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Crystal structure of the nico transition-metal riboswitch bound to cobalt

Analyse Crystal structure of the nico transition-metal riboswitch bound to cobalt in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4RUM
Type: RNA
Length: 92 nucleotides
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nico riboswitch RNA
Ligands: K, CO, MG, SR
Pockets: 4 · best druggability 0.59

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Nico riboswitch RNA	rna	92	—	—

Ligands and binding sites

K · Potassium ion · metal · 7 copies · chains A
CO · Cobalt (II) ion · metal · 4 copies · chains A
MG · Magnesium ion · metal · 2 copies · chains A
SR · Strontium ion · metal · chains A
GOL · Glycerol · additive · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	482	0.59	0.75	28	CO
2	344	0.53	0.75	21	K
3	251	0.49	0.75	26	K, CO
4	77	0.27	0.72	13	empty

Modifications

Observed in the structure: 1 modified (nucleotide modification).

Compared structures

4RUM · Crystal structure of the NiCo transition-metal riboswitch bound to cobalt · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Elsewhere: RCSB PDB 4RUM · PDBe 4RUM

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