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Structure paper

TitleStructure and ligand binding of the ADP-binding domain of the NAD + riboswitch.
Journal, issue, pagesRna, Vol. 26, Page 878-887, Year 2020
Publish dateNov 1, 2019 (structure data deposition date)
AuthorsHuang, L. / Wang, J. / Lilley, D.M.J.
External linksRna / PubMed:32295864
MethodsX-ray diffraction
Resolution2.1 - 2.95 Å
Structure data

PDB-6tb7:
Crystal structure of the ADP-binding domain of the NAD+ riboswitch with Adenosine monophosphate (AMP)
Method: X-RAY DIFFRACTION / Resolution: 2.53 Å

PDB-6tf0:
Crystal structure of the ADP-binding domain of the NAD+ riboswitch with Nicotinamide adenine dinucleotide, reduced (NADH)
Method: X-RAY DIFFRACTION / Resolution: 2.1 Å

PDB-6tf1:
Crystal structure of the ADP-binding domain of the NAD+ riboswitch with Adenosine diphosphate (ADP)
Method: X-RAY DIFFRACTION / Resolution: 2.4 Å

PDB-6tf2:
Crystal structure of the ADP-binding domain of the NAD+ riboswitch with Adenosine 5-triphosphate (ATP)
Method: X-RAY DIFFRACTION / Resolution: 2.55 Å

PDB-6tf3:
Crystal structure of the ADP-binding domain of the NAD+ riboswitch with Cordycepin 5-triphosphate (3-dATP)
Method: X-RAY DIFFRACTION / Resolution: 2.66 Å

PDB-6tfe:
Crystal structure of the ADP-binding domain of the NAD+ riboswitch with N6-Methyl-adenosine-5'-triphosphate (m6ATP)
Method: X-RAY DIFFRACTION / Resolution: 2.3 Å

PDB-6tff:
Crystal structure of the ADP-binding domain of the NAD+ riboswitch with Nicotinamide adenine dinucleotide (NAD+)
Method: X-RAY DIFFRACTION / Resolution: 2.52 Å

PDB-6tfg:
Crystal structure of the ADP-binding domain of the NAD+ riboswitch with Adenosine 3-phosphate 5-phosphosulfate (APPS)
Method: X-RAY DIFFRACTION / Resolution: 2.45 Å

PDB-6tfh:
Crystal structure of the ADP-binding domain of the NAD+ riboswitch with Nicotinamide adenine dinucleotide, reduced (NADH); soaking with Manganese(II) (Mn2+)
Method: X-RAY DIFFRACTION / Resolution: 2.95 Å

Chemicals

ChemComp-AMP:
ADENOSINE MONOPHOSPHATE / AMP*YM / Adenosine monophosphate

ChemComp-MG:
Unknown entry

ChemComp-NA:
Unknown entry

ChemComp-BR:
BROMIDE ION / Bromide

ChemComp-HOH:
WATER / Water

ChemComp-NAI:
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Nicotinamide adenine dinucleotide

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM / Adenosine diphosphate

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM / Adenosine triphosphate

ChemComp-3AT:
3'-DEOXYADENOSINE-5'-TRIPHOSPHATE / Deoxyadenosine triphosphate

ChemComp-N6E:
N6-Methyladenosine 5'-triphosphate

ChemComp-NAD:
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NAD*YM / Nicotinamide adenine dinucleotide

ChemComp-PPS:
3'-PHOSPHATE-ADENOSINE-5'-PHOSPHATE SULFATE / 3'-Phosphoadenosine-5'-phosphosulfate

ChemComp-MN:
Unknown entry

Source
  • candidatus koribacter versatilis ellin345 (bacteria)
KeywordsRNA / RNA structure; tRNA-mimicking; X-ray crystallography / RNA structure; Riboswitch; X-ray crystallography / Non-coding RNA

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