SMTL ID : 8sv4.1

7-Deazapurines and 5-Halogenpyrimidine DNA duplex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

monomer

Ligands

1 x FWN: 2-[2-(2-ethoxyethoxy)ethoxy]ethanol(Non-covalent)

FWN.1: 5 residues within 4Å: Chain A: H.61, R.64, E.68, R.69 Ligands: SO4.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.61, A:R.64, A:R.69 Water bridges: A:H.61

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.2: 5 residues within 4Å: Chain A: N.52, E.55, S.79 Chain C: G.10, C.11 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:E.55 Hydrogen bonds: A:N.52 Water bridges: A:N.51 ACT.3: 3 residues within 4Å: Chain A: R.64, E.68, W.114 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.68 Water bridges: A:H.118 Salt bridges: A:R.64, A:H.118

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

SO4.4: 6 residues within 4Å: Chain A: Y.29, R.43, L.57, H.61, L.107 Ligands: FWN.1 6 PLIP interactions: 6 interactions with chain A Water bridges: A:L.57, A:H.61, A:H.61, A:H.61 Salt bridges: A:R.43, A:H.61 SO4.5: 3 residues within 4Å: Chain A: K.67, H.118, T.119 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.119, A:T.119 Salt bridges: A:K.67

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

EDO.6: 3 residues within 4Å: Chain A: Q.21, I.26, P.45 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pallan, P.S. et al., Conformational Morphing by a DNA Analogue Featuring 7-Deazapurines and 5-Halogenpyrimidines and the Origins of Adenine-Tract Geometry. Biochemistry (2023)

Release Date

2023-10-04

Peptides

Ribonuclease H: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Ribonuclease H

Related Entries With Identical Sequence