SMTL ID : 6l25.1

Deoxyribonuclease from Staphylococcus aureus

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

4 x NI: NICKEL (II) ION(Non-covalent)

NI.1: 7 residues within 4Å: Chain A: H.22, H.24, E.108, H.169, D.220 Ligands: NI.2, PO4.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.22, A:H.24, A:E.108, A:D.220 NI.2: 6 residues within 4Å: Chain A: E.108, H.144, H.169 Ligands: NI.1, PO4.3, PO4.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.108, A:H.144, A:H.169 NI.5: 7 residues within 4Å: Chain B: H.22, H.24, E.108, H.169, D.220 Ligands: NI.6, PO4.7 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.22, B:H.24, B:E.108, B:D.220 NI.6: 6 residues within 4Å: Chain B: E.108, H.144, H.169 Ligands: NI.5, PO4.7, PO4.8 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.108, B:H.144, B:H.169

4 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 10 residues within 4Å: Chain A: H.24, F.54, H.79, E.108, H.144, D.220, Y.223 Ligands: NI.1, NI.2, PO4.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.108 Salt bridges: A:H.24, A:H.79, A:H.144 PO4.4: 7 residues within 4Å: Chain A: H.144, H.169, S.170, D.220, L.224 Ligands: NI.2, PO4.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.170 Salt bridges: A:H.144, A:H.169 PO4.7: 9 residues within 4Å: Chain B: H.24, H.79, E.108, H.144, D.220, Y.223 Ligands: NI.5, NI.6, PO4.8 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.220 Salt bridges: B:H.24, B:H.79, B:H.144 PO4.8: 7 residues within 4Å: Chain B: H.144, N.145, H.169, S.170, D.220 Ligands: NI.6, PO4.7 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.169, B:S.170 Salt bridges: B:H.144, B:H.169

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lee, K.-Y. et al., A structural study of TatD from Staphylococcus aureus elucidates a putative DNA-binding mode of a Mg2+-dependent nuclease. Iucrj (2020)

Release Date

2020-05-13

Peptides

Deoxyribonuclease YcfH: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Deoxyribonuclease YcfH