SMTL ID : 4cxo.1

bifunctional endonuclease in complex with ssDNA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.67 Å

Oligo State

monomer

Ligands

1 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN.1: 11 residues within 4Å: Chain A: H.52, W.53, L.57, G.82, R.83, A.88, N.91, Y.92, Q.95, Y.109 Ligands: TMP.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.83 Water bridges: A:W.53, A:R.83, A:R.83

1 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN.2: 4 residues within 4Å: Chain A: P.30, W.43, N.110, E.113 2 PLIP interactions: 2 interactions with chain A Water bridges: A:S.32, A:W.43

1 x NAG- NAG- MAN: alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-MAN.3: 8 residues within 4Å: Chain A: Y.170, A.180, L.181, N.184, E.188, W.189, P.241, Y.244 No protein-ligand interaction detected (PLIP)

2 x TMP: THYMIDINE-5'-PHOSPHATE(Non-covalent)

TMP.4: 12 residues within 4Å: Chain A: K.48, Y.59, N.61, L.129, H.130, K.137, G.138, N.140, H.154, D.158 Ligands: ZN.8, SO4.10 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.61, A:N.140 Water bridges: A:S.55, A:L.129 pi-Stacking: A:Y.59 TMP.6: 9 residues within 4Å: Chain A: K.81, G.82, G.87, Y.90, N.91, T.94, Y.109 Ligands: NAG-NAG-BMA-MAN-MAN.1, D5M.5 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:T.94 Hydrogen bonds: A:G.82, A:N.91, A:T.94, A:Y.109, A:Y.109 Water bridges: A:R.83

1 x D5M: 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE(Non-covalent)

D5M.5: 6 residues within 4Å: Chain A: Y.70, N.71, Y.90, K.201, D.207 Ligands: TMP.6 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.90 Hydrogen bonds: A:N.71, A:N.71 Water bridges: A:T.203 Salt bridges: A:K.201

3 x ZN: ZINC ION(Non-covalent)

ZN.7: 6 residues within 4Å: Chain A: D.45, H.58, H.120, D.124 Ligands: ZN.9, SO4.10 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.45, A:H.58, A:H.120, A:D.124 ZN.8: 5 residues within 4Å: Chain A: H.130, H.154, D.158 Ligands: TMP.4, SO4.10 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.130, A:H.154, A:D.158, A:D.158 ZN.9: 6 residues within 4Å: Chain A: W.1, H.6, H.120, D.124 Ligands: ZN.7, SO4.10 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:W.1, A:H.6, A:D.124

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

SO4.10: 13 residues within 4Å: Chain A: W.1, H.6, D.45, K.48, H.58, H.120, D.124, H.130, D.158 Ligands: TMP.4, ZN.7, ZN.8, ZN.9 4 PLIP interactions: 4 interactions with chain A Salt bridges: A:K.48, A:H.58, A:H.120, A:H.130

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yu, T. et al., Structural Insights of the Ssdna Binding Site in the Multifunctional Endonuclease Atbfn2 from Arabidopsis Thaliana. Plos One (2014)

Release Date

2014-07-23

Peptides

ENDONUCLEASE 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

ENDONUCLEASE 2