SMTL ID : 5ean.1

Crystal structure of Dna2 in complex with a 5' overhang DNA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.36 Å

Oligo State

homo-dimer

Ligands

2 x SF4: IRON/SULFUR CLUSTER(Non-covalent)

SF4.1: 9 residues within 4Å: Chain A: C.140, R.142, R.143, I.390, I.391, C.397, C.400, C.406, M.426 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.140, A:C.397, A:C.400, A:C.406 SF4.5: 9 residues within 4Å: Chain C: C.140, R.142, R.143, I.390, I.391, C.397, C.400, C.406, M.426 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.140, C:C.397, C:C.400, C:C.406

4 x CA: CALCIUM ION(Non-covalent)

CA.2: 6 residues within 4Å: Chain A: H.167, D.281, E.302, L.303 Chain B: A.12 Ligands: CA.4 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.167, A:D.281, A:E.302, A:L.303, H2O.1 CA.4: 6 residues within 4Å: Chain A: E.302, K.304 Chain B: G.11, A.12, G.13 Ligands: CA.2 No protein-ligand interaction detected (PLIP) CA.6: 6 residues within 4Å: Chain C: H.167, D.281, E.302, L.303 Chain D: A.12 Ligands: CA.8 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.167, C:D.281, C:E.302, C:L.303, H2O.1 CA.8: 6 residues within 4Å: Chain C: E.302, K.304 Chain D: G.11, A.12, G.13 Ligands: CA.6 No protein-ligand interaction detected (PLIP)

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.3: 9 residues within 4Å: Chain A: G.629, L.630, N.631, Q.634, G.657, T.659, T.660, K.692, Y.831 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:N.631, A:N.631, A:Q.634, A:Q.634, A:T.659, A:T.659, A:T.660, A:T.660 Salt bridges: A:K.692, A:K.692 pi-Stacking: A:Y.831 ADP.7: 9 residues within 4Å: Chain C: G.629, L.630, N.631, Q.634, G.657, T.659, T.660, K.692, Y.831 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:N.631, C:N.631, C:Q.634, C:Q.634, C:T.659, C:T.659, C:T.660, C:Y.831 Salt bridges: C:K.692, C:K.692 pi-Stacking: C:Y.831

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhou, C. et al., Dna2 nuclease-helicase structure, mechanism and regulation by Rpa. Elife (2015)

Release Date

2015-11-18

Peptides

DNA replication ATP-dependent helicase/nuclease DNA2: AC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

DNA replication ATP-dependent helicase/nuclease DNA2