SMTL ID : 3zdb.1

Structure of E. coli ExoIX in complex with the palindromic 5ov4 DNA oligonucleotide, di-magnesium and potassium

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.47 Å

Oligo State

homo-dimer

Ligands

2 x K: POTASSIUM ION(Non-covalent)

K.1: 7 residues within 4Å: Chain A: L.171, A.172, P.180, V.182, I.185 Chain B: C.10 Ligands: MG.2 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:A.172, A:V.182, A:I.185, H2O.6, H2O.6 K.6: 7 residues within 4Å: Chain C: L.171, A.172, P.180, V.182, I.185 Chain D: C.10 Ligands: MG.7 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:A.172, C:V.182, C:I.185, H2O.14, H2O.14

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: A.172, I.185 Chain B: C.10 Ligands: K.1 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:A.172, A:I.185, H2O.6, H2O.6, H2O.6 MG.3: 2 residues within 4Å: Chain A: D.104 Ligands: MG.5 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.104, H2O.1, H2O.1, H2O.3, H2O.8 MG.5: 2 residues within 4Å: Chain A: D.50 Ligands: MG.3 No protein-ligand interaction detected (PLIP) MG.7: 4 residues within 4Å: Chain C: A.172, I.185 Chain D: C.10 Ligands: K.6 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:A.172, C:I.185, H2O.14, H2O.14, H2O.14 MG.8: 2 residues within 4Å: Chain C: D.104 Ligands: MG.10 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:D.104, H2O.9, H2O.9, H2O.11, H2O.16 MG.10: 2 residues within 4Å: Chain C: D.50 Ligands: MG.8 No protein-ligand interaction detected (PLIP)

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

ACT.4: 6 residues within 4Å: Chain A: Q.35, L.36, H.39, R.141, Y.143, K.146 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Q.35, A:H.39, A:Y.143 Water bridges: A:H.39, A:H.39 Salt bridges: A:H.39, A:R.141, A:K.146 ACT.9: 6 residues within 4Å: Chain C: Q.35, L.36, H.39, R.141, Y.143, K.146 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:Q.35, C:H.39, C:Y.143 Water bridges: C:H.39, C:H.39 Salt bridges: C:H.39, C:R.141, C:K.146

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Anstey-Gilbert, C.S. et al., The Structure of E. Coli Exoix - Implications for DNA Binding and Catalysis in Flap Endonucleases. Nucleic Acids Res. (2013)

Release Date

2013-07-10

Peptides

PROTEIN XNI: AC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

PROTEIN XNI

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