SMTL ID : 2xqc.1

DEINOCOCCUS RADIODURANS ISDRA2 TRANSPOSASE COMPLEXED WITH LEFT END RECOGNITION AND CLEAVAGE SITE AND ZN

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 x DT- DT- DG- DA- DT- DG: 5'-D(TP*TP*GP*AP*TP*GP)-3'(Non-covalent)

DT-DT-DG-DA-DT-DG.1: 24 residues within 4Å: Chain A: I.25, C.27, Y.30, R.31, H.32, H.67, H.69, K.105, L.106, W.107, G.108, C.117 Chain B: G.2, C.3, A.4, C.5, A.6, C.7 Chain C: Y.132, I.133, Q.136, H.137 Ligands: ZN.3, ZN.7 28 PLIP interactions: 17 interactions with chain C, 11 interactions with chain A Hydrophobic interactions: C:R.14 Hydrogen bonds: C:R.14, C:R.14, C:Y.16, C:Y.16, C:Q.77, A:Y.30, A:R.93, A:L.111, A:W.112, A:N.113, A:S.115 Water bridges: C:K.12, C:K.12, C:K.12, C:K.12, C:R.14, C:R.14, C:R.14, C:R.14, C:G.15, A:P.114 Salt bridges: C:K.12, C:R.14, A:K.29, A:K.29, A:K.88, A:R.93 DT-DT-DG-DA-DT-DG.2: 25 residues within 4Å: Chain A: V.17, Y.132, Q.136, H.137 Chain C: H.23, I.25, C.27, Y.30, R.31, H.32, H.67, H.69, K.105, L.106, W.107, G.108, C.117, L.119 Chain D: G.2, C.3, A.4, C.5, A.6, C.7 Ligands: ZN.8 Protein-ligand interaction information (PLIP) not available

9 x ZN: ZINC ION(Non-covalent)(Non-functional Binders)

ZN.3: 5 residues within 4Å: Chain A: H.67, H.69 Chain C: H.137 Ligands: DT-DT-DG-DA-DT-DG.1, DT-DT-DG-DA-DT-DG.1 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain A Metal complexes: C:H.137, A:H.67, A:H.69 ZN.4: 2 residues within 4Å: Chain A: P.114 Chain B: C.21 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:P.114, H2O.6, H2O.6, H2O.6, H2O.6 ZN.5: 2 residues within 4Å: Chain A: D.45, D.49 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.45, A:D.45, A:D.49, A:D.49 ZN.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) ZN.7: 1 residues within 4Å: Ligands: DT-DT-DG-DA-DT-DG.1 No protein-ligand interaction detected (PLIP) ZN.8: 5 residues within 4Å: Chain A: H.137 Chain C: H.67, H.69 Ligands: DT-DT-DG-DA-DT-DG.2, DT-DT-DG-DA-DT-DG.2 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C Metal complexes: A:H.137, C:H.67, C:H.69 ZN.9: 1 residues within 4Å: Chain C: D.45 6 PLIP interactions: 1 interactions with chain C, 5 Ligand-Water interactions Metal complexes: C:D.45, H2O.14, H2O.14, H2O.14, H2O.14, H2O.14 ZN.10: 3 residues within 4Å: Chain C: P.114 Chain D: C.21, A.22 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:P.114, H2O.18, H2O.18, H2O.18, H2O.18 ZN.11: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hickman, A.B. et al., DNA Recognition and the Precleavage State During Single-Stranded DNA Transposition in D. Radiodurans. Embo J. (2010)

Release Date

2010-10-13

Peptides

TRANSPOSASE: AC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
D

TRANSPOSASE

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