SMTL ID : 5l2l.1

Nab2 Zn fingers 5-7 bound to A11G RNA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

homo-tetramer

Ligands

14 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: C.9, C.15, C.20, Y.22, H.24 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.9, A:C.15, A:C.20, A:H.24 ZN.2: 6 residues within 4Å: Chain A: R.23, C.31, C.37, C.42, F.44, H.46 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.31, A:C.37, A:C.42, A:H.46 ZN.3: 6 residues within 4Å: Chain A: C.52, F.54, C.58, C.63, F.65, H.67 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.52, A:C.58, A:C.63, A:H.67 ZN.4: 2 residues within 4Å: Chain A: E.7 Chain G: A.3 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.7, H2O.1, H2O.1, H2O.4, H2O.25 ZN.5: 5 residues within 4Å: Chain B: C.9, C.15, C.20, H.24 Chain H: A.3 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.9, B:C.15, B:C.20, B:H.24 ZN.6: 7 residues within 4Å: Chain B: R.23, C.31, E.33, C.37, C.42, F.44, H.46 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.31, B:C.37, B:C.42, B:H.46 ZN.7: 6 residues within 4Å: Chain B: C.52, F.54, C.58, C.63, F.65, H.67 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.52, B:C.58, B:C.63, B:H.67 ZN.8: 5 residues within 4Å: Chain E: C.9, C.15, C.20, Y.22, H.24 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.9, E:C.15, E:C.20, E:H.24 ZN.9: 6 residues within 4Å: Chain E: R.23, C.31, C.37, C.42, F.44, H.46 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.31, E:C.37, E:C.42, E:H.46 ZN.10: 6 residues within 4Å: Chain E: C.52, F.54, C.58, C.63, F.65, H.67 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.52, E:C.58, E:C.63, E:H.67 ZN.11: 5 residues within 4Å: Chain C: A.3 Chain F: C.9, C.15, C.20, H.24 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.9, F:C.15, F:C.20, F:H.24 ZN.12: 6 residues within 4Å: Chain F: R.23, C.31, C.37, C.42, F.44, H.46 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.31, F:C.37, F:C.42, F:H.46 ZN.13: 5 residues within 4Å: Chain F: C.52, C.58, C.63, F.65, H.67 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.52, F:C.58, F:C.63, F:H.67 ZN.14: 1 residues within 4Å: Chain F: G.1 2 PLIP interactions: 1 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:G.1, H2O.22

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Aibara, S. et al., Structural basis for the dimerization of Nab2 generated by RNA binding provides insight into its contribution to both poly(A) tail length determination and transcript compaction in Saccharomyces cerevisiae. Nucleic Acids Res. (2017)

Release Date

2016-12-21

Peptides

Nab2p: ABEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

E
E

F
F

Nab2p