SMTL ID : 1zbh.1

3'-end specific recognition of histone mRNA stem-loop by 3'-exonuclease

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

homo-tetramer

Ligands

8 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain C: D.84, D.180, D.184 Ligands: MG.2, AMP.3 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Ligand interactions Metal complexes: C:D.84, AMP.3 MG.2: 5 residues within 4Å: Chain C: D.84, E.86, D.248 Ligands: MG.1, AMP.3 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Ligand interactions Metal complexes: C:D.84, C:E.86, C:D.248, AMP.3, AMP.3 MG.4: 5 residues within 4Å: Chain D: D.84, D.180, D.184 Ligands: MG.5, AMP.6 2 PLIP interactions: 1 interactions with chain D, 1 Ligand-Ligand interactions Metal complexes: D:D.84, AMP.6 MG.5: 5 residues within 4Å: Chain D: D.84, E.86, D.248 Ligands: MG.4, AMP.6 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Ligand interactions Metal complexes: D:D.84, D:E.86, D:D.248, AMP.6, AMP.6 MG.7: 4 residues within 4Å: Chain E: D.84, W.183, D.184 Ligands: AMP.9 2 PLIP interactions: 1 interactions with chain E, 1 Ligand-Ligand interactions Metal complexes: E:D.84, AMP.9 MG.8: 5 residues within 4Å: Chain E: D.84, E.86, N.243, D.248 Ligands: AMP.9 3 PLIP interactions: 2 interactions with chain E, 1 Ligand-Ligand interactions Metal complexes: E:D.84, E:E.86, AMP.9 MG.10: 5 residues within 4Å: Chain F: D.84, D.180, D.184 Ligands: MG.11, AMP.12 2 PLIP interactions: 1 interactions with chain F, 1 Ligand-Ligand interactions Metal complexes: F:D.84, AMP.12 MG.11: 5 residues within 4Å: Chain F: D.84, E.86, D.248 Ligands: MG.10, AMP.12 4 PLIP interactions: 3 interactions with chain F, 1 Ligand-Ligand interactions Metal complexes: F:D.84, F:E.86, F:D.248, AMP.12

4 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.3: 16 residues within 4Å: Chain C: D.84, F.85, E.86, A.87, T.88, C.89, N.93, F.135, L.139, T.140, W.183, F.188, N.243, D.248 Ligands: MG.1, MG.2 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:E.86, C:A.87, C:A.87, C:N.243, C:D.248 AMP.6: 16 residues within 4Å: Chain D: D.84, F.85, E.86, A.87, T.88, C.89, E.90, N.93, H.99, F.135, L.139, T.140, F.188, N.243 Ligands: MG.4, MG.5 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:E.86, D:A.87, D:A.87, D:H.99, D:N.243 AMP.9: 16 residues within 4Å: Chain E: D.84, F.85, E.86, A.87, T.88, C.89, E.90, N.93, F.135, L.139, T.140, W.183, F.188, N.243 Ligands: MG.7, MG.8 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:E.86, E:A.87, E:A.87 AMP.12: 15 residues within 4Å: Chain F: D.84, F.85, E.86, A.87, T.88, C.89, E.90, N.93, H.99, F.135, L.139, T.140, F.188 Ligands: MG.10, MG.11 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:E.86, F:A.87, F:A.87, F:N.93

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cheng, Y. et al., Structural basis for 3'-end specific recognition of histone mRNA stem-loop by 3'-exonuclease, a human nuclease that also targets siRNA. To be Published

Release Date

2006-09-26

Peptides

3'-5' exonuclease ERI1: CDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
A

D
B

E
C

F
D

3'-5' exonuclease ERI1