1bf4, 1bqj, 1brn, 1c8c, 1cdw, 1ckq, 1cl8, 1cn0, 1d02, 1d11, 1d14, 1d15, 1d21, 1d22, 1d2i, 1d32, 1d37, 1d38, 1d40, 1d41, 1d45, 1d48, 1d53, 1d54, 1d58, 1d67, 1d76, 1d90, 1d9r, 1da0, 1da2, 1da9, 1dc0, 1dc1, 1dcg, 1dcr, 1dcw, 1dfm, 1dj6, 1dl8, 1dn4, 1dn5, 1dn8, 1dnf, 1dp7, 1dsz, 1e3o, 1egw, 1em0, 1emh, 1eo4, 1eon, 1esg, 1eyu, 1f0v, 1fd5, 1fdg, 1fhz, 1fiu, 1fms, 1fn1, 1fn2, 1g2f, 1g9z, 1gtw, 1gu4, 1h6f, 1hcr, 1hlv, 1hwt, 1hzs, 1i0t, 1i3w, 1ick, 1ign, 1ih4, 1ih6, 1imr, 1ims, 1j59, 1j75, 1jb7, 1jes, 1jft, 1jh9, 1jk1, 1jk2, 1jpq, 1jtl, 1juc, 1jux, 1jx4, 1k3w, 1k3x, 1k9g, 1kbu, 1kci, 1kx3, 1kx5, 1l1h, 1l1t, 1l1z, 1l3l, 1l3s, 1l3t, 1l3u, 1l3v, 1lat, 1lau, 1ljx, 1llm, 1lmb, 1m07, 1m19, 1m3q, 1m5r, 1m69, 1m6f, 1mf5, 1mj2, 1mjm, 1mjo, 1mjq, 1mnn, 1mus, 1mw8, 1nh2, 1njw, 1njx, 1nk0, 1nk4, 1nk7, 1nk8, 1nk9, 1nkc, 1nke, 1nkp, 1nnj, 1nqs, 1nr8, 1nt8, 1nvp, 1o0k, 1omk, 1orn, 1p20, 1p3i, 1p3l, 1p71, 1per, 1pfe, 1ph4, 1ph6, 1ph8, 1pji, 1pjj, 1puf, 1pup, 1puy, 1q3f, 1qda, 1qn3, 1qn4, 1qn5, 1qn6, 1qn8, 1qn9, 1qna, 1qnb, 1qne, 1qum, 1qyk, 1qyl, 1qzg, 1r2z, 1r3z, 1r41, 1r68, 1rff, 1rh6, 1rnb, 1rpe, 1rqy, 1run, 1s1k, 1s1l, 1s32, 1ssp, 1suz, 1sx5, 1sxq, 1t9i, 1tdz, 1tez, 1tro, 1u1p, 1u1q, 1u1r, 1u4b, 1ue2, 1ue4, 1uhy, 1v3n, 1v3o, 1v3p, 1vzk, 1w0u, 1wd0, 1wte, 1wto, 1wtp, 1wtq, 1wtr, 1wtv, 1xa2, 1xam, 1xc9, 1xjv, 1xo0, 1xuw, 1xux, 1xvn, 1xvr, 1xyi, 1ytb, 1ytf, 1zez, 1zf2, 1zna, 200d, 210d, 211d, 212d, 215d, 221d, 224d, 234d, 235d, 236d, 241d, 242d, 244d, 245d, 254d, 258d, 276d, 277d, 278d, 279d, 284d, 288d, 292d, 293d, 2bdp, 2bop, 2cgp, 2crx, 2dcg, 2des, 2hap, 2hdd, 2nll, 2or1, 2pvi, 304d, 306d, 308d, 313d, 314d, 331d, 334d, 336d, 351d, 352d, 360d, 362d, 366d, 367d, 383d, 385d, 386d, 3bam, 3bdp, 3cro, 3crx, 3hts, 3pvi, 400d, 417d, 427d, 432d, 441d, 442d, 443d, 452d, 453d, 465d, 467d, 473d, 481d, 482d, 4bdp, adh013, zdf013, zdfb03, zdfb06 The DNA conformational space was investigated at the level of a dinucleotide unit with its 5′-end phosphate group removed; it was described by six backbone torsion angles between γ and δ + 1, plus two χ angles characterizing the glycosidic bond ( Figure 1 ).

The central step of the quadruplex (Residues 2 and 3) in complexes with the telomere-end binding protein [structures 1JB7 ( 74 ), 1PH4, 1PH6 and 1PH8 ( 56 )] as well as in the non-complexed quadruplex [1JPQ ( 75 )] adopts the conformation of Cluster 122 ( Supplementary Table T2 ), a B-like cluster with the canonical α + 1 and γ + 1 values flipped (‘α + 1/γ + 1 crank’) and with the syn orientation (χ ∼ 70°) of the second guanine base enabling non-W–Ck purine–purine base pair.

Publication Year: 2008

Explaining the varied glycosidic conformational, G-tract length and sequence preferences for anti-parallel G-quadruplexes.

(2011) Nucleic Acids Res 39

PubMed: 21296760 | PubMedCentral: PMC3105399 | DOI: 10.1093/nar/gkr031

The coordinates of the first and the second quartets with sandwiched K + ions were obtained from the crystal structure of the diagonal anti-parallel G-quadruplex [d(G 4 T 4 G 4 )] 2 [( 33 ); PDB: 1JPQ... and were used as the initial structure for the SA-aabb model.

Publication Year: 2011

Insight into G-DNA structural polymorphism and folding from sequence and loop connectivity through free energy analysis.

(2011) J Am Chem Soc 133

PubMed: 21761922 | PubMedCentral: PMC3168932 | DOI: 10.1021/ja107805r

( 56 ) Methods Starting Structures All of the L n , L w , D , and P 3 a models were built from the NMR structure 2GKU ;( 56 ) the P 2 a models were built from the 1L34 structure;( 57 ) the P 4 a stems... were built from the crystal structure 1JPQ with two loop K + ions removed from the initial structure;( 58 ) and the stem structures of the P 3 p / P 4 p models were obtained from the first three/four G-quartets of the 139D structure, respectively.

The T 4 - models were all built from the loop present in the 1JPQ structure.

Publication Year: 2011

Thrombin-aptamer recognition: a revealed ambiguity.

(2011) Nucleic Acids Res 39

PubMed: 21715374 | PubMedCentral: PMC3177225 | DOI: 10.1093/nar/gkr522

A brief analysis of other quadruplex structures (PDB codes: 2AVH, 1JPQ, 1I34) shows that this type of interaction is not unusual in antiparallel quadruplex, where guanine residues with syn and anti co... formations alternate along the strand.

Publication Year: 2011

Structural dynamics of possible late-stage intermediates in folding of quadruplex DNA studied by molecular simulations.

(2013) Nucleic Acids Res 41

PubMed: 23700306 | PubMedCentral: PMC3737530 | DOI: 10.1093/nar/gkt412

Six of them were taken from the Protein Data Bank (PDB): (i) the nuclear magnetic resonance (NMR) solution structure of d[T 2 (G 3 T 2 A) 3 G 3 A] (2GKU, first frame) ( 12 ), a 3+1 (hybrid) monomolecu... ar quadruplex with three tetrads; (ii) the X-ray structure of d[A(G 3 T 2 A) 3 G 3 ] (1KF1) ( 45 ) folded in a monomolecular parallel quadruplex with three tetrads; (iii) the X-ray structure of [d(G 4 T 4 G 4 )] 2 (1JPQ) ( 46 ) Oxytricha nova telomeric dimeric antiparallel quadruplex with four tetrads; (iv) the X-ray structure of [d(TG 4 T)] 4 (352D) ( 47 ), forming four consecutive parallel stranded guanine tetrads with thymidines unstructured and bulged into space (one disordered thymidine residue was modeled); (v) the structure of RNA parallel quadruplex [r(UG 4 U)] 4 (1J8G) ( 48 ), forming four G-tetrads complemented by uridines that are bulged out; and (vi) the X-ray structure of [d(G 4 )] 4 (3TVB) ( 49 ), forming a parallel stranded stem with the first tetrad all- syn .

Publication Year: 2013