SMTL ID : 6dp8.1

Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hybrid: Reaction in 5 mM Mg2+ and 200 mM Li+ for 240 s at 21 C

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.32 Å

Oligo State

monomer

Ligands

1 x A- C- A- U: RNA (5'-R(*AP*CP*AP*U)-3')(Non-covalent)

A-C-A-U.1: 17 residues within 4Å: Chain A: D.17, N.51, E.55, D.78, S.79, Q.80, T.81, K.126, T.129 Ligands: C-G.2, DC-DG-DA-DT-DG-DT.3, DC-DG-DA-DT-DG-DT.3, DC-DG-DA-DT-DG-DT.3, DC-DG-DA-DT-DG-DT.3, MG.4, LI.5, EDO.19 Protein-ligand interaction information (PLIP) not available

1 x C- G: RNA (5'-R(P*CP*G)-3')(Non-covalent)

C-G.2: 18 residues within 4Å: Chain A: D.17, V.18, G.19, S.20, Q.21, G.22, N.23, N.51, D.138, Y.139 Ligands: A-C-A-U.1, DC-DG-DA-DT-DG-DT.3, DC-DG-DA-DT-DG-DT.3, DC-DG-DA-DT-DG-DT.3, MG.4, LI.5, GOL.10, MG.20 Protein-ligand interaction information (PLIP) not available

1 x DC- DG- DA- DT- DG- DT: DNA (5'-D(*CP*GP*AP*TP*GP*T)-3')(Non-covalent)

DC-DG-DA-DT-DG-DT.3: 22 residues within 4Å: Chain A: N.23, P.24, T.50, N.51, N.52, M.53, Q.80, T.81, K.84, W.85, K.92, S.93, T.94, L.95 Ligands: A-C-A-U.1, A-C-A-U.1, A-C-A-U.1, A-C-A-U.1, C-G.2, C-G.2, GOL.10, EDO.17 Protein-ligand interaction information (PLIP) not available

2 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 6 residues within 4Å: Chain A: D.17, I.135, D.138, Y.139 Ligands: A-C-A-U.1, C-G.2 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.17, A:D.138, H2O.1, H2O.2 MG.20: 3 residues within 4Å: Chain A: G.140 Ligands: C-G.2, C-G.2 No protein-ligand interaction detected (PLIP)

1 x LI: LITHIUM ION(Non-covalent)

LI.5: 7 residues within 4Å: Chain A: D.17, V.18, E.55, D.78, S.79 Ligands: A-C-A-U.1, C-G.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.17, A:E.55, A:D.78

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

CL.6: 5 residues within 4Å: Chain A: Y.29, R.43, L.57, L.107 Ligands: GOL.15 Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain A: Q.80, I.83, K.126 Ligand excluded by PLIP CL.8: 4 residues within 4Å: Chain A: I.10, P.74, P.123, L.125 Ligand excluded by PLIP

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 5 residues within 4Å: Chain A: H.61, R.64, Y.65, E.68, R.69 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.64, A:R.64, A:R.69 GOL.10: 6 residues within 4Å: Chain A: G.22, N.23, P.24 Ligands: C-G.2, DC-DG-DA-DT-DG-DT.3, DC-DG-DA-DT-DG-DT.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.23, A:N.23, A:P.24 GOL.15: 7 residues within 4Å: Chain A: Y.29, L.57, H.61, R.64, L.107, A.111 Ligands: CL.6 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.29 Water bridges: A:R.64, A:R.64

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

EDO.11: 3 residues within 4Å: Chain A: K.89, T.119, Y.120 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.89, A:Y.120, A:Y.120 EDO.14: 3 residues within 4Å: Chain A: R.43, L.103, L.107 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.43, A:R.43 EDO.16: 6 residues within 4Å: Chain A: L.40, Y.65, L.66, R.69, S.71, K.73 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.73 Water bridges: A:D.33, A:D.33 EDO.17: 4 residues within 4Å: Chain A: T.94 Ligands: DC-DG-DA-DT-DG-DT.3, DC-DG-DA-DT-DG-DT.3, DC-DG-DA-DT-DG-DT.3 No protein-ligand interaction detected (PLIP) EDO.18: 6 residues within 4Å: Chain A: S.93, T.94, L.95, V.96, R.97, W.105 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.97 EDO.19: 1 residues within 4Å: Ligands: A-C-A-U.1 No protein-ligand interaction detected (PLIP)

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.12: 6 residues within 4Å: Chain A: P.24, L.95, V.96, N.98, E.100, T.101 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.98 PEG.13: 3 residues within 4Å: Chain A: V.96, R.97, N.98 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Samara, N.L. et al., Cation trafficking propels RNA hydrolysis. Nat. Struct. Mol. Biol. (2018)

Release Date

2018-08-15

Peptides

Ribonuclease H: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Ribonuclease H

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