SMTL ID : 7r97.1

Crystal structure of postcleavge complex of Escherichia coli RNase III

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

6 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: E.41, E.117 Chain C: A.1 Ligands: MG.2, MG.21 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.41, A:E.117, H2O.1, H2O.3 MG.2: 5 residues within 4Å: Chain A: D.45, E.117 Chain C: A.1 Chain D: U.28 Ligands: MG.1 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.45, A:E.117, H2O.2, H2O.15 MG.12: 5 residues within 4Å: Chain B: E.41, E.117 Chain D: A.1 Ligands: MG.13, MG.27 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.41, B:E.117, H2O.7, H2O.15 MG.13: 5 residues within 4Å: Chain B: D.45, E.117 Chain C: U.28 Chain D: A.1 Ligands: MG.12 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.45, B:E.117, H2O.8, H2O.12 MG.21: 4 residues within 4Å: Chain A: E.41 Chain C: A.1, A.2 Ligands: MG.1 No protein-ligand interaction detected (PLIP) MG.27: 4 residues within 4Å: Chain B: E.41 Chain D: A.1, A.2 Ligands: MG.12 No protein-ligand interaction detected (PLIP)

7 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 2 residues within 4Å: Chain A: R.8, R.11 Ligand excluded by PLIP CL.4: 3 residues within 4Å: Chain A: F.60, P.61, R.62 Ligand excluded by PLIP CL.5: 2 residues within 4Å: Chain A: R.208 Chain C: C.22 Ligand excluded by PLIP CL.6: 6 residues within 4Å: Chain A: W.139, Y.140, Q.141, T.142, R.143 Ligands: EDO.10 Ligand excluded by PLIP CL.14: 2 residues within 4Å: Chain B: F.188, R.208 Ligand excluded by PLIP CL.15: 4 residues within 4Å: Chain B: R.86, E.89, L.90, G.91 Ligand excluded by PLIP CL.16: 3 residues within 4Å: Chain B: F.60, P.61, R.62 Ligand excluded by PLIP

14 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.7: 8 residues within 4Å: Chain A: V.5, R.8, L.9, K.12, F.88, E.89, E.92, C.93 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.88 Water bridges: A:R.8, A:E.92 EDO.8: 7 residues within 4Å: Chain A: K.157, Y.174, R.208, R.209, E.212 Chain D: U.24, U.25 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.157, A:R.208 Water bridges: A:R.209, A:R.209 EDO.9: 3 residues within 4Å: Chain A: R.59, Q.141, D.145 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.59, A:R.59, A:Q.141 EDO.10: 7 residues within 4Å: Chain A: L.84, E.87, F.88, N.138, W.139, R.143 Ligands: CL.6 No protein-ligand interaction detected (PLIP) EDO.11: 6 residues within 4Å: Chain A: R.77, G.78, N.79, E.109 Chain D: A.27, U.28 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.77, A:N.79 EDO.17: 7 residues within 4Å: Chain B: M.1, N.2, V.5, I.6, L.27, C.93, R.95 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.2, B:R.95, B:R.95 EDO.18: 5 residues within 4Å: Chain B: K.157, Y.174, R.208, E.212 Chain C: U.25 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.157, B:R.208, B:R.208 Water bridges: B:R.209 EDO.19: 4 residues within 4Å: Chain B: L.94, R.95, L.96, L.101 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.96 Water bridges: B:L.94 EDO.20: 3 residues within 4Å: Chain B: Y.163, R.167, L.225 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.167 EDO.24: 7 residues within 4Å: Chain B: Q.161, E.162, A.165, L.171 Chain C: G.4, G.5, U.24 No protein-ligand interaction detected (PLIP) EDO.25: 7 residues within 4Å: Chain C: U.6, C.7, A.8, U.9, G.18, U.19, G.20 No protein-ligand interaction detected (PLIP) EDO.26: 4 residues within 4Å: Chain A: S.207, K.210 Chain C: G.21, C.22 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.207, A:K.210, A:K.210 EDO.30: 5 residues within 4Å: Chain D: G.4, G.5, U.6 Ligands: K.28, EDO.31 No protein-ligand interaction detected (PLIP) EDO.31: 9 residues within 4Å: Chain D: A.3, G.4, G.5, U.6, G.21, C.22, C.23 Ligands: K.28, EDO.30 No protein-ligand interaction detected (PLIP)

2 x K: POTASSIUM ION(Non-functional Binders)

K.22: 5 residues within 4Å: Chain C: G.5, U.6, G.20, G.21, C.22 No protein-ligand interaction detected (PLIP) K.28: 7 residues within 4Å: Chain D: G.5, U.6, G.20, G.21, C.22 Ligands: EDO.30, EDO.31 No protein-ligand interaction detected (PLIP)

2 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.23: 3 residues within 4Å: Chain C: C.11, G.12, A.14 No protein-ligand interaction detected (PLIP) TRS.29: 3 residues within 4Å: Chain D: C.11, G.12, A.14 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dharavath, S. et al., Structural basis for Dicer-like function of an engineered RNase III variant and insights into the reaction trajectory of two-Mg 2+ -ion catalysis. Rna Biol. (2022)

Release Date

2022-07-20

Peptides

Ribonuclease 3: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Ribonuclease 3