SMTL ID : 1wrn.1

Metal Ion dependency of the antiterminator protein, HutP, for binding to the terminator region of hut mRNA- A structural basis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-hexamer

Ligands

6 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 4 residues within 4Å: Chain A: H.72, H.76 Chain B: H.137 Ligands: HIS.8 5 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: A:H.72, A:H.76, B:H.137, HIS.8, H2O.4 MN.7: 4 residues within 4Å: Chain B: H.72, H.76 Chain C: H.137 Ligands: HIS.11 5 PLIP interactions: 1 Ligand-Ligand interactions, 1 interactions with chain C, 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: HIS.11, C:H.137, B:H.72, B:H.76, H2O.9 MN.10: 4 residues within 4Å: Chain A: H.137 Chain C: H.72, H.76 Ligands: HIS.2 5 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: A:H.137, C:H.72, C:H.76, HIS.2, H2O.13 MN.13: 4 residues within 4Å: Chain D: H.72, H.76 Chain E: H.137 Ligands: HIS.20 4 PLIP interactions: 2 interactions with chain D, 1 interactions with chain E, 1 Ligand-Water interactions Metal complexes: D:H.72, D:H.76, E:H.137, H2O.18 MN.19: 4 residues within 4Å: Chain E: H.72, H.76 Chain F: H.137 Ligands: HIS.23 5 PLIP interactions: 2 interactions with chain E, 1 Ligand-Ligand interactions, 1 interactions with chain F, 1 Ligand-Water interactions Metal complexes: E:H.72, E:H.76, HIS.23, F:H.137, H2O.23 MN.22: 4 residues within 4Å: Chain D: H.137 Chain F: H.72, H.76 Ligands: HIS.14 4 PLIP interactions: 2 interactions with chain F, 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: F:H.72, F:H.76, D:H.137, H2O.27

6 x HIS: HISTIDINE(Non-covalent)

HIS.2: 12 residues within 4Å: Chain A: R.87, L.96, R.97, I.128, G.129, A.130, H.137 Chain C: Y.68, H.72, Y.75, H.76 Ligands: MN.10 8 PLIP interactions: 4 interactions with chain A, 2 interactions with chain C, 2 Ligand-Ligand interactions Hydrogen bonds: A:A.130, C:Y.68, H.2, H.2 Salt bridges: A:R.87, A:R.97, A:H.137, C:H.76 HIS.8: 12 residues within 4Å: Chain A: Y.68, H.72, Y.75, H.76 Chain B: R.87, L.96, R.97, I.128, G.129, A.130, H.137 Ligands: MN.1 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Salt bridges: B:R.87, B:R.97, B:H.137, A:H.76 HIS.11: 12 residues within 4Å: Chain B: Y.68, H.72, Y.75, H.76 Chain C: R.87, L.96, R.97, I.128, G.129, A.130, H.137 Ligands: MN.7 9 PLIP interactions: 4 interactions with chain B, 1 Ligand-Ligand interactions, 4 interactions with chain C Hydrogen bonds: B:Y.68, B:Y.68, H.11 Salt bridges: B:H.76, C:R.87, C:R.97, C:H.137 pi-Stacking: B:Y.75 Water bridges: C:R.97 HIS.14: 12 residues within 4Å: Chain D: R.87, L.96, R.97, I.128, G.129, A.130, H.137 Chain F: Y.68, H.72, Y.75, H.76 Ligands: MN.22 8 PLIP interactions: 4 interactions with chain D, 3 interactions with chain F, 1 Ligand-Ligand interactions Hydrogen bonds: D:A.130, F:Y.68, F:H.76, H.14 Salt bridges: D:R.87, D:R.97, D:H.137, F:H.76 HIS.20: 12 residues within 4Å: Chain D: Y.68, H.72, Y.75, H.76 Chain E: R.87, L.96, R.97, I.128, G.129, A.130, H.137 Ligands: MN.13 6 PLIP interactions: 1 Ligand-Ligand interactions, 2 interactions with chain D, 3 interactions with chain E Hydrogen bonds: H.20, D:H.76 Salt bridges: D:H.76, E:R.87, E:R.97, E:H.137 HIS.23: 12 residues within 4Å: Chain E: Y.68, H.72, Y.75, H.76 Chain F: R.87, L.96, R.97, I.128, G.129, A.130, H.137 Ligands: MN.19 9 PLIP interactions: 4 interactions with chain E, 4 interactions with chain F, 1 Ligand-Ligand interactions Hydrogen bonds: E:Y.68, E:Y.68, H.23 Salt bridges: E:H.76, F:R.87, F:R.97, F:H.137 pi-Stacking: E:Y.75 Water bridges: F:R.97

12 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.3: 12 residues within 4Å: Chain A: E.80, A.81, H.83, G.84, F.140, G.141, V.142 Chain D: G.84, R.87, F.140, G.141 Ligands: PEG.15 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.80, A:G.84, A:V.142 PEG.4: 9 residues within 4Å: Chain A: A.115, E.116 Chain F: Q.64, E.66, G.67, Y.68, R.69, E.70, R.107 8 PLIP interactions: 7 interactions with chain F, 1 interactions with chain A Hydrogen bonds: F:Q.64, F:R.69, F:E.70, F:E.70, F:R.107, A:E.116 Water bridges: F:S.71, F:I.147 PEG.5: 4 residues within 4Å: Chain A: M.44, G.93, S.94 Chain C: H.47 1 PLIP interactions: 1 interactions with chain C Water bridges: C:H.47 PEG.6: 9 residues within 4Å: Chain A: V.49, I.50, I.53, E.54, K.58, S.71, L.74, Y.75, T.78 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:V.49, A:E.54, A:E.54, A:S.71, A:T.78 PEG.9: 4 residues within 4Å: Chain B: G.61, V.62, I.63, R.107 No protein-ligand interaction detected (PLIP) PEG.12: 3 residues within 4Å: Chain C: R.10, L.11, L.14 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.10 Water bridges: C:L.14 PEG.15: 12 residues within 4Å: Chain A: G.84, R.87, F.140, G.141 Chain D: E.80, A.81, H.83, G.84, F.140, G.141, V.142 Ligands: PEG.3 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:E.80, D:G.84, D:V.142 PEG.16: 9 residues within 4Å: Chain C: Q.64, E.66, G.67, Y.68, R.69, E.70, R.107 Chain D: A.115, E.116 8 PLIP interactions: 7 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:Q.64, C:R.69, C:E.70, C:E.70, C:R.107, D:E.116 Water bridges: C:S.71, C:I.147 PEG.17: 4 residues within 4Å: Chain D: M.44, G.93, S.94 Chain F: H.47 1 PLIP interactions: 1 interactions with chain F Water bridges: F:H.47 PEG.18: 9 residues within 4Å: Chain D: V.49, I.50, I.53, E.54, K.58, S.71, L.74, Y.75, T.78 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:V.49, D:E.54, D:E.54, D:S.71, D:T.78 PEG.21: 4 residues within 4Å: Chain E: G.61, V.62, I.63, R.107 No protein-ligand interaction detected (PLIP) PEG.24: 3 residues within 4Å: Chain F: R.10, L.11, L.14 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:R.10 Water bridges: F:L.14

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kumarevel, T. et al., Characterization of the metal ion binding site in the anti-terminator protein, HutP, of Bacillus subtilis. Nucleic Acids Res. (2005)

Release Date

2005-08-30

Peptides

Hut operon positive regulatory protein: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
A

E
B

F
C

Hut operon positive regulatory protein

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