SMTL ID : 9fz6.1

A 2.58A crystal structure of S. aureus DNA gyrase and DNA with metals identified through anomalous scattering

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.58 Å

Oligo State

hetero-2-2-mer

Ligands

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

DA-DG-DC-DC-DG-DT-DA-DG.1: 28 residues within 4Å: Chain A: R.25, K.35, V.37, H.38, H.71, H.73, G.74, S.77, R.84, S.165, I.167, Q.259, R.264 Chain B: E.19, R.42, G.43, K.44, D.96, I.100 Chain E: G.3 Chain F: C.7, T.8, A.9, C.10, G.11, G.12, C.13 Ligands: GOL.13 Protein-ligand interaction information (PLIP) not available DA-DG-DC-DC-DG-DT-DA-DG.2: 28 residues within 4Å: Chain C: R.25, K.35, H.38, H.71, H.73, G.74, S.77, A.81, R.84, S.165, I.167, R.264 Chain D: E.19, R.42, G.43, K.44, D.96, I.100 Chain E: C.7, T.8, A.9, C.10, G.11, G.12, C.13, T.14 Chain F: G.3 Ligands: MN.15 Protein-ligand interaction information (PLIP) not available

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: D.53, K.54, S.55, R.119 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.53, A:S.55, A:R.119 Water bridges: A:R.119, A:R.119 GOL.4: 4 residues within 4Å: Chain A: D.88, F.89, P.211, R.477 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.211, A:R.477 GOL.8: 6 residues within 4Å: Chain C: A.24, P.36, R.39, R.40, E.148, P.149 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.39, C:R.40 GOL.9: 5 residues within 4Å: Chain C: E.243, G.247, R.248, Q.249 Ligands: GOL.10 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.248, C:Q.249 Water bridges: C:E.243 GOL.10: 6 residues within 4Å: Chain C: G.247, Q.249, D.303, A.304, N.305 Ligands: GOL.9 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:G.247, C:D.303, C:D.303, C:A.304 Water bridges: C:Q.249, C:A.306 GOL.11: 2 residues within 4Å: Chain C: E.439, N.442 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.442, C:N.442 GOL.13: 5 residues within 4Å: Chain A: M.105, Q.259, V.260 Ligands: DA-DG-DC-DC-DG-DT-DA-DG.1, DA-DG-DC-DC-DG-DT-DA-DG.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.259

5 x MN: MANGANESE (II) ION(Non-covalent)(Non-functional Binders)

MN.5: 2 residues within 4Å: Chain B: D.92, D.94 6 PLIP interactions: 2 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.92, B:D.94, H2O.5, H2O.5, H2O.5, H2O.5 MN.6: 2 residues within 4Å: Chain C: H.382 Ligands: BTB.7 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:H.382 MN.12: 2 residues within 4Å: Chain D: D.92, D.94 6 PLIP interactions: 2 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:D.92, D:D.94, H2O.11, H2O.11, H2O.11, H2O.11 MN.14: 2 residues within 4Å: Chain A: S.76 Chain E: G.3 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:S.76, H2O.13, H2O.13, H2O.13 MN.15: 3 residues within 4Å: Chain E: C.6 Chain F: G.3 Ligands: DA-DG-DC-DC-DG-DT-DA-DG.2 No protein-ligand interaction detected (PLIP)

1 x BTB: 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-covalent)

BTB.7: 3 residues within 4Å: Chain C: D.381, H.382 Ligands: MN.6 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Morgan, H. et al., How Do Gepotidacin and Zoliflodacin Stabilize DNA Cleavage Complexes with Bacterial Type IIA Topoisomerases? 1. Experimental Definition of Metal Binding Sites. Int J Mol Sci (2024)

Release Date

2024-10-23

Peptides

DNA gyrase subunit A: AC
DNA gyrase subunit B: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

DNA gyrase subunit A

DNA gyrase subunit B

Related Entries With Identical Sequence