SMTL ID : 3v7e.1 (1 other biounit)

Crystal structure of YbxF bound to the SAM-I riboswitch aptamer

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

monomer

Ligands

12 x NCO: COBALT HEXAMMINE(III)(Non-functional Binders)

NCO.1: 8 residues within 4Å: Chain B: C.3, U.4, U.5, A.6, A.119, U.120, G.121, A.122 No protein-ligand interaction detected (PLIP) NCO.2: 6 residues within 4Å: Chain B: G.23, C.25, U.26, G.27, G.28, C.29 No protein-ligand interaction detected (PLIP) NCO.3: 8 residues within 4Å: Chain B: C.59, G.60, U.61, C.62, U.72, G.73, A.74 Ligands: NCO.9 No protein-ligand interaction detected (PLIP) NCO.4: 5 residues within 4Å: Chain B: A.45, A.46, U.86, G.87, G.88 No protein-ligand interaction detected (PLIP) NCO.5: 6 residues within 4Å: Chain B: A.10, G.11, A.12, A.94, U.95, U.96 No protein-ligand interaction detected (PLIP) NCO.6: 3 residues within 4Å: Chain B: U.113, G.114, A.115 No protein-ligand interaction detected (PLIP) NCO.7: 8 residues within 4Å: Chain B: A.24, C.25, U.96, C.98, U.99, G.100, A.116, A.117 No protein-ligand interaction detected (PLIP) NCO.8: 3 residues within 4Å: Chain B: C.41, G.42, G.43 No protein-ligand interaction detected (PLIP) NCO.9: 5 residues within 4Å: Chain B: A.57, C.59, G.73, C.75 Ligands: NCO.3 No protein-ligand interaction detected (PLIP) NCO.10: 6 residues within 4Å: Chain B: A.46, C.48, C.50, U.83, A.84, G.85 No protein-ligand interaction detected (PLIP) NCO.11: 6 residues within 4Å: Chain B: G.53, U.54, A.79, G.80, G.81, C.82 No protein-ligand interaction detected (PLIP) NCO.12: 4 residues within 4Å: Chain B: C.62, A.63, G.64, C.65 No protein-ligand interaction detected (PLIP)

1 x SAM: S-ADENOSYLMETHIONINE(Non-functional Binders)

SAM.13: 11 residues within 4Å: Chain B: U.7, C.8, G.11, A.45, A.46, C.47, U.89, G.90, C.91, U.120, G.121 No protein-ligand interaction detected (PLIP)

13 x MG: MAGNESIUM ION(Non-functional Binders)

MG.14: 3 residues within 4Å: Chain B: G.13, G.42, C.92 No protein-ligand interaction detected (PLIP) MG.15: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.16: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.17: 1 residues within 4Å: Chain B: A.36 No protein-ligand interaction detected (PLIP) MG.18: 3 residues within 4Å: Chain B: G.100, C.101, A.102 No protein-ligand interaction detected (PLIP) MG.19: 1 residues within 4Å: Chain B: G.1 No protein-ligand interaction detected (PLIP) MG.20: 1 residues within 4Å: Chain B: G.19 No protein-ligand interaction detected (PLIP) MG.21: 2 residues within 4Å: Chain B: U.83, A.84 No protein-ligand interaction detected (PLIP) MG.22: 2 residues within 4Å: Chain B: C.104, G.105 No protein-ligand interaction detected (PLIP) MG.23: 1 residues within 4Å: Chain B: A.117 No protein-ligand interaction detected (PLIP) MG.24: 3 residues within 4Å: Chain B: G.18, G.19, G.35 No protein-ligand interaction detected (PLIP) MG.25: 1 residues within 4Å: Chain B: G.114 No protein-ligand interaction detected (PLIP) MG.26: 1 residues within 4Å: Chain B: C.3 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Baird, N.J. et al., YbxF and YlxQ are bacterial homologs of L7Ae and bind K-turns but not K-loops. Rna (2012)

Release Date

2012-03-07

Peptides

Ribosome-associated protein L7Ae-like: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Ribosome-associated protein L7Ae-like

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