SMTL ID : 4edv.1

The structure of the S. aureus DnaG RNA Polymerase Domain bound to pppGpp and Manganese

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.01 Å

Oligo State

monomer

Ligands

1 x BEN: BENZAMIDINE(Non-functional Binders)

BEN.1: 3 residues within 4Å: Chain A: E.17, F.18, Y.21 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:E.17, A:F.18, A:F.18 Water bridges: A:Y.21

1 x 0O2: guanosine 5'-(tetrahydrogen triphosphate) 3'-(trihydrogen diphosphate)(Non-covalent)

0O2.2: 15 residues within 4Å: Chain A: R.39, R.115, E.121, P.122, K.123, Y.124, M.162, D.163, D.203, D.205, A.207, D.236 Ligands: MN.3, MN.4, MN.5 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:K.123, A:Y.124 Water bridges: A:R.39, A:R.39, A:R.39, A:R.115, A:R.115, A:K.123, A:K.123, A:K.123, A:K.123, A:Y.124, A:G.160, A:G.160, A:M.162, A:D.205, A:A.207 Salt bridges: A:R.39, A:R.115, A:E.121, A:K.123

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

MN.3: 4 residues within 4Å: Chain A: D.203, D.236 Ligands: 0O2.2, MN.4 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.203, A:D.236, H2O.5, H2O.5 MN.4: 3 residues within 4Å: Chain A: D.236 Ligands: 0O2.2, MN.3 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.236, H2O.1, H2O.5, H2O.8 MN.5: 3 residues within 4Å: Chain A: D.203, D.205 Ligands: 0O2.2 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.205, H2O.4, H2O.5, H2O.5

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rymer, R.U. et al., Binding Mechanism of Metal-NTP Substrates and Stringent-Response Alarmones to Bacterial DnaG-Type Primases. Structure (2012)

Release Date

2012-07-25

Peptides

DNA primase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA primase

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