- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.68 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)
- 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)
- 1 x DC- DG- DA- DT- DG- DT: DNA (5'-D(*CP*GP*AP*TP*GP*T)-3')(Non-covalent)
- 2 x MG: MAGNESIUM ION(Non-covalent)
- 6 x RB: RUBIDIUM ION(Non-covalent)(Non-functional Binders)
RB.6: 8 residues within 4Å:- Chain A: D.138, Y.139, G.140, R.141, A.142
- Ligands: C-G.2, MG.4, RB.8
2 PLIP interactions:2 interactions with chain A- Metal complexes: A:D.138, A:Y.139
RB.7: 5 residues within 4Å:- Chain A: D.78, T.129, E.134
- Ligands: A-C-A-U.1, C-G.2
No protein-ligand interaction detected (PLIP)RB.8: 4 residues within 4Å:- Chain A: E.134, D.138, A.142
- Ligands: RB.6
2 PLIP interactions:1 interactions with chain A, 1 Ligand-Water interactions- Metal complexes: A:D.138, H2O.3
RB.9: 2 residues within 4Å:- Chain A: K.67, N.70
3 PLIP interactions:1 interactions with chain A, 2 Ligand-Water interactions- Metal complexes: A:K.67, H2O.5, H2O.5
RB.19: 2 residues within 4Å:- Ligands: A-C-A-U.1, DC-DG-DA-DT-DG-DT.3
No protein-ligand interaction detected (PLIP)RB.20: 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)
- 4 x GOL: GLYCEROL(Non-functional Binders)
GOL.13: 6 residues within 4Å:- Chain A: H.61, R.64, Y.65, E.68, R.69
- Ligands: GOL.15
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:R.69, A:R.69
- Water bridges: A:R.64
GOL.14: 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.15: 4 residues within 4Å:- Chain A: H.61, R.64
- Ligands: CL.10, GOL.13
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:R.64
- Water bridges: A:Y.29, A:Y.29, A:H.61
GOL.21: 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
- 4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
EDO.16: 4 residues within 4Å:- Chain A: K.89, H.118, T.119, Y.120
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:Y.120
EDO.17: 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:T.122
EDO.18: 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.22: 3 residues within 4Å:- Chain A: T.94
- Ligands: DC-DG-DA-DT-DG-DT.3, DC-DG-DA-DT-DG-DT.3
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:T.94
- 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
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.68 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)
- 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)
- 1 x DC- DG- DA- DT- DG- DT: DNA (5'-D(*CP*GP*AP*TP*GP*T)-3')(Non-covalent)
- 2 x MG: MAGNESIUM ION(Non-covalent)
- 6 x RB: RUBIDIUM ION(Non-covalent)(Non-functional Binders)
- 3 x CL: CHLORIDE ION(Non-functional Binders)
- 4 x GOL: GLYCEROL(Non-functional Binders)
- 4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 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