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Structure paper

TitleCation trafficking propels RNA hydrolysis.
Journal, issue, pagesNat. Struct. Mol. Biol., Vol. 25, Page 715-721, Year 2018
Publish dateJun 5, 2018 (structure data deposition date)
AuthorsSamara, N.L. / Yang, W.
External linksNat. Struct. Mol. Biol. / PubMed:30076410
MethodsX-ray diffraction
Resolution1.25 - 1.948 Å
Structure data

PDB-6dmn:
Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hybrid: Soaked in 2 mM Ca2+ and 200 mM K+ at 21 C
Method: X-RAY DIFFRACTION / Resolution: 1.27 Å

PDB-6dmv:
Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hybrid: Soaked for 40 s in 2 mM Mg2+ and 200 mM K+ at 21 C
Method: X-RAY DIFFRACTION / Resolution: 1.52 Å

PDB-6do8:
Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hybrid: Reaction in 2 mM Mg2+ and 200 mM K+ for 80 s at 21 C
Method: X-RAY DIFFRACTION / Resolution: 1.414 Å

PDB-6do9:
Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hybrid: Reaction in 2 mM Mg2+ and 200 mM K+ for 120 s at 21 C
Method: X-RAY DIFFRACTION / Resolution: 1.36 Å

PDB-6doa:
Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hybrid: Reaction in 2 mM Mg2+ and 200 mM K+ for 480 s at 21 C
Method: X-RAY DIFFRACTION / Resolution: 1.474 Å

PDB-6dob:
Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hybrid: Reaction in 2 mM Mg2+ and 200 mM K+ for 200 s at 21 C
Method: X-RAY DIFFRACTION / Resolution: 1.343 Å

PDB-6doc:
Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hybrid: Reaction in 2 mM Mg2+ and 200 mM K+ for 240 s at 21 C
Method: X-RAY DIFFRACTION / Resolution: 1.496 Å

PDB-6dod:
Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hybrid: Reaction in 2 mM Mg2+ and 200 mM K+ for 360 s at 21 C
Method: X-RAY DIFFRACTION / Resolution: 1.535 Å

PDB-6doe:
Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hybrid: Reaction in 2 mM Mg2+ and 200 mM K+ for 420 s at 21 C
Method: X-RAY DIFFRACTION / Resolution: 1.451 Å

PDB-6dof:
Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hybrid: Reaction in 2 mM Mg2+ and 200 mM K+ for 540 s at 21 C
Method: X-RAY DIFFRACTION / Resolution: 1.433 Å

PDB-6dog:
Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hybrid: Reaction in 2 mM Mg2+ and 200 mM K+ for 600 s at 21 C
Method: X-RAY DIFFRACTION / Resolution: 1.285 Å

PDB-6doh:
Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hybrid: Soak in 0.5 mM EGTA and 200 mM K+ at 21 C
Method: X-RAY DIFFRACTION / Resolution: 1.363 Å

PDB-6doi:
Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hybrid (1.54 Angstrom wavelength): Soak in 0.5 mM EGTA and 200 mM K+ at 21 C
Method: X-RAY DIFFRACTION / Resolution: 1.948 Å

PDB-6doj:
Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hybrid: Reaction in 2 mM Mg2+ and 5 mM K+ for 120 s at 21 C
Method: X-RAY DIFFRACTION / Resolution: 1.403 Å

PDB-6dok:
Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hybrid: Reaction in 2 mM Mg2+ and 25 mM K+ for 120 s at 21 C (dataset 1)
Method: X-RAY DIFFRACTION / Resolution: 1.38 Å

PDB-6dol:
Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hybrid: Reaction in 2 mM Mg2+ and 25 mM K+ for 120 s at 21 C (dataset 2)
Method: X-RAY DIFFRACTION / Resolution: 1.433 Å

PDB-6dom:
Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hybrid: Reaction in 2 mM Mg2+ and 50 mM K+ for 120 s at 21 C
Method: X-RAY DIFFRACTION / Resolution: 1.425 Å

PDB-6don:
Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hybrid: Reaction in 2 mM Mg2+ and 100 mM K+ for 120 s at 21 C (dataset 1)
Method: X-RAY DIFFRACTION / Resolution: 1.422 Å

PDB-6doo:
Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hybrid: Reaction in 2 mM Mg2+ and 100 mM K+ for 120 s at 21 C (dataset 2)
Method: X-RAY DIFFRACTION / Resolution: 1.44 Å

PDB-6dop:
Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hybrid: Reaction in 2 mM Mg2+ and 200 mM K+ for 120 s at 21 C (dataset 1)
Method: X-RAY DIFFRACTION / Resolution: 1.25 Å

PDB-6doq:
Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hybrid: Reaction in 2 mM Mg2+ and 200 mM K+ for 120 s at 21 C (dataset 2)
Method: X-RAY DIFFRACTION / Resolution: 1.422 Å

PDB-6dor:
Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hybrid: Reaction in 2 mM Mg2+ and 300 mM K+ for 120 s at 21 C (dataset 1)
Method: X-RAY DIFFRACTION / Resolution: 1.5 Å

PDB-6dos:
Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hybrid: Reaction in 2 mM Mg2+ and 300 mM K+ for 120 s at 21 C (dataset 2)
Method: X-RAY DIFFRACTION / Resolution: 1.318 Å

PDB-6dot:
Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hybrid: Reaction in 5 mM Mg2+ and 200 mM Rb+ for 40 s at 21 C
Method: X-RAY DIFFRACTION / Resolution: 1.423 Å

PDB-6dou:
Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hybrid: Reaction in 5 mM Mg2+ and 200 mM Rb+ for 120 s at 21 C
Method: X-RAY DIFFRACTION / Resolution: 1.487 Å

PDB-6dov:
Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hybrid: Reaction in 5 mM Mg2+ and 200 mM Rb+ for 80 s at 21 C
Method: X-RAY DIFFRACTION / Resolution: 1.521 Å

PDB-6dow:
Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hybrid: Reaction in 5 mM Mg2+ and 200 mM Rb+ for 160 s at 21 C
Method: X-RAY DIFFRACTION / Resolution: 1.495 Å

PDB-6dox:
Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hybrid: Reaction in 5 mM Mg2+ and 200 mM Rb+ for 360 s at 21 C
Method: X-RAY DIFFRACTION / Resolution: 1.45 Å

PDB-6doy:
Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hybrid: Reaction in 2 mM Mg2+ and 200 mM Li+ for 120 s at 21 C
Method: X-RAY DIFFRACTION / Resolution: 1.45 Å

PDB-6doz:
Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hybrid: Reaction in 1 mM Mg2+ and 75 mM K+ for 40 s at 21 C
Method: X-RAY DIFFRACTION / Resolution: 1.573 Å

PDB-6dp0:
Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hybrid: Reaction in 2.5 mM Mg2+ and 75 mM K+ for 40 s at 21 C
Method: X-RAY DIFFRACTION / Resolution: 1.451 Å

PDB-6dp1:
Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hybrid: Reaction in 5 mM Mg2+ and 75 mM K+ for 40 s at 21 C
Method: X-RAY DIFFRACTION / Resolution: 1.42 Å

PDB-6dp2:
Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hybrid: Reaction in 7.5 mM Mg2+ and 75 mM K+ for 40 s at 21 C
Method: X-RAY DIFFRACTION / Resolution: 1.662 Å

PDB-6dp3:
Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hybrid: Reaction in 10 mM Mg2+ and 75 mM K+ for 40 s at 21 C
Method: X-RAY DIFFRACTION / Resolution: 1.461 Å

PDB-6dp4:
Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hybrid: Reaction in 20 mM Mg2+ and 75 mM K+ for 40 s at 21 C
Method: X-RAY DIFFRACTION / Resolution: 1.374 Å

PDB-6dp5:
Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hybrid: Reaction in 40 mM Mg2+ and 75 mM K+ for 40 s at 21 C
Method: X-RAY DIFFRACTION / Resolution: 1.432 Å

PDB-6dp6:
Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hybrid: Reaction in 80 mM Mg2+ and 75 mM K+ for 40 s at 21 C
Method: X-RAY DIFFRACTION / Resolution: 1.403 Å

PDB-6dp7:
Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hybrid: Reaction in 500 mM Mn2+ and 200 mM K+ for 40 s at 21 C
Method: X-RAY DIFFRACTION / Resolution: 1.381 Å

PDB-6dp8:
Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hybrid: Reaction in 5 mM Mg2+ and 200 mM Li+ for 240 s at 21 C
Method: X-RAY DIFFRACTION / Resolution: 1.323 Å

PDB-6dp9:
Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hybrid: Reaction in 2 mM Mn2+ and 200 mM K+ for 40 s at 21 C
Method: X-RAY DIFFRACTION / Resolution: 1.4 Å

PDB-6dpa:
Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hybrid: Reaction in 4 mM Mn2+ and 200 mM K+ for 40 s at 21 C
Method: X-RAY DIFFRACTION / Resolution: 1.489 Å

PDB-6dpb:
Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hybrid: Reaction in 8 mM Mn2+ and 200 mM K+ for 40 s at 21 C
Method: X-RAY DIFFRACTION / Resolution: 1.324 Å

PDB-6dpc:
Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hybrid: Reaction in 12 mM Mn2+ and 200 mM K+ for 40 s at 21 C
Method: X-RAY DIFFRACTION / Resolution: 1.34 Å

PDB-6dpd:
Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hybrid: Reaction in 16 mM Mn2+ and 200 mM K+ for 40 s at 21 C
Method: X-RAY DIFFRACTION / Resolution: 1.46 Å

PDB-6dpe:
Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hybrid: Reaction in 20 mM Mn2+ and 200 mM K+ for 40 s at 21 C
Method: X-RAY DIFFRACTION / Resolution: 1.56 Å

PDB-6dpf:
Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hybrid: Reaction in 40 mM Mn2+ and 200 mM K+ for 40 s at 21 C
Method: X-RAY DIFFRACTION / Resolution: 1.56 Å

PDB-6dpg:
Crystal Structure of Bacillus Halodurans Ribonuclease H1 E188A in Complex with an RNA/DNA Hybrid: Reaction in 4 mM Mn2+ and 200 mM K+ for 240 s at 21 C
Method: X-RAY DIFFRACTION / Resolution: 1.38 Å

PDB-6dph:
Crystal Structure of Bacillus Halodurans Ribonuclease H1 E188A in Complex with an RNA/DNA Hybrid: Reaction in 2 mM Mn2+ and 200 mM K+ for 120 s at 21 C
Method: X-RAY DIFFRACTION / Resolution: 1.339 Å

PDB-6dpi:
Crystal Structure of Bacillus Halodurans Ribonuclease H1 K196A in Complex with an RNA/DNA Hybrid: Reaction in 10 mM Mg2+ and 200 mM Rb+ for 40 s at 21 C
Method: X-RAY DIFFRACTION / Resolution: 1.347 Å

PDB-6dpj:
Crystal Structure of Bacillus Halodurans Ribonuclease H1 K196A in Complex with an RNA/DNA Hybrid: Reaction in 4 mM Mn2+ and 200 mM K+ for 80 s at 21 C
Method: X-RAY DIFFRACTION / Resolution: 1.55 Å

PDB-6dpk:
Crystal Structure of Bacillus Halodurans Ribonuclease H1 K196A in Complex with an RNA/DNA Hybrid: Reaction in 4 mM Mn2+ and 200 mM K+ for 240 s at 21 C
Method: X-RAY DIFFRACTION / Resolution: 1.391 Å

PDB-6dpl:
Crystal Structure of Bacillus Halodurans Ribonuclease H1 K196A in Complex with an RNA/DNA Hybrid: Reaction in 10 mM Mg2+ and 200 mM Rb+ for 720 s at 21 C
Method: X-RAY DIFFRACTION / Resolution: 1.45 Å

PDB-6dpm:
Crystal Structure of Bacillus Halodurans Ribonuclease H1 K196A in Complex with an RNA/DNA Hybrid: Reaction in 10 mM Mg2+ and 200 mM Rb+ for 1800 s at 21 C
Method: X-RAY DIFFRACTION / Resolution: 1.677 Å

PDB-6dpn:
Crystal Structure of Bacillus Halodurans Ribonuclease H1 E188A in Complex with an RNA/DNA Hybrid: Reaction in 2 mM Mg2+ and 200 mM K+ for 200 s at 21 C
Method: X-RAY DIFFRACTION / Resolution: 1.493 Å

PDB-6dpo:
Crystal Structure of Bacillus Halodurans Ribonuclease H1 E188A in Complex with an RNA/DNA Hybrid: Reaction in 2 mM Mg2+ and 200 mM K+ for 360 s at 21 C
Method: X-RAY DIFFRACTION / Resolution: 1.45 Å

PDB-6dpp:
Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hybrid: Reaction in 5 mM Mg2+ and 200 mM Rb+ for 240 s at 21 C
Method: X-RAY DIFFRACTION / Resolution: 1.45 Å

Chemicals

ChemComp-CA:
Unknown entry

ChemComp-IOD:
IODIDE ION

ChemComp-GOL:
GLYCEROL

ChemComp-EDO:
1,2-ETHANEDIOL

ChemComp-K:
Unknown entry

ChemComp-HOH:
WATER

ChemComp-MG:
Unknown entry

ChemComp-PGE:
TRIETHYLENE GLYCOL

ChemComp-RB:
RUBIDIUM ION

ChemComp-CL:
Unknown entry

ChemComp-PEG:
DI(HYDROXYETHYL)ETHER

ChemComp-LI:
Unknown entry

ChemComp-MN:
Unknown entry

Source
  • bacillus halodurans (bacteria)
  • synthetic construct (others)
  • bacillus halodurans (strain atcc baa-125 / dsm 18197 / ferm 7344 / jcm 9153 / c-125) (bacteria)
  • unidentified (others)
  • bacillus halodurans c-125 (bacteria)
  • synthetic (others)
Keywordshydrolase/dna/rna / protein-RNA-DNA complex / double helix / RNA hydrolysis / in crystallo catalysis / metal dependent catalysis / monovalent cations / divalent cations / HYDROLASE / hydrolase-dna-rna complex / hydrolase/rna/dna / hydrolase-rna-dna complex

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