SMTL ID : 6dp9.1

Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA Hybrid: Reaction in 2 mM Mn2+ and 200 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: RNA (5'-R(*AP*CP*AP*U)-3')(Non-covalent)

A-C-A-U.1: 16 residues within 4Å: Chain A: N.45, E.49, D.72, S.73, Q.74, T.75, K.120, W.121, T.123 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, MN.5, K.6 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.11, V.12, G.13, S.14, Q.15, G.16, N.17, N.45, E.49, D.72 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, MN.4, MN.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: 22 residues within 4Å: Chain A: N.17, P.18, T.44, N.45, N.46, M.47, Q.74, T.75, K.78, W.79, K.86, S.87, T.88, L.89 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.12, K.18 Protein-ligand interaction information (PLIP) not available

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

MN.4: 7 residues within 4Å: Chain A: D.11, D.132, Y.133 Ligands: C-G.2, MN.5, K.6, K.7 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.11, A:D.132, H2O.2, H2O.3 MN.5: 8 residues within 4Å: Chain A: D.11, V.12, E.49, D.72 Ligands: A-C-A-U.1, C-G.2, MN.4, K.6 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.11, A:E.49, A:D.72, A:D.72

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

K.6: 8 residues within 4Å: Chain A: D.11, V.12, E.49, D.72 Ligands: A-C-A-U.1, C-G.2, MN.4, MN.5 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.11, A:E.49, A:D.72, A:D.72, H2O.2 K.7: 8 residues within 4Å: Chain A: D.11, V.12, G.13, D.132, Y.133 Ligands: C-G.2, C-G.2, MN.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.11, A:D.11, A:V.12, H2O.3 K.18: 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.23, R.37, L.51, L.101 Ligand excluded by PLIP IOD.9: 3 residues within 4Å: Chain A: Q.74, I.77, K.120 Ligand excluded by PLIP IOD.10: 2 residues within 4Å: Chain A: K.61, H.112 Ligand excluded by PLIP IOD.11: 4 residues within 4Å: Chain A: I.4, P.68, P.117, L.119 Ligand excluded by PLIP

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.12: 5 residues within 4Å: Chain A: G.16, N.17, P.18 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.17, A:N.17, A:P.18 GOL.13: 6 residues within 4Å: Chain A: H.55, R.58, Y.59, E.62, R.63 Ligands: GOL.15 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.63, A:R.63 Water bridges: A:E.62 GOL.14: 6 residues within 4Å: Chain A: L.34, Y.59, L.60, R.63, S.65, K.67 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.65, A:K.67 Water bridges: A:D.27, A:K.67 GOL.15: 3 residues within 4Å: Chain A: H.55, R.58 Ligands: GOL.13 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.55, A:R.58 Water bridges: A:Y.23, A:H.55

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

EDO.16: 3 residues within 4Å: Chain A: K.83, T.113, Y.114 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.83, A:Y.114 Water bridges: A:Y.114 EDO.17: 1 residues within 4Å: Chain A: K.29 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.29

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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