SMTL ID : 3zq4.1

Unusual, dual endo- and exo-nuclease activity in the degradosome explained by crystal structure analysis of RNase J1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

homo-tetramer

Ligands

8 x ZN: ZINC ION(Non-covalent)

ZN.1: 7 residues within 4Å: Chain A: N.23, H.74, D.78, H.79, D.164, H.390 Ligands: ZN.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.78, A:H.79, A:D.164, A:H.390 ZN.2: 6 residues within 4Å: Chain A: H.74, H.76, H.79, H.142, D.164 Ligands: ZN.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.74, A:H.76, A:H.142, A:D.164 ZN.4: 7 residues within 4Å: Chain B: N.23, H.74, D.78, H.79, D.164, H.390 Ligands: ZN.5 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.78, B:H.79, B:D.164, B:H.390 ZN.5: 7 residues within 4Å: Chain B: H.74, H.76, D.78, H.79, H.142, D.164 Ligands: ZN.4 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.76, B:H.142, B:D.164 ZN.8: 7 residues within 4Å: Chain C: N.23, H.74, D.78, H.79, D.164, H.390 Ligands: ZN.9 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.78, C:H.79, C:D.164, C:H.390 ZN.9: 6 residues within 4Å: Chain C: H.74, H.76, H.79, H.142, D.164 Ligands: ZN.8 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:H.74, C:H.74, C:H.76, C:H.142, C:D.164 ZN.10: 7 residues within 4Å: Chain D: N.23, H.74, D.78, H.79, D.164, H.390 Ligands: ZN.11 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.78, D:H.79, D:D.164, D:H.390 ZN.11: 7 residues within 4Å: Chain D: H.74, H.76, D.78, H.79, H.142, D.164 Ligands: ZN.10 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:H.74, D:H.76, D:H.142, D:D.164

4 x CA: CALCIUM ION(Non-covalent)

CA.3: 5 residues within 4Å: Chain A: G.49, D.51, D.443 Chain B: E.463, E.464 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:G.49, A:D.443 CA.6: 4 residues within 4Å: Chain A: E.464 Chain B: G.49, D.51, D.443 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:G.49, B:D.443 CA.7: 4 residues within 4Å: Chain C: G.49, D.51, D.443 Chain D: E.464 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.51, C:D.443 CA.12: 3 residues within 4Å: Chain C: E.464 Chain D: G.49, D.443 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.443

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Newman, J.A. et al., Unusual, Dual Endo- and Exonuclease Activity in the Degradosome Explained by Crystal Structure Analysis of Rnase J1. Structure (2011)

Release Date

2011-09-14

Peptides

RIBONUCLEASE J 1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
D

D
E

RIBONUCLEASE J 1