SMTL ID : 6vtd.1

Naegleria gruberi RNA ligase R149A mutant with ATP and Mn

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

monomer

Ligands

1 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1: 19 residues within 4Å: Chain A: K.122, T.146, D.147, Q.148, T.169, V.170, K.171, L.172, S.176, R.191, E.228, F.249, V.282, V.316, K.318, K.327 Ligands: MN.2, MN.3, MN.4 22 PLIP interactions: 22 interactions with chain A Hydrogen bonds: A:T.146, A:T.146, A:D.147, A:Q.148, A:T.169, A:T.169, A:K.171, A:L.172, A:S.176, A:S.176, A:R.191, A:K.318 Water bridges: A:K.122, A:K.171, A:D.173 Salt bridges: A:K.122, A:K.171, A:K.171, A:R.191, A:K.327, A:K.327 pi-Stacking: A:F.249

3 x MN: MANGANESE (II) ION(Non-covalent)(Non-functional Binders)

MN.2: 4 residues within 4Å: Chain A: D.147, Q.148, K.327 Ligands: ATP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.147 MN.3: 3 residues within 4Å: Chain A: D.173, E.228 Ligands: ATP.1 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.173, H2O.1, H2O.1 MN.4: 1 residues within 4Å: Ligands: ATP.1 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Unciuleac, M.C. et al., Caveat mutator: alanine substitutions for conserved amino acids in RNA ligase elicit unexpected rearrangements of the active site for lysine adenylylation. Nucleic Acids Res. (2020)

Release Date

2020-04-08

Peptides

RNA Ligase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

RNA Ligase

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