SMTL ID : 4lj0.1

Nab2 Zn fingers complexed with polyadenosine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-dimer

Ligands

3 x A- A- A- A: polyadenosine RNA(Non-covalent)

A-A-A-A.1: 10 residues within 4Å: Chain A: Y.7, N.10, C.11, A.12, N.13 Ligands: A-A-A-A.2, A-A-A-A.2, MG.12, MG.13, MG.14 Protein-ligand interaction information (PLIP) not available A-A-A-A.2: 20 residues within 4Å: Chain A: N.10, C.11, A.12, P.14, T.44, P.45, C.46, K.47, F.48, P.50, C.51, T.52, N.53, C.56, F.58 Ligands: A-A-A-A.1, A-A-A-A.1, ZN.6, MG.13, MG.15 Protein-ligand interaction information (PLIP) not available A-A-A-A.3: 8 residues within 4Å: Chain A: P.24, P.25, C.26, R.27, N.28, C.37, F.39 Ligands: ZN.5 Protein-ligand interaction information (PLIP) not available

6 x ZN: ZINC ION(Non-covalent)

ZN.4: 5 residues within 4Å: Chain A: C.5, C.11, C.16, F.18, H.20 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.5, A:C.11, A:C.16, A:H.20 ZN.5: 7 residues within 4Å: Chain A: C.26, N.28, C.32, C.37, F.39, H.41 Ligands: A-A.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.26, A:C.32, A:C.37, A:H.41 ZN.6: 7 residues within 4Å: Chain A: C.46, C.51, C.56, F.58, H.60 Ligands: A-A-A-A.2, A-A-A-A.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.46, A:C.51, A:C.56, A:H.60 ZN.9: 6 residues within 4Å: Chain B: C.5, Y.7, C.11, C.16, F.18, H.20 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.5, B:C.11, B:C.16, B:H.20 ZN.10: 6 residues within 4Å: Chain B: C.26, N.28, C.32, C.37, F.39, H.41 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:C.26, B:C.32, B:C.37, B:H.41, H2O.1 ZN.11: 6 residues within 4Å: Chain B: C.46, F.48, C.51, C.56, F.58, H.60 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.46, B:C.51, B:C.56, B:H.60

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.7: 5 residues within 4Å: Chain A: C.5, K.6, W.8, T.44 Ligands: ACT.8 No protein-ligand interaction detected (PLIP) ACT.8: 7 residues within 4Å: Chain A: W.8, T.40, H.41, L.42, K.43, T.44 Ligands: ACT.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.43, A:T.44, A:T.44

4 x MG: MAGNESIUM ION(Non-functional Binders)

MG.12: 2 residues within 4Å: Ligands: A-A-A-A.1, A-A-A-A.1 No protein-ligand interaction detected (PLIP) MG.13: 2 residues within 4Å: Ligands: A-A-A-A.1, A-A-A-A.2 No protein-ligand interaction detected (PLIP) MG.14: 2 residues within 4Å: Ligands: A-A-A-A.1, A-A-A-A.1 No protein-ligand interaction detected (PLIP) MG.15: 2 residues within 4Å: Ligands: A-A-A-A.2, A-A-A-A.2 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kuhlmann, S.I. et al., Structural basis for the molecular recognition of polyadenosine RNA by Nab2 Zn fingers. Nucleic Acids Res. (2014)

Release Date

2013-10-09

Peptides

Nab2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Nab2