SMTL ID : 8ctz.1

12-mer DNA structure of ExBIM & O6Me-G bound to RNase-H

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.32 Å

Oligo State

homo-trimer

Ligands

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 5 residues within 4Å: Chain A: L.63, K.67, Y.120, E.121, T.122 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.63, A:K.67, A:E.121, A:T.122 GOL.6: 5 residues within 4Å: Chain B: H.61, R.64, Y.65, E.68 Ligands: EDO.8 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.64, B:E.68 GOL.10: 9 residues within 4Å: Chain C: G.2 Chain D: G.10, C.11, G.12 Chain E: N.78, S.79, Q.80, T.81, K.126 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:Q.80, E:K.126 GOL.11: 2 residues within 4Å: Chain E: D.88, K.90 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:D.88

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

ACT.2: 4 residues within 4Å: Chain A: R.64, E.68, W.114, H.118 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.68 Salt bridges: A:R.64 ACT.7: 1 residues within 4Å: Chain B: E.110 No protein-ligand interaction detected (PLIP)

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

EDO.3: 2 residues within 4Å: Chain A: D.109, E.112 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.109, A:D.109 EDO.8: 5 residues within 4Å: Chain B: R.43, V.60, H.61, R.64 Ligands: GOL.6 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.64 EDO.12: 6 residues within 4Å: Chain E: Y.29, L.57, V.60, H.61, R.64, A.111 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:R.64

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

NA.4: 5 residues within 4Å: Chain A: D.17, V.18, E.134 Chain D: T.8, X.9 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.18

2 x K: POTASSIUM ION(Non-covalent)

K.5: 1 residues within 4Å: Chain A: Y.120 No protein-ligand interaction detected (PLIP) K.9: 4 residues within 4Å: Chain B: T.81 Chain C: C.11, G.12 Chain D: G.2 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kellum Jr., A.H. et al., Conformation and Pairing Properties of an O 6 -Methyl-2'-deoxyguanosine-Directed Benzimidazole Nucleoside Analog in Duplex DNA. Chem.Res.Toxicol. (2022)

Release Date

2022-08-31

Peptides

Ribonuclease H: ABE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
B

E
A

Ribonuclease H

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