7EIA
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 7eia by Molmil](/molmil-images/mine/7eia) | RNA kink-turn motif with pyrrolo cytosine | Descriptor: | POTASSIUM ION, RNA (5'-R(*GP*GP*CP*GP*A)-D(P*(4PC))-R(P*GP*AP*AP*CP*CP*GP*GP*GP*GP*AP*GP*CP*C)-3') | Authors: | Kondo, J, Miyauchi, T. | Deposit date: | 2021-03-30 | Release date: | 2022-03-30 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (3 Å) | Cite: | RNA kink-turn motif with pyrrolo cytosine To Be Published
|
|
7F8Z
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 7f8z by Molmil](/molmil-images/mine/7f8z) | RNA kink-turn motif with 2-aminopurine | Descriptor: | POTASSIUM ION, RNA (5'-R(*GP*GP*CP*GP*A)-D(P*(2PR))-R(P*GP*AP*AP*CP*CP*GP*GP*GP*GP*AP*GP*CP*C)-3') | Authors: | Kondo, J, Miyauchi, T. | Deposit date: | 2021-07-03 | Release date: | 2022-07-06 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (3 Å) | Cite: | RNA kink-turn motif with 2-aminopurine To Be Published
|
|
7XKM
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 7xkm by Molmil](/molmil-images/mine/7xkm) | |
7XLW
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 7xlw by Molmil](/molmil-images/mine/7xlw) | |
7XLV
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 7xlv by Molmil](/molmil-images/mine/7xlv) | Crystal structure of a NIR-emitting DNA-stabilized Ag16 nanocluster (G7I mutant) | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, DNA (5'-D(*CP*AP*CP*CP*TP*AP*IP*CP*GP*A)-3'), SILVER ION | Authors: | Kondo, J, Cerretani, C, Vosch, T. | Deposit date: | 2022-04-23 | Release date: | 2022-07-13 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (1.1 Å) | Cite: | The effect of inosine on the spectroscopic properties and crystal structure of a NIR-emitting DNA-stabilized silver nanocluster. Nanoscale Adv, 4, 2022
|
|
7BSH
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 7bsh by Molmil](/molmil-images/mine/7bsh) | |
7BSE
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 7bse by Molmil](/molmil-images/mine/7bse) | |
7BSG
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 7bsg by Molmil](/molmil-images/mine/7bsg) | |
7BSF
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 7bsf by Molmil](/molmil-images/mine/7bsf) | |
6M2P
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 6m2p by Molmil](/molmil-images/mine/6m2p) | Crystal structure of a NIR-emitting DNA-stabilized Ag16 nanocluster (A10-deletion mutant) | Descriptor: | CALCIUM ION, CHLORIDE ION, DNA (5'-D(*CP*AP*CP*CP*TP*AP*GP*CP*G)-3'), ... | Authors: | Kondo, J, Cerretani, C, Vosch, T. | Deposit date: | 2020-02-28 | Release date: | 2020-07-01 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (1.13 Å) | Cite: | Removal of the A10 adenosine in a DNA-stabilized Ag16 nanocluster. Rsc Adv, 10, 2020
|
|
7Y8P
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 7y8p by Molmil](/molmil-images/mine/7y8p) | Crystal structure of 4'-selenoRNA duplex | Descriptor: | COBALT HEXAMMINE(III), RNA (5'-R(*GP*GP*AP*(IKS)P*(ILK)P*(IKS)P*GP*AP*GP*UP*CP*C)-3') | Authors: | Kondo, J, Minakawa, N, Ohta, M, Takahashi, H, Tarashima, N. | Deposit date: | 2022-06-24 | Release date: | 2023-05-03 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (1.5 Å) | Cite: | Synthesis and properties of fully-modified 4'-selenoRNA, an endonuclease-resistant RNA analog. Bioorg.Med.Chem., 76, 2022
|
|
7YGP
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 7ygp by Molmil](/molmil-images/mine/7ygp) | DNA duplex containing 5OHU-T base pairs | Descriptor: | COBALT (II) ION, COBALT HEXAMMINE(III), DNA (5'-D(*GP*GP*AP*CP*CP*TP*(OHU)P*GP*GP*TP*CP*C)-3') | Authors: | Kondo, J, Torigoe, H, Arakawa, F. | Deposit date: | 2022-07-12 | Release date: | 2023-05-24 | Last modified: | 2024-05-29 | Method: | X-RAY DIFFRACTION (1.997 Å) | Cite: | Specific binding of Hg 2+ to mismatched base pairs involving 5-hydroxyuracil in duplex DNA. J.Inorg.Biochem., 241, 2023
|
|
7YGO
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 7ygo by Molmil](/molmil-images/mine/7ygo) | DNA duplex containing 5OHU-Hg(II)-T base pairs | Descriptor: | DNA (5'-D(*GP*GP*AP*CP*CP*TP*(6HU)P*GP*GP*TP*CP*C)-3'), MERCURY (II) ION | Authors: | Kondo, J, Torigoe, H, Arakawa, F. | Deposit date: | 2022-07-12 | Release date: | 2023-05-24 | Last modified: | 2024-05-29 | Method: | X-RAY DIFFRACTION (2.403 Å) | Cite: | Specific binding of Hg 2+ to mismatched base pairs involving 5-hydroxyuracil in duplex DNA. J.Inorg.Biochem., 241, 2023
|
|
6JBF
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 6jbf by Molmil](/molmil-images/mine/6jbf) | Crystal structure of the bacterial ribosomal decoding site in complex with 4'-deoxy-4'-fluoro neamine analog (axial 4'-F) | Descriptor: | (1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyl 2,6-diamino-2,4,6-trideoxy-4-fluoro-alpha-D-galactopyranoside, RNA (5'-R(*UP*UP*GP*CP*GP*UP*CP*AP*CP*GP*CP*CP*GP*GP*CP*GP*AP*AP*GP*UP*CP*GP*C)-3') | Authors: | Kanazawa, H, Auffinger, P, Hanessian, S, Kondo, J. | Deposit date: | 2019-01-25 | Release date: | 2020-01-29 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (2.6 Å) | Cite: | Crystal structure of the bacterial ribosomal decoding site in complex with 4'-deoxy-4'-fluoro neamine analog (axial 4'-F) To Be Published
|
|
6JBG
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 6jbg by Molmil](/molmil-images/mine/6jbg) | Crystal structure of the bacterial ribosomal decoding site in complex with 4'-deoxy-4'-fluoro neamine analog (equatorial 4'-F) | Descriptor: | (1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyl 2,6-diamino-2,4,6-trideoxy-4-fluoro-alpha-D-glucopyranoside, RNA (5'-R(*UP*UP*GP*CP*GP*UP*CP*AP*CP*GP*CP*CP*GP*GP*CP*GP*AP*AP*GP*UP*CP*GP*C)-3'), RNA (5'-R(P*UP*GP*CP*GP*UP*CP*AP*CP*GP*CP*CP*GP*GP*CP*GP*AP*AP*GP*UP*CP*GP*C)-3') | Authors: | Kanazawa, H, Auffinger, P, Hanessian, S, Kondo, J. | Deposit date: | 2019-01-25 | Release date: | 2020-01-29 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (3.1 Å) | Cite: | Crystal structure of the bacterial ribosomal decoding site in complex with 4'-deoxy-4'-fluoro neamine analog (axial 4'-F) To Be Published
|
|
6IYQ
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 6iyq by Molmil](/molmil-images/mine/6iyq) | |
6JR4
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 6jr4 by Molmil](/molmil-images/mine/6jr4) | Crystal structure of a NIR-emitting DNA-stabilized Ag16 nanocluster | Descriptor: | CALCIUM ION, DNA (5'-D(*CP*AP*CP*CP*TP*AP*GP*CP*GP*A)-3'), SILVER ION | Authors: | Kondo, J, Cerretani, C, Kanazawa, H, Vosch, T. | Deposit date: | 2019-04-02 | Release date: | 2019-08-28 | Last modified: | 2024-03-27 | Method: | X-RAY DIFFRACTION (1.798 Å) | Cite: | Crystal structure of a NIR-Emitting DNA-Stabilized Ag16Nanocluster. Angew.Chem.Int.Ed.Engl., 58, 2019
|
|
2RT8
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 2rt8 by Molmil](/molmil-images/mine/2rt8) | Structure of metallo-dna in solution | Descriptor: | DNA (5'-D(*CP*GP*CP*GP*TP*TP*GP*TP*CP*C)-3'), DNA (5'-D(*GP*GP*AP*CP*TP*TP*CP*GP*CP*G)-3'), MERCURY (II) ION | Authors: | Yamaguchi, H, Sebera, J, Kondo, J, Oda, S, Komuro, T, Kawamura, T, Dairaku, T, Kondo, Y, Okamoto, I, Ono, A, Burda, J.V, Kojima, C, Sychrovsky, V, Tanaka, Y. | Deposit date: | 2013-06-18 | Release date: | 2014-03-05 | Last modified: | 2024-05-15 | Method: | SOLUTION NMR | Cite: | The structure of metallo-DNA with consecutive thymine-HgII-thymine base pairs explains positive entropy for the metallo base pair formation. Nucleic Acids Res., 42, 2014
|
|
2RVP
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 2rvp by Molmil](/molmil-images/mine/2rvp) | Solution structure of DNA Containing Metallo-Base-Pair | Descriptor: | DNA (5'-D(*TP*AP*AP*TP*AP*TP*AP*CP*TP*TP*AP*AP*TP*TP*A)-3'), DNA (5'-D(*TP*AP*AP*TP*TP*AP*AP*CP*TP*AP*TP*AP*TP*TP*A)-3'), SILVER ION | Authors: | Dairaku, T, Furuita, K, Sato, H, Sebera, J, Nakashima, K, Kondo, J, Yamanaka, D, Kondo, Y, Okamoto, I, Ono, A, Sychrovsky, V, Kojima, C, Tanaka, Y. | Deposit date: | 2016-03-22 | Release date: | 2016-08-31 | Last modified: | 2024-05-15 | Method: | SOLUTION NMR | Cite: | Structure Determination of an Ag(I) -Mediated Cytosine-Cytosine Base Pair within DNA Duplex in Solution with (1) H/(15) N/(109) Ag NMR Spectroscopy. Chemistry, 22, 2016
|
|
3S4P
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 3s4p by Molmil](/molmil-images/mine/3s4p) | Crystal structure of the bacterial ribosomal decoding site complexed with an amphiphilic paromomycin O2''-ether analogue | Descriptor: | (1R,2R,3S,4R,6S)-4,6-diamino-2-{[3-O-(2,6-diamino-2,6-dideoxy-beta-L-idopyranosyl)-2-O-{2-[(2-phenylethyl)amino]ethyl}-beta-D-ribofuranosyl]oxy}-3-hydroxycyclohexyl 2-amino-2-deoxy-alpha-D-glucopyranoside, RNA (5'-R(P*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*C)-3') | Authors: | Szychowski, J, Kondo, J, Zahr, O, Auclair, K, Westhof, E, Hanessian, S, Keillor, J.W. | Deposit date: | 2011-05-20 | Release date: | 2011-09-21 | Last modified: | 2023-11-01 | Method: | X-RAY DIFFRACTION (2.56 Å) | Cite: | Inhibition of aminoglycoside-deactivating enzymes APH(3')-IIIa and AAC(6')-Ii by amphiphilic paromomycin O2''-ether analogues Chemmedchem, 6, 2011
|
|
5ZEG
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 5zeg by Molmil](/molmil-images/mine/5zeg) | |
5ZEM
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 5zem by Molmil](/molmil-images/mine/5zem) | |
5ZEJ
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 5zej by Molmil](/molmil-images/mine/5zej) | Crystal structure of the bacterial A1408me1A-mutant ribosomal decoding site in complex with paromomycin | Descriptor: | PAROMOMYCIN, RNA (5'-R(P*UP*GP*CP*GP*UP*CP*(1MA)P*CP*GP*UP*CP*GP*AP*CP*GP*AP*AP*GP*UP*CP*GP*C)-3') | Authors: | Kanazawa, H, Baba, F, Koganei, M, Kondo, J. | Deposit date: | 2018-02-27 | Release date: | 2018-03-21 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (3.5 Å) | Cite: | A structural basis for the antibiotic resistance conferred by an N1-methylation of A1408 in 16S rRNA. Nucleic Acids Res., 45, 2017
|
|
4K31
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 4k31 by Molmil](/molmil-images/mine/4k31) | Crystal structure of apramycin bound to the leishmanial rRNA A-site | Descriptor: | APRAMYCIN, RNA (5'-R(*UP*UP*GP*CP*GP*UP*CP*GP*UP*UP*CP*CP*GP*GP*AP*AP*AP*AP*GP*UP*CP*GP*C)-3') | Authors: | Shalev, M, Kondo, J, Adir, N, Baasov, T. | Deposit date: | 2013-04-10 | Release date: | 2013-07-31 | Last modified: | 2023-09-20 | Method: | X-RAY DIFFRACTION (1.415 Å) | Cite: | Identification of the molecular attributes required for aminoglycoside activity against Leishmania. Proc.Natl.Acad.Sci.USA, 110, 2013
|
|
4K32
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 4k32 by Molmil](/molmil-images/mine/4k32) | Crystal structure of geneticin bound to the leishmanial rRNA A-site | Descriptor: | GENETICIN, RNA (5'-R(*UP*UP*GP*CP*GP*UP*CP*GP*UP*UP*CP*CP*GP*GP*AP*AP*AP*AP*GP*UP*CP*GP*C)-3') | Authors: | Shalev, M, Kondo, J, Adir, N, Baasov, T. | Deposit date: | 2013-04-10 | Release date: | 2013-07-31 | Last modified: | 2024-02-28 | Method: | X-RAY DIFFRACTION (2.5 Å) | Cite: | Identification of the molecular attributes required for aminoglycoside activity against Leishmania. Proc.Natl.Acad.Sci.USA, 110, 2013
|
|