SMTL ID : 6vt9.1

Naegleria gruberi RNA ligase E227A mutant with ATP and Mn

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.49 Å

Oligo State

monomer

Ligands

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

ATP.1: 21 residues within 4Å: Chain A: R.5, K.122, T.146, D.147, Q.148, R.150, T.169, V.170, K.171, L.172, G.174, S.175, S.176, R.191, A.228, F.249, V.282, V.316, K.318, K.327 Ligands: MN.2 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:Q.148, A:T.169, A:K.171, A:L.172, A:S.176, A:K.318 Water bridges: A:R.191, A:R.191 Salt bridges: A:R.5, A:K.122, A:K.122, A:R.150, A:R.191, A:R.191, A:K.327, A:K.327, A:K.327 pi-Stacking: A:F.249

1 x MN: MANGANESE (II) ION(Non-covalent)

MN.2: 3 residues within 4Å: Chain A: D.147, R.191 Ligands: ATP.1 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.147, H2O.1, H2O.1

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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