SMTL ID : 6wox.1

Thermus thermophilus RNA polymerase initially transcribing complex with 2'dCTP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.14 Å

Oligo State

hetero-2-1-1-1-1-mer

Ligands

1 x G- C- A: RNA (5'-R(*GP*CP*A)-3')(Non-covalent)

G-C-A.1: 15 residues within 4Å: Chain C: P.444, Q.567, K.838, K.846, H.999 Chain D: R.704, A.705, D.741, D.743 Chain G: T.15, G.16, C.17, A.18 Ligands: DCP.3, MG.4 Protein-ligand interaction information (PLIP) not available

1 x NA: SODIUM ION(Non-functional Binders)

NA.2: 5 residues within 4Å: Chain C: D.686, R.879 Chain D: D.739, R.1029 Ligands: DCP.3 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:R.1029, C:D.686, C:R.879, C:R.879

1 x DCP: 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE(Non-covalent)

DCP.3: 12 residues within 4Å: Chain C: R.557, R.879 Chain D: R.704, P.706, N.737, D.739, R.1029 Chain G: G.14, T.15 Ligands: G-C-A.1, NA.2, MG.4 7 PLIP interactions: 5 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:R.704, D:R.704, D:N.737, D:D.739, C:R.557 Salt bridges: D:R.1029, C:R.879

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 5 residues within 4Å: Chain D: D.739, D.741, D.743 Ligands: G-C-A.1, DCP.3 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:D.739, D:D.741, D:D.741, D:D.743, D:D.743

2 x ZN: ZINC ION(Non-covalent)

ZN.5: 5 residues within 4Å: Chain D: C.58, C.60, K.62, C.73, C.76 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.58, D:C.60, D:C.73, D:C.76 ZN.6: 7 residues within 4Å: Chain D: C.1112, T.1114, R.1189, C.1194, Q.1195, C.1201, C.1204 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.1112, D:C.1194, D:C.1201, D:C.1204

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Makinen, J.J. et al., The mechanism of the nucleo-sugar selection by multi-subunit RNA polymerases. Nat Commun (2021)

Release Date

2020-06-10

Peptides

DNA-directed RNA polymerase subunit alpha: AB
DNA-directed RNA polymerase subunit beta: C
DNA-directed RNA polymerase subunit beta': D
DNA-directed RNA polymerase subunit omega: E
RNA polymerase sigma factor SigA: F

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

DNA-directed RNA polymerase subunit alpha

DNA-directed RNA polymerase subunit beta

DNA-directed RNA polymerase subunit beta'

DNA-directed RNA polymerase subunit omega

RNA polymerase sigma factor SigA

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