SMTL ID : 6lrd.1

Structure of RecJ complexed with a 5'-P-dSpacer-modified ssDNA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

1 x 3DR- DT- DT- DT- DT- DT: DNA (5'-D(P*(3DR)P*TP*TP*TP*TP*T)-3')(Non-covalent)

3DR-DT-DT-DT-DT-DT.1: 43 residues within 4Å: Chain A: D.79, Y.80, D.81, R.109, Y.114, D.135, H.159, A.222, D.223, V.224, K.257, A.268, F.269, P.273, R.274, N.276, R.280, N.310, R.313, R.314, A.344, G.345, V.346, M.347, G.348, I.349, K.353, E.356, K.369, G.370, S.371, R.373, R.393, F.394, G.395, G.396, H.397, A.400, A.401, G.402, F.403 Ligands: MN.3, MN.4 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.80, A:R.109, A:M.347, A:G.348, A:S.371 Water bridges: A:R.109

1 x ASP- LEU- PRO- PHE: ASP-LEU-PRO-PHE(Non-covalent)

ASP-LEU-PRO-PHE.2: 10 residues within 4Å: Chain A: P.553, M.557, V.572, Y.575, L.576, Y.600, G.627, P.628, K.629, T.630 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:P.553, A:V.572, A:Y.575, A:Y.575, A:L.576, A:Y.600, A:Y.600 Hydrogen bonds: A:K.629 Salt bridges: A:K.629

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

MN.3: 6 residues within 4Å: Chain A: D.83, D.135, H.159, D.223 Ligands: 3DR-DT-DT-DT-DT-DT.1, MN.4 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.83, A:D.135, A:H.159, A:D.223, H2O.2 MN.4: 5 residues within 4Å: Chain A: D.79, D.81, D.135 Ligands: 3DR-DT-DT-DT-DT-DT.1, MN.3 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.79, A:D.81, A:D.81, A:D.135, H2O.2

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

SO4.5: 4 residues within 4Å: Chain A: P.294, S.295, D.296, H.297 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.295, A:D.296, A:D.296, A:H.297 Salt bridges: A:H.297 SO4.6: 3 residues within 4Å: Chain A: P.438, V.439, W.663 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:V.439 Water bridges: A:L.437, A:A.440, A:R.468, A:W.663 SO4.7: 4 residues within 4Å: Chain A: G.163, E.164, R.385, R.388 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.164 Salt bridges: A:R.385, A:R.388 SO4.8: 3 residues within 4Å: Chain A: R.432, A.539, G.540 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.540 Salt bridges: A:R.432

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cheng, K. et al., Participation of RecJ in the base excision repair pathway of Deinococcus radiodurans. Nucleic Acids Res. (2020)

Release Date

2020-08-26

Peptides

Single-stranded-DNA-specific exonuclease: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Single-stranded-DNA-specific exonuclease

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