MERNA

A Database of Metal Ion Binding Sites in RNA

66 PDB files have been found to contain the metal ion Sodium as specified per your search criterion:

• 1DK1 (2 Na ions) (Within 6 Angstroms of any RNA atom) - Detailed view of a key element of the ribosome assembly: crystal structure of the s15-rrna complex
• 1DUQ (10 Na ions) (Within 6 Angstroms of any RNA atom) - Crystal structure of the rev binding element of hiv-1
• 1F7Y (2 Na ions) (Within 6 Angstroms of any RNA atom) - The crystal structure of two uucg loops highlights the role played by 2'-hydroxyl groups in its unusual stability
• 1FIR (1 Na ion) (Within 6 Angstroms of any RNA atom) - Crystal structure of hiv-1 reverse transcription primer trna(lys3)
• 1J6S (8 Na ions) (Within 6 Angstroms of any RNA atom) - Crystal structure of an rna tetraplex (ugaggu)4 with a- tetrads, g-tetrads, u-tetrads and g-u octads
• 1J8G (3 Na ions) (Within 6 Angstroms of any RNA atom) - X-ray analysis of a rna tetraplex r(uggggu)4 at ultra-high resolution
• 1JJ2 (86 Na ions) (Within 6 Angstroms of any RNA atom) - Fully refined crystal structure of the haloarcula marismortui large ribosomal subunit at 2.4 angstrom resolution
• 1JTW (15 Na ions) (Within 6 Angstroms of any RNA atom) - Structure of sl4 rna from the hiv-1 packaging signal
• 1K73 (86 Na ions) (Within 6 Angstroms of any RNA atom) - Co-crystal structure of anisomycin bound to the 50s ribosomal subunit
• 1K8A (83 Na ions) (Within 6 Angstroms of any RNA atom) - Co-crystal structure of carbomycin a bound to the 50s ribosomal subunit of haloarcula marismortui
• 1K9M (85 Na ions) (Within 6 Angstroms of any RNA atom) - Co-crystal structure of tylosin bound to the 50s ribosomal subunit of haloarcula marismortui
• 1KC8 (86 Na ions) (Within 6 Angstroms of any RNA atom) - Co-crystal structure of blasticidin s bound to the 50s ribosomal subunit
• 1KD1 (85 Na ions) (Within 6 Angstroms of any RNA atom) - Co-crystal structure of spiramycin bound to the 50s ribosomal subunit of haloarcula marismortui
• 1KQS (86 Na ions) (Within 6 Angstroms of any RNA atom) - The haloarcula marismortui 50s complexed with a pretranslocational intermediate in protein synthesis
• 1L2X (3 Na ions) (Within 6 Angstroms of any RNA atom) - Atomic resolution crystal structure of a viral rna pseudoknot
• 1L3Z (1 Na ion) (Within 6 Angstroms of any RNA atom) - Crystal structure analysis of an rna heptamer
• 1M1K (86 Na ions) (Within 6 Angstroms of any RNA atom) - Co-crystal structure of azithromycin bound to the 50s ribosomal subunit of haloarcula marismortui
• 1M90 (86 Na ions) (Within 6 Angstroms of any RNA atom) - Co-crystal structure of cca-phe-caproic acid-biotin and sparsomycin bound to the 50s ribosomal subunit
• 1MDG (5 Na ions) (Within 6 Angstroms of any RNA atom) - An alternating antiparallel octaplex in an rna crystal structure
• 1N8R (86 Na ions) (Within 6 Angstroms of any RNA atom) - Structure of large ribosomal subunit in complex with virginiamycin m
• 1NJI (85 Na ions) (Within 6 Angstroms of any RNA atom) - Structure of chloramphenicol bound to the 50s ribosomal subunit
• 1NTA (2 Na ions) (Within 6 Angstroms of any RNA atom) - 2.9 a crystal structure of streptomycin rna-aptamer
• 1NTB (2 Na ions) (Within 6 Angstroms of any RNA atom) - 2.9 a crystal structure of streptomycin rna-aptamer complex
• 1Q7Y (86 Na ions) (Within 6 Angstroms of any RNA atom) - Crystal structure of ccdap-puromycin bound at the peptidyl transferase center of the 50s ribosomal subunit
• 1Q81 (86 Na ions) (Within 6 Angstroms of any RNA atom) - Crystal structure of minihelix with 3' puromycin bound to a- site of the 50s ribosomal subunit.
• 1Q82 (86 Na ions) (Within 6 Angstroms of any RNA atom) - Crystal structure of cc-puromycin bound to the a-site of the 50s ribosomal subunit
• 1Q86 (86 Na ions) (Within 6 Angstroms of any RNA atom) - Crystal structure of cca-phe-cap-biotin bound simultaneously at half occupancy to both the a-site and p- site of the the 50s ribosomal subunit.
• 1Q93 (1 Na ion) (Within 6 Angstroms of any RNA atom) - Crystal structure of a mutant of the sarcin/ricin domain from rat 28s rrna
• 1QVF (86 Na ions) (Within 6 Angstroms of any RNA atom) - Structure of a deacylated trna minihelix bound to the e site of the large ribosomal subunit of haloarcula marismortui
• 1QVG (86 Na ions) (Within 6 Angstroms of any RNA atom) - Structure of cca oligonucleotide bound to the trna binding sites of the large ribosomal subunit of haloarcula marismortui
• 1S72 (86 Na ions) (Within 6 Angstroms of any RNA atom) - Refined crystal structure of the haloarcula marismortui large ribosomal subunit at 2.4 angstrom resolution
• 1VQ4 (86 Na ions) (Within 6 Angstroms of any RNA atom) - The structure of the transition state analogue "daa" bound to the large ribosomal subunit of haloarcula marismortui
• 1VQ5 (86 Na ions) (Within 6 Angstroms of any RNA atom) - The structure of the transition state analogue "raa" bound to the large ribosomal subunit of haloarcula marismortui
• 1VQ6 (86 Na ions) (Within 6 Angstroms of any RNA atom) - The structure of c-hpmn and cca-phe-cap-bio bound to the large ribosomal subunit of haloarcula marismortui
• 1VQ7 (86 Na ions) (Within 6 Angstroms of any RNA atom) - The structure of the transition state analogue "dca" bound to the large ribosomal subunit of haloarcula marismortui
• 1VQ8 (75 Na ions) (Within 6 Angstroms of any RNA atom) - The structure of ccda-phe-cap-bio and the antibiotic sparsomycin bound to the large ribosomal subunit of haloarcula marismortui
• 1VQ9 (75 Na ions) (Within 6 Angstroms of any RNA atom) - The structure of cca-phe-cap-bio and the antibiotic sparsomycin bound to the large ribosomal subunit of haloarcula marismortui
• 1VQK (75 Na ions) (Within 6 Angstroms of any RNA atom) - The structure of ccda-phe-cap-bio bound to the a site of the ribosomal subunit of haloarcula marismortui
• 1VQL (75 Na ions) (Within 6 Angstroms of any RNA atom) - The structure of the transition state analogue "dcsn" bound to the large ribosomal subunit of haloarcula marismortui
• 1VQM (75 Na ions) (Within 6 Angstroms of any RNA atom) - The structure of the transition state analogue "dan" bound to the large ribosomal subunit of haloarcula marismortui
• 1VQN (75 Na ions) (Within 6 Angstroms of any RNA atom) - The structure of cc-hpmn and cca-phe-cap-bio bound to the large ribosomal subunit of haloarcula marismortui
• 1VQO (75 Na ions) (Within 6 Angstroms of any RNA atom) - The structure of ccpmn bound to the large ribosomal subunit of haloarcula marismortui
• 1VQP (75 Na ions) (Within 6 Angstroms of any RNA atom) - The structure of the transition state analogue "rap" bound to the large ribosomal subunit of haloarcula marismortui
• 1W2B (83 Na ions) (Within 6 Angstroms of any RNA atom) - Trigger factor ribosome binding domain in complex with 50s
• 1XP7 (1 Na ion) (Within 6 Angstroms of any RNA atom) - Hiv-1 subtype f genomic rna dimerization initiation site
• 1XPE (3 Na ions) (Within 6 Angstroms of any RNA atom) - Hiv-1 subtype b genomic rna dimerization initiation site
• 1XPF (1 Na ion) (Within 6 Angstroms of any RNA atom) - Hiv-1 subtype a genomic rna dimerization initiation site
• 1Y3O (3 Na ions) (Within 6 Angstroms of any RNA atom) - Hiv-1 dis rna subtype f- mn soaked
• 1Y6T (2 Na ions) (Within 6 Angstroms of any RNA atom) - Hiv-1 dis(mal) duplex co hexamine-soaked
• 1YHQ (75 Na ions) (Within 6 Angstroms of any RNA atom) - Crystal structure of azithromycin bound to the g2099a mutant 50s ribosomal subunit of haloarcula marismortui
• 1YI2 (86 Na ions) (Within 6 Angstroms of any RNA atom) - Crystal structure of erythromycin bound to the g2099a mutant 50s ribosomal subunit of haloarcula marismortui
• 1YIJ (86 Na ions) (Within 6 Angstroms of any RNA atom) - Crystal structure of telithromycin bound to the g2099a mutant 50s ribosomal subunit of haloarcula marismortui
• 1YIT (85 Na ions) (Within 6 Angstroms of any RNA atom) - Crystal structure of virginiamycin m and s bound to the 50s ribosomal subunit of haloarcula marismortui
• 1YJ9 (86 Na ions) (Within 6 Angstroms of any RNA atom) - Crystal structure of the mutant 50s ribosomal subunit of haloarcula marismortui containing a three residue deletion
• 1YJN (86 Na ions) (Within 6 Angstroms of any RNA atom) - Crystal structure of clindamycin bound to the g2099a mutant 50s ribosomal subunit of haloarcula marismortui
• 1YJW (86 Na ions) (Within 6 Angstroms of any RNA atom) - Crystal structure of quinupristin bound to the g2099a mutant 50s ribosomal subunit of haloarcula marismortui
• 246D (2 Na ions) (Within 6 Angstroms of any RNA atom) - Structure of the purine-pyrimidine alternating rna double helix, r(guauaua)d(c), with a 3'-terminal deoxy residue
• 2B8R (1 Na ion) (Within 6 Angstroms of any RNA atom) - Structure of hiv-1(lai) genomic rna dis
• 2B8S (2 Na ions) (Within 6 Angstroms of any RNA atom) - Structure of hiv-1(mal) genomic rna dis
• 2GDI (2 Na ions) (Within 6 Angstroms of any RNA atom) - Crystal structure of thiamine pyrophosphate-specific riboswitch in complex with thiamine pyrophosphate
• 420D (1 Na ion) (Within 6 Angstroms of any RNA atom) - Crystal structure of a 16-mer rna duplex with non-adjacent a(anti).g(syn) mismatches
• 434D (1 Na ion) (Within 6 Angstroms of any RNA atom) - 5'-r(*up*ap*gp*cp*up*cp*c)-3', 5'-r(*gp*gp*gp*gp*cp*up*a)-3'
• 435D (2 Na ions) (Within 6 Angstroms of any RNA atom) - 5'-r(*up*ap*gp*cp*cp*cp*c)-3', 5'-r(*gp*gp*gp*gp*cp*up*a)-3'
• 437D (1 Na ion) (Within 6 Angstroms of any RNA atom) - Crystal structure of an rna pseudoknot from beet western yellow virus involved in ribosomal frameshifting
• 464D (1 Na ion) (Within 6 Angstroms of any RNA atom) - Disorder and twin refinement of rna heptamer double helix
• 466D (1 Na ion) (Within 6 Angstroms of any RNA atom) - Disorder and twin refinement of rna heptamer double helix

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