SMTL ID : 6dpi.1

Crystal Structure of Bacillus Halodurans Ribonuclease H1 K196A in Complex with an RNA/DNA Hybrid: Reaction in 10 mM Mg2+ and 200 mM Rb+ for 40 s at 21 C

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.35 Å

Oligo State

monomer

Ligands

1 x A- C- A- U: 5'-R(*AP*CP*AP*U)-3' portion of intact RNA (5'-R(*AP*CP*AP*UP*CP*G)-3')(Non-covalent)

A-C-A-U.1: 15 residues within 4Å: Chain A: N.51, E.55, D.78, S.79, Q.80, T.81, K.126, W.127, 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.5 Protein-ligand interaction information (PLIP) not available

1 x C- G: 5'-R(P*CP*G)-3' portion of intact RNA (5'-R(*AP*CP*AP*UP*CP*G)-3')(Non-covalent)

C-G.2: 20 residues within 4Å: Chain A: D.17, V.18, G.19, S.20, Q.21, G.22, N.23, N.51, E.55, D.78, Y.139, R.141, A.142 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, MG.5, RB.6 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: 23 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.11, RB.17, EDO.18 Protein-ligand interaction information (PLIP) not available

2 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 5 residues within 4Å: Chain A: D.17, D.138, Y.139 Ligands: C-G.2, MG.5 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.17, A:D.138, H2O.1, H2O.2, H2O.3 MG.5: 7 residues within 4Å: Chain A: D.17, V.18, E.55, D.78 Ligands: A-C-A-U.1, C-G.2, MG.4 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.17, A:E.55, A:E.55, A:D.78, A:D.78

3 x RB: RUBIDIUM ION(Non-covalent)(Non-functional Binders)

RB.6: 6 residues within 4Å: Chain A: D.138, Y.139, G.140, R.141, A.142 Ligands: C-G.2 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:Y.139, H2O.1, H2O.2 RB.7: 2 residues within 4Å: Chain A: K.67, N.70 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:K.67, H2O.4, H2O.5, H2O.5, H2O.6 RB.17: 2 residues within 4Å: Ligands: DC-DG-DA-DT-DG-DT.3, DC-DG-DA-DT-DG-DT.3 No protein-ligand interaction detected (PLIP)

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

CL.8: 5 residues within 4Å: Chain A: Y.29, R.43, L.57, L.107 Ligands: GOL.14 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain A: Q.80, I.83, K.126 Ligand excluded by PLIP CL.10: 4 residues within 4Å: Chain A: I.10, P.74, P.123, L.125 Ligand excluded by PLIP

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.11: 5 residues within 4Å: Chain A: G.22, N.23, P.24 Ligands: 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.12: 6 residues within 4Å: Chain A: H.61, R.64, Y.65, E.68, R.69 Ligands: GOL.14 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.64, A:R.64, A:R.69, A:R.69 GOL.13: 7 residues within 4Å: Chain A: D.33, L.40, Y.65, L.66, R.69, S.71, K.73 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.33, A:D.33, A:S.71, A:K.73 Water bridges: A:Y.65 GOL.14: 5 residues within 4Å: Chain A: Y.29, H.61, R.64 Ligands: CL.8, GOL.12 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.64 Water bridges: A:Y.29, A:R.43, A:H.61

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

EDO.15: 3 residues within 4Å: Chain A: K.89, T.119, Y.120 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.120 Water bridges: A:Y.120 EDO.16: 2 residues within 4Å: Chain A: R.72, E.121 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.72 Water bridges: A:E.121 EDO.18: 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)

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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