SMTL ID : 3jsl.1

Crystal structure of the adenylation domain of NAD+-dependent DNA ligase from Staphylococcus aureus

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

8 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 5 residues within 4Å: Chain A: G.115, L.116, A.117, R.133, R.194 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.117 Water bridges: A:R.133, A:G.134 Salt bridges: A:R.194 SO4.2: 5 residues within 4Å: Chain A: M.79, L.80, R.165, Y.219, S.220 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.80, A:S.220 Salt bridges: A:R.165 SO4.3: 3 residues within 4Å: Chain A: A.2, H.49 Chain B: N.74 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:A.2, B:N.74 Water bridges: A:H.49, B:N.74, B:N.74 Salt bridges: A:H.49 SO4.4: 3 residues within 4Å: Chain A: N.74 Chain B: A.2, H.49 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:N.74, B:A.2 Water bridges: A:N.74, B:A.2, B:H.49 Salt bridges: B:H.49 SO4.5: 1 residues within 4Å: Chain A: K.241 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.241 SO4.6: 5 residues within 4Å: Chain B: G.115, L.116, A.117, R.133, R.194 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:A.117 Water bridges: B:R.133, B:G.134 Salt bridges: B:R.194 SO4.7: 5 residues within 4Å: Chain B: M.79, L.80, R.165, Y.219, S.220 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:L.80, B:Y.219 Water bridges: B:L.80, B:R.165, B:Y.219, B:S.220, B:S.220 Salt bridges: B:R.165 SO4.8: 4 residues within 4Å: Chain B: K.182, F.190, Q.203, R.212 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:K.182, B:R.212

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Han, S. et al., Structure of the adenylation domain of NAD(+)-dependent DNA ligase from Staphylococcus aureus. Acta Crystallogr.,Sect.F (2009)

Release Date

2009-12-15

Peptides

DNA ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

DNA ligase

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