SMTL ID : 4nc7.4 (3 other biounits)

N-terminal domain of delta-subunit of RNA polymerase complexed with I3C and nickel ions

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

2 x I3C: 5-amino-2,4,6-triiodobenzene-1,3-dicarboxylic acid(Non-covalent)

I3C.1: 9 residues within 4Å: Chain A: Q.33, E.34, N.37, K.47, Y.81 Chain C: K.28, P.29, S.71, D.72 10 PLIP interactions: 4 interactions with chain C, 6 interactions with chain A Hydrogen bonds: C:D.72, C:D.72, A:N.37, A:Y.81, A:Y.81 Salt bridges: C:K.28, A:K.47, A:K.47 Halogen bonds: C:S.71, A:E.34 I3C.4: 9 residues within 4Å: Chain A: K.28, P.29, S.71, D.72 Chain C: Q.33, E.34, N.37, K.47, Y.81 8 PLIP interactions: 3 interactions with chain A, 5 interactions with chain C Hydrogen bonds: A:D.72, C:N.37, C:Y.81 Salt bridges: A:K.28, C:K.47, C:K.47 Halogen bonds: A:S.71, C:E.34

4 x NI: NICKEL (II) ION(Non-covalent)

NI.2: 5 residues within 4Å: Chain A: L.61, N.62, D.64, F.67 Chain B: N.62 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:L.61, A:N.62, A:D.64, A:F.67, H2O.3 NI.3: 5 residues within 4Å: Chain A: N.62 Chain B: L.61, N.62, D.64, F.67 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:L.61, B:N.62, B:D.64, B:F.67, H2O.2 NI.5: 5 residues within 4Å: Chain C: L.61, N.62, D.64, F.67 Chain D: N.62 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:L.61, C:N.62, C:D.64, C:F.67, H2O.6 NI.6: 5 residues within 4Å: Chain C: N.62 Chain D: L.61, N.62, D.64, F.67 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:L.61, D:N.62, D:D.64, D:F.67, H2O.5

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Demo, G. et al., X-ray vs. NMR structure of N-terminal domain of delta-subunit of RNA polymerase. J.Struct.Biol. (2014)

Release Date

2014-07-02

Peptides

DNA-directed RNA polymerase subunit delta: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

DNA-directed RNA polymerase subunit delta

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