SMTL ID : 2igi.1

Crystal Structure of E. coli Oligoribonuclease

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 7 residues within 4Å: Chain A: D.11, L.12, E.13, D.162 Ligands: CD.2, ZN.4, ACY.12 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.11, A:E.13, A:D.162, H2O.2 ZN.4: 6 residues within 4Å: Chain A: L.12, E.13, H.157 Ligands: ZN.1, CD.2, ACY.13 4 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:E.13, A:H.157, H2O.2, ACY.13 ZN.15: 7 residues within 4Å: Chain B: D.11, L.12, E.13, D.162 Ligands: CD.16, ZN.18, ACY.23 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.11, B:E.13, B:D.162, H2O.11 ZN.18: 5 residues within 4Å: Chain B: L.12, E.13, H.157 Ligands: ZN.15, ACY.24 4 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: B:E.13, B:H.157, H2O.11, ACY.24

13 x CD: CADMIUM ION(Non-covalent)

CD.2: 4 residues within 4Å: Chain A: D.11 Ligands: ZN.1, ZN.4, ACY.12 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.11, H2O.1, H2O.2, H2O.2, H2O.4 CD.3: 4 residues within 4Å: Chain A: R.112, F.116, E.123 Ligands: ACY.11 4 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:E.123, A:E.123, H2O.1, ACY.11 CD.5: 1 residues within 4Å: Chain A: H.48 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:H.48, H2O.3, H2O.7, H2O.8, H2O.9 CD.6: 3 residues within 4Å: Chain A: T.78, E.83 Ligands: ACY.14 5 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:T.78, A:E.83, A:E.83, H2O.6, ACY.14 CD.7: 4 residues within 4Å: Chain A: E.41, M.160, R.164 Ligands: CD.8 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.41, A:E.41 CD.8: 3 residues within 4Å: Chain A: E.41, R.164 Ligands: CD.7 No protein-ligand interaction detected (PLIP) CD.9: 1 residues within 4Å: Chain A: H.176 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.176, H2O.4, H2O.7, H2O.9 CD.10: 1 residues within 4Å: Chain A: H.176 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.176, H2O.8, H2O.16 CD.16: 5 residues within 4Å: Chain B: D.11, L.12 Ligands: ZN.15, ACY.23, ACY.24 6 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: B:D.11, H2O.9, H2O.11, H2O.11, H2O.12, ACY.23 CD.17: 4 residues within 4Å: Chain B: R.112, F.116, E.123 Ligands: ACY.22 4 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: B:E.123, B:E.123, H2O.9, ACY.22 CD.19: 3 residues within 4Å: Chain B: T.78, E.83 Ligands: ACY.25 5 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: B:T.78, B:E.83, H2O.16, H2O.16, ACY.25 CD.20: 1 residues within 4Å: Chain B: H.48 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:H.48, H2O.13, H2O.16, H2O.17, H2O.17 CD.21: 1 residues within 4Å: Chain B: D.161 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.161, B:D.161, H2O.11, H2O.13

8 x ACY: ACETIC ACID(Non-functional Binders)

ACY.11: 6 residues within 4Å: Chain A: R.112, F.116, E.123, Y.128 Chain B: Q.110 Ligands: CD.3 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:Y.128 Water bridges: A:R.112, B:R.113 Salt bridges: A:R.112 ACY.12: 5 residues within 4Å: Chain A: D.11, H.157, D.162 Ligands: ZN.1, CD.2 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.157 ACY.13: 5 residues within 4Å: Chain A: L.12, E.13, L.17, H.157 Ligands: ZN.4 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.17 Salt bridges: A:H.157 ACY.14: 5 residues within 4Å: Chain A: H.48, T.78, M.79, E.83 Ligands: CD.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.80 ACY.22: 6 residues within 4Å: Chain A: Q.110 Chain B: R.112, F.116, E.123, Y.128 Ligands: CD.17 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Water bridges: B:R.112, A:R.113 Salt bridges: B:R.112 ACY.23: 6 residues within 4Å: Chain B: D.11, K.153, H.157, D.162 Ligands: ZN.15, CD.16 4 PLIP interactions: 4 interactions with chain B Water bridges: B:H.157, B:H.157, B:D.162 Salt bridges: B:H.157 ACY.24: 6 residues within 4Å: Chain B: L.12, E.13, L.17, H.157 Ligands: CD.16, ZN.18 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.17 Salt bridges: B:H.157 ACY.25: 5 residues within 4Å: Chain B: H.48, T.78, M.79, E.83 Ligands: CD.19 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.80

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fiedler, T.J. et al., Crystal Structure of Oligoribonuclease, the lone essential exoribonuclease in Escherichia coli. To be Published

Release Date

2007-10-02

Peptides

Oligoribonuclease: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Oligoribonuclease

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