SMTL ID : 2xo6.1

DEINOCOCCUS RADIODURANS ISDRA2 TRANSPOSASE Y132F MUTANT COMPLEXED WITH LEFT END RECOGNITION AND CLEAVAGE SITE

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*G)-3'(Non-covalent)

DT-DT-DG-DA-DT-DG.1: 22 residues within 4Å: Chain A: H.23, 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 B: G.2, C.3, A.4, C.5, A.6, C.7 Chain C: F.132, Q.136 Ligands: CD.3 28 PLIP interactions: 13 interactions with chain A, 15 interactions with chain C Hydrogen bonds: A:Y.30, A:L.111, A:W.112, A:N.113, A:S.115, C:K.12, C:K.12, C:R.14, C:R.14, C:Y.16, C:Y.16, C:Q.77 Water bridges: A:Y.30, A:R.93, A:P.114, A:P.114, C:R.14, C:R.14, C:R.14, C:G.15, C:G.15 Salt bridges: A:K.29, A:K.29, A:K.88, A:R.93, C:R.14 Hydrophobic interactions: C:R.14, C:Y.16 DT-DT-DG-DA-DT-DG.2: 24 residues within 4Å: Chain A: L.8, M.10, V.17, F.132, Q.136 Chain C: H.23, 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: C.3, A.4, C.5, A.6, C.7 Ligands: CD.12 Protein-ligand interaction information (PLIP) not available

9 x CD: CADMIUM ION(Non-covalent)(Non-functional Binders)

CD.3: 5 residues within 4Å: Chain A: H.67, H.69 Chain C: Q.136 Ligands: DT-DT-DG-DA-DT-DG.1, DT-DT-DG-DA-DT-DG.1 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.67, A:H.69, H2O.12 CD.4: 3 residues within 4Å: Chain A: P.114 Chain B: C.21 Ligands: MG.8 6 PLIP interactions: 6 Ligand-Water interactions Metal complexes: H2O.7, H2O.7, H2O.7, H2O.7, H2O.7, H2O.7 CD.5: 2 residues within 4Å: Chain A: D.41 Ligands: MG.9 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.41, H2O.2, H2O.2 CD.6: 1 residues within 4Å: Chain A: D.66 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.66, A:D.66, H2O.1 CD.7: 5 residues within 4Å: Chain A: P.7, L.8, E.9, E.123 Ligands: MG.10 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.9, A:E.9, A:E.123 CD.12: 6 residues within 4Å: Chain A: Q.136 Chain C: M.64, H.67, H.69 Ligands: DT-DT-DG-DA-DT-DG.2, DT-DT-DG-DA-DT-DG.2 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.67, C:H.69, H2O.16 CD.13: 4 residues within 4Å: Chain C: P.114 Chain D: C.21, A.22 Ligands: MG.19 6 PLIP interactions: 6 Ligand-Water interactions Metal complexes: H2O.14, H2O.14, H2O.15, H2O.15, H2O.15, H2O.15 CD.14: 3 residues within 4Å: Chain C: D.45, D.49 Ligands: MG.15 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:D.45, C:D.49, H2O.10, H2O.10, H2O.10 CD.18: 2 residues within 4Å: Chain D: T.16 Ligands: MG.20 No protein-ligand interaction detected (PLIP)

8 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.8: 3 residues within 4Å: Chain A: P.114 Chain B: C.21 Ligands: CD.4 6 PLIP interactions: 6 Ligand-Water interactions Metal complexes: H2O.7, H2O.7, H2O.7, H2O.7, H2O.7, H2O.7 MG.9: 2 residues within 4Å: Chain A: D.41 Ligands: CD.5 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.41, H2O.2, H2O.2 MG.10: 5 residues within 4Å: Chain A: P.7, L.8, E.9, E.123 Ligands: CD.7 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.9, A:E.9, A:E.123 MG.11: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.15: 3 residues within 4Å: Chain C: D.45, D.49 Ligands: CD.14 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:D.45, C:D.49, H2O.10, H2O.10, H2O.10 MG.17: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.19: 4 residues within 4Å: Chain C: P.114 Chain D: C.21, A.22 Ligands: CD.13 6 PLIP interactions: 6 Ligand-Water interactions Metal complexes: H2O.14, H2O.14, H2O.15, H2O.15, H2O.15, H2O.15 MG.20: 2 residues within 4Å: Chain D: T.16 Ligands: CD.18 No protein-ligand interaction detected (PLIP)

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

ACT.16: 1 residues within 4Å: Chain C: W.107 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:W.107

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