SMTL ID : 2faq.1 (1 other biounit)

Crystal Structure of Pseudomonas aeruginosa LigD polymerase domain with ATP and Manganese

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

2 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 4 residues within 4Å: Chain A: D.138, D.140 Ligands: MN.2, ATP.5 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.138, A:D.138, A:D.140, H2O.4, H2O.6 MN.2: 5 residues within 4Å: Chain A: D.138, D.140, D.228, R.231 Ligands: MN.1 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.138, A:D.140, A:D.228, H2O.6

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

SO4.3: 4 residues within 4Å: Chain A: S.21, H.22, R.25, K.35 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:S.21, A:S.21 Water bridges: A:R.25, A:R.25, A:R.25, A:R.25, A:P.64 Salt bridges: A:H.22, A:R.25, A:K.35 SO4.4: 3 residues within 4Å: Chain A: S.216, R.219, N.220 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.219

1 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.5: 15 residues within 4Å: Chain A: F.73, H.120, D.138, D.140, S.173, G.175, K.176, G.177, H.179, R.231, S.237, T.238, R.245, R.247 Ligands: MN.1 22 PLIP interactions: 22 interactions with chain A Hydrogen bonds: A:H.120, A:S.173, A:K.176, A:G.177, A:R.231 Water bridges: A:R.231, A:R.231, A:S.237, A:V.239, A:R.245, A:R.245, A:R.245, A:R.247 Salt bridges: A:H.179, A:R.231, A:R.245, A:R.245, A:R.247, A:R.247, A:R.247 pi-Stacking: A:F.73, A:F.73

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhu, H. et al., Atomic structure and nonhomologous end-joining function of the polymerase component of bacterial DNA ligase D. Proc.Natl.Acad.Sci.USA (2006)

Release Date

2006-05-23

Peptides

probable ATP-dependent DNA ligase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

probable ATP-dependent DNA ligase

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