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PDB ID Mentions in PubMed Central Article count: 3

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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.

Publication Year: 2011

Structural fluctuation observed in Z-DNA d(CGCGCG)? in the absence of divalent metal cations and polyamines.

(2013) J Synchrotron Radiat 20

PubMed: 24121329 | PubMedCentral: PMC3795545 | DOI: 10.1107/S0909049513020773

The global helical parameters of our structure were similar to those of the binary complex of Z-DNA and Mg 2+ ( 1dcg ; Gessner et al. , 1989 ▶ ) and the tertiary complex of Z-DNA, Mg 2+ and sp... rmine ( 2dcg ; Wang et al. , 1979 ▶ ).

Publication Year: 2013