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PDB ID Mentions in PubMed Central

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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 ).

Publication Year: 2008


High regularity of Z-DNA revealed by ultra high-resolution crystal structure at 0.55 A.

(2011) Nucleic Acids Res 39

PubMed: 21459852 | PubMedCentral: PMC3152349 | DOI: 10.1093/nar/gkr202

Structures of d(CGCGCG) 2 available in the PDB and NDB (code in italics) Data Base Code Resolution (Å) R (%) i/a a SF b Crystal form a (Å) b (Å) c (Å) Amine Metal ions ... eference 2DCG 0.90 14.0 i n A 17.87 31.55 44.58 Spermine Mg 2+ ( 1 ) 1DCG 1.00 17.5 i n A 18.01 31.03 44.80 – Mg 2+ ( 33 ) ZDF013 c 1.00 19.5 i n A 17.45 31.63 45.56 – – ( 34 ) 292D 1.00 16.1 i n A 17.94 31.23 44.55 Polyamine Mg 2+ , Na + ( 35 ) 293D 1.00 19.1 i n A 17.93 31.23 44.64 Spermidine Mg 2+ , Na + ( 36 ) 336D 1.00 19.0 i n A 17.98 31.51 44.38 Thermospermine Mg 2+ ( 37 ) 1ICK 0.95 8.6 a y A 17.87 31.55 44.58 Spermine Mg 2+ ( 4 ) 1DJ6 1.00 16.9 i y A 17.93 31.36 44.62 Polyamine Mg 2+ ( 38 ) 2ELG 1.00 23.2 i y A 17.85 30.99 44.02 Spermidine Mg 2+ , Na + ( 39 ) 2IE1 1.60 19.0 i y A 17.64 30.38 43.63 Polyamine – ( 40 ) 3P4J 0.55 7.77 a y A 17.88 31.42 43.90 Spermine – This work 1D48 1.00 18.5 i n B 18.41 30.77 43.15 Spermine – ( 14 ) 131D 1.00 18.0 i n B 18.27 30.69 42.46 Spermine Na + ( 41 ) 1I0T 0.60 16.0 i n B 18.32 30.68 42.49 Spermine – ( 5 ) 1V9G 1.80N d 22.2 i y B 18.46 30.76 43.18 Spermine(D) e – ( 42 ) 1WOE 1.50N d 17.6 i y B 18.46 30.76 43.18 Spermine – ( 42 ) a Model refined isotropically (i) or anisotropically (a).

In the structures crystallized in the presence of Mg 2+ (1DCG, 2DCG, 1ICK), this ion is octahedrally coordinated by the N7 atom of guanine Gua6 and five water molecules.

Although almost all of those structures were refined against diffraction data reaching atomic resolution of ∼1.0 Å, only one model (1ICK) was refined with anisotropic atomic displacement parameters (ADPs) ( 4 ).

In the current structure, as well as in other type A crystals (2DCG, 1ICK), its terminal N1 atom forms hydrogen bonds with two phosphate groups of two neighboring DNA duplexes (atoms OP1_6 and OP2_9), N5 is H-bonded to OP2_5, N10 (partially disordered in the current structure) is H-bonded to the N7_8 atom of a guanine base, and N14 is in the neighborhood of the O6_4 atom of a cytosine base.

b Spermine atoms between C7 and N14 are split into two alternative sites with occupancies of 0.56/0.44 Refinement The refinement started with the Z-DNA model 1ICK stripped of all water and ligand molecules.

Publication Year: 2011