SMTL ID : 2qk9.1

Human RNase H catalytic domain mutant D210N in complex with 18-mer RNA/DNA hybrid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.55 Å

Oligo State

monomer

Ligands

7 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 4 residues within 4Å: Chain A: C.8, A.9 Chain B: T.10 Ligands: 16D.4 No protein-ligand interaction detected (PLIP) SO4.2: 4 residues within 4Å: Chain A: G.13, A.14 Chain B: C.6, A.7 No protein-ligand interaction detected (PLIP) SO4.3: 2 residues within 4Å: Chain B: T.12, C.13 No protein-ligand interaction detected (PLIP) SO4.7: 4 residues within 4Å: Chain C: R.25, R.43, S.152, E.153 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.153 Salt bridges: C:R.25, C:R.43 SO4.8: 3 residues within 4Å: Chain A: C.10, C.11 Chain C: H.132 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:H.132 SO4.9: 3 residues within 4Å: Chain B: G.8, G.9 Chain C: R.21 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:R.21 SO4.10: 3 residues within 4Å: Chain C: S.18, R.21, R.22 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:S.18, C:S.18, C:R.22 Water bridges: C:R.23, C:R.23 Salt bridges: C:R.21, C:R.22

1 x 16D: HEXANE-1,6-DIAMINE(Non-functional Binders)

16D.4: 5 residues within 4Å: Chain A: A.7 Chain B: T.10, G.11, T.12 Ligands: SO4.1 No protein-ligand interaction detected (PLIP)

1 x NA: SODIUM ION(Non-functional Binders)

NA.5: 6 residues within 4Å: Chain A: A.9, C.10 Chain C: D.13, G.14, E.54, N.78 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:D.13, C:N.78 Water bridges: C:S.79

1 x FLC: CITRATE ANION(Non-covalent)

FLC.6: 4 residues within 4Å: Chain C: V.40, G.41, E.147, Q.151 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:G.41, C:G.41, C:Q.151

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.11: 6 residues within 4Å: Chain C: R.47, R.52, I.107, N.108, E.110, D.111 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:R.47, C:R.47, C:N.108, C:E.110, C:D.111 Water bridges: C:R.47 GOL.12: 4 residues within 4Å: Chain C: H.56, C.59, K.60, E.63 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:H.56, C:K.60, C:K.60

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nowotny, M. et al., Structure of Human RNase H1 Complexed with an RNA/DNA Hybrid: Insight into HIV Reverse Transcription. Mol.Cell (2007)

Release Date

2007-11-13

Peptides

Ribonuclease H1: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
A

Ribonuclease H1

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