SMTL ID : 9gef.1

Experimental localization of metal-binding sites reveals the role of metal ions in the delafloxacin-stabilized Streptococcus pneumoniae topoisomerase IV DNA cleavage complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.62 Å

Oligo State

homo-dimer

Ligands

1 x DT- DG- DT- DG- DG- DA- DT: DNA (5'-D(*TP*GP*TP*GP*GP*AP*T)-3')(Non-covalent)

DT-DG-DT-DG-DG-DA-DT.1: 26 residues within 4Å: Chain A: E.23, G.47, K.48, D.100, R.266, K.276, V.278, Q.279, H.312, H.314, G.315, S.318, A.322, R.325, K.331, T.406, I.408, E.500 Chain C: A.5, T.6, C.7, C.8, A.9, C.10, A.11 Ligands: TE9.21 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.355, A:S.26 Salt bridges: B:R.355

1 x DG- DT- DA- DA- DT- DA- DC: DNA (5'-D(*GP*TP*AP*AP*TP*AP*C)-3')(Non-covalent)

DG-DT-DA-DA-DT-DA-DC.2: 25 residues within 4Å: Chain B: E.23, G.47, K.48, D.100, R.266, K.276, V.278, H.312, H.314, G.315, S.318, A.322, R.325, K.331, T.406, I.408, E.500 Chain D: G.5, T.6, A.7, T.8, T.9, A.10, C.11 Ligands: TE9.22 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:L.2, B:K.48, B:I.408 Hydrogen bonds: B:R.46, B:K.48, B:N.51, B:N.51, B:G.411, B:R.473, B:R.473 Water bridges: B:N.564 Salt bridges: B:K.54, B:K.54, B:H.103, B:R.219, B:R.220, B:K.471

4 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.3: 5 residues within 4Å: Chain A: R.609, L.616, L.660, R.664 Ligands: MPD.10 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.616 MPD.10: 5 residues within 4Å: Chain A: I.620, R.664, N.667, L.673 Ligands: MPD.3 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.673 MPD.11: 5 residues within 4Å: Chain B: R.609, L.616, R.664 Ligands: MPD.12, K.17 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.609, B:R.609 MPD.12: 7 residues within 4Å: Chain B: L.616, V.619, I.620, R.664, N.667, T.668 Ligands: MPD.11 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:V.619, B:I.620 Hydrogen bonds: B:R.664, B:N.667

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

MG.4: 2 residues within 4Å: Chain A: S.317 Ligands: TE9.21 No protein-ligand interaction detected (PLIP) MG.5: 2 residues within 4Å: Chain A: D.96, D.98 6 PLIP interactions: 2 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.96, A:D.98, H2O.1, H2O.1, H2O.1, H2O.4 MG.13: 2 residues within 4Å: Chain B: D.96, D.98 6 PLIP interactions: 2 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.96, B:D.98, H2O.3, H2O.3, H2O.3, H2O.4 MG.23: 1 residues within 4Å: Ligands: TE9.22 No protein-ligand interaction detected (PLIP)

8 x K: POTASSIUM ION(Non-covalent)

K.6: 4 residues within 4Å: Chain A: M.339, G.341, N.343 Chain B: N.177 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:M.339, A:G.341, H2O.2 K.7: 2 residues within 4Å: Chain A: Q.661, R.664 No protein-ligand interaction detected (PLIP) K.8: 4 residues within 4Å: Chain A: F.554, K.555, T.557, Q.560 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:F.554, A:K.555, A:T.557, H2O.1, H2O.2 K.14: 4 residues within 4Å: Chain A: N.177 Chain B: M.339, G.341, N.343 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:G.341 K.15: 2 residues within 4Å: Chain A: N.667 Chain B: E.634 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.634 K.16: 3 residues within 4Å: Chain B: G.74, D.85, N.87 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.85 K.17: 3 residues within 4Å: Chain B: Q.661, R.664 Ligands: MPD.11 No protein-ligand interaction detected (PLIP) K.18: 4 residues within 4Å: Chain B: F.554, K.555, T.557, Q.560 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:F.554, B:K.555, B:T.557, B:Q.560, H2O.4

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.9: 7 residues within 4Å: Chain A: I.198, E.199, D.200, A.204, S.246, L.247, E.248 Ligand excluded by PLIP CL.19: 7 residues within 4Å: Chain B: I.198, E.199, D.200, A.204, S.246, L.247, E.248 Ligand excluded by PLIP

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

ACT.20: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

2 x TE9: delafloxacin(Non-covalent)

TE9.21: 12 residues within 4Å: Chain A: L.2, G.24, D.25, L.45, R.46, G.47, S.317 Chain C: T.4, A.5 Chain D: A.1 Ligands: DT-DG-DT-DG-DG-DA-DT.1, MG.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.25, A:S.317 Water bridges: A:S.317 TE9.22: 12 residues within 4Å: Chain B: L.2, G.24, D.25, L.45, R.46, G.47, S.317 Chain C: G.1 Chain D: C.4, G.5 Ligands: DG-DT-DA-DA-DT-DA-DC.2, MG.23 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.25, B:D.25, B:S.317

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, B. et al., Experimental localization of metal-binding sites reveals the role of metal ions in type II DNA topoisomerases. Proc.Natl.Acad.Sci.USA (2024)

Release Date

2024-10-16

Peptides

DNA TOPOISOMERASE (ATP-HYDROLYZING),DNA TOPOISOMERASE 4: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

DNA TOPOISOMERASE (ATP-HYDROLYZING),DNA TOPOISOMERASE 4