SMTL ID : 3zda.1

Structure of E. coli ExoIX in complex with a fragment of the Flap1 DNA oligonucleotide, potassium and magnesium

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

monomer

Ligands

1 x DG- DC- DG- DC: 5'-D(*GP*CP*GP*CP)-3'(Non-covalent)

DG-DC-DG-DC.1: 14 residues within 4Å: Chain A: V.182, A.183, G.184, I.185, G.186, P.187, K.188, S.189 Ligands: DA-DA-DG-DC-DG-DC.2, DA-DA-DG-DC-DG-DC.2, DA-DA-DG-DC-DG-DC.2, DA-DA-DG-DC-DG-DC.2, DA-DA-DG-DC-DG-DC.2, K.3 Protein-ligand interaction information (PLIP) not available

1 x DA- DA- DG- DC- DG- DC: 5'-D(*AP*AP*GP*CP*GP*CP)-3'(Non-functional Binders)

DA-DA-DG-DC-DG-DC.2: 4 residues within 4Å: Ligands: DG-DC-DG-DC.1, DG-DC-DG-DC.1, DG-DC-DG-DC.1, DG-DC-DG-DC.1 Protein-ligand interaction information (PLIP) not available

1 x K: POTASSIUM ION(Non-covalent)

K.3: 6 residues within 4Å: Chain A: L.171, A.172, P.180, V.182, I.185 Ligands: DG-DC-DG-DC.1 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:A.172, A:P.180, A:V.182, A:I.185, H2O.8

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 1 residues within 4Å: Chain A: D.104 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.104, H2O.1, H2O.1, H2O.4, H2O.10

1 x PIV: PIVALIC ACID(Non-covalent)

PIV.5: 6 residues within 4Å: Chain A: Q.35, L.36, H.39, R.141, Y.143, K.146 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.36, A:H.39, A:Y.143, A:Y.143, A:K.146 Water bridges: A:H.39 Salt bridges: A:H.39, A:R.141, A:K.146

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

PO4.6: 5 residues within 4Å: Chain A: L.110, K.113, I.240, L.244, L.247 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:L.110 Water bridges: A:K.113, A:K.113, A:G.242, A:L.244 Salt bridges: A:K.113

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: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

PROTEIN XNI

Related Entries With Identical Sequence