SMTL ID : 6dp6.1

Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hybrid: Reaction in 80 mM Mg2+ and 75 mM K+ for 40 s at 21 C

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

monomer

Ligands

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

A-C-A-U.1: 16 residues within 4Å: Chain A: N.51, E.55, D.78, S.79, Q.80, T.81, K.126, T.129, D.130 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, K.7 Protein-ligand interaction information (PLIP) not available

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

C-G.2: 22 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, D.138, Y.139, R.141, K.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, K.6, K.7 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: 20 residues within 4Å: Chain A: N.23, P.24, T.50, N.51, N.52, M.53, 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, K.14 Protein-ligand interaction information (PLIP) not available

2 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 8 residues within 4Å: Chain A: D.17, D.138, Y.139, K.142 Ligands: C-G.2, C-G.2, MG.5, K.6 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.17, A:D.138, H2O.1, H2O.1, H2O.2 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 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.17, A:E.55, A:D.78, A:D.78

3 x K: POTASSIUM ION(Non-covalent)(Non-functional Binders)

K.6: 8 residues within 4Å: Chain A: D.138, Y.139, G.140, R.141, K.142 Ligands: C-G.2, C-G.2, MG.4 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.138, H2O.2, H2O.5 K.7: 6 residues within 4Å: Chain A: D.78, T.129, E.134, K.142 Ligands: A-C-A-U.1, C-G.2 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.134, H2O.5 K.14: 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)

4 x IOD: IODIDE ION(Non-functional Binders)

IOD.8: 4 residues within 4Å: Chain A: Y.29, R.43, L.57, L.107 Ligand excluded by PLIP IOD.9: 3 residues within 4Å: Chain A: Q.80, I.83, K.126 Ligand excluded by PLIP IOD.10: 4 residues within 4Å: Chain A: I.10, P.74, P.123, L.125 Ligand excluded by PLIP IOD.11: 2 residues within 4Å: Chain A: K.67, H.118 Ligand excluded by PLIP

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

EDO.12: 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:Y.65, A:Y.65, A:S.71 EDO.13: 5 residues within 4Å: Chain A: H.61, R.64, Y.65, E.68, R.69 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.69, A:R.69

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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