SMTL ID : 7kee.1

RNA polymerase II elongation complex with unnatural base dTPT3, rNaMTP bound to E-site

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.45 Å

Oligo State

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

Ligands

8 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.107, C.110, C.148, C.167 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.110, A:C.148, A:C.167 ZN.2: 4 residues within 4Å: Chain A: C.67, C.70, C.77, H.80 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.67, A:C.70, A:C.77 ZN.5: 4 residues within 4Å: Chain B: C.1163, C.1166, C.1182, C.1185 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.1163, B:C.1182, B:C.1185 ZN.6: 4 residues within 4Å: Chain C: C.86, C.88, C.92, C.95 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.86, C:C.88, C:C.92, C:C.95 ZN.7: 6 residues within 4Å: Chain G: C.7, C.10, C.29, T.31, C.32, Y.34 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:C.7, G:T.31 ZN.8: 5 residues within 4Å: Chain G: C.75, C.78, S.80, C.103, C.106 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:C.75, G:C.103 ZN.9: 5 residues within 4Å: Chain H: C.7, C.10, R.43, C.45, C.46 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:C.7, H:C.10, H:C.45, H:C.46 ZN.10: 4 residues within 4Å: Chain J: C.31, C.34, C.48, C.51 2 PLIP interactions: 2 interactions with chain J Metal complexes: J:C.34, J:C.48

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: D.481, D.483, D.485 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.483, A:D.483, A:D.485, A:D.485

1 x WCG: (1S)-1,4-anhydro-5-O-[(R)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-1-(3-methoxynaphthalen-2-yl)-D-ribitol(Non-covalent)

WCG.4: 7 residues within 4Å: Chain A: N.479, D.481, K.752 Chain B: R.766, D.837, S.1019, R.1020 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.1020, A:N.479 Salt bridges: B:R.766, B:R.1020 pi-Cation interactions: A:K.752

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Oh, J. et al., Transcriptional processing of an unnatural base pair by eukaryotic RNA polymerase II. Nat.Chem.Biol. (2021)

Release Date

2021-06-23

Peptides

DNA-directed RNA polymerase II subunit RPB1: A
DNA-directed RNA polymerase II subunit RPB2: B
DNA-directed RNA polymerase II subunit RPB3: C
DNA-directed RNA polymerases I, II, and III subunit RPABC1: D
DNA-directed RNA polymerases I, II, and III subunit RPABC2: E
DNA-directed RNA polymerases I, II, and III subunit RPABC3: F
DNA-directed RNA polymerase II subunit RPB9: G
DNA-directed RNA polymerases I, II, and III subunit RPABC5: H
DNA-directed RNA polymerase II subunit RPB11: I
DNA-directed RNA polymerases I, II, and III subunit RPABC4: J

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
E

E
F

F
H

G
I

H
J

I
K

J
L

DNA-directed RNA polymerase II subunit RPB1

DNA-directed RNA polymerase II subunit RPB2

DNA-directed RNA polymerase II subunit RPB3

DNA-directed RNA polymerases I, II, and III subunit RPABC1

DNA-directed RNA polymerases I, II, and III subunit RPABC2

DNA-directed RNA polymerases I, II, and III subunit RPABC3

DNA-directed RNA polymerase II subunit RPB9

DNA-directed RNA polymerases I, II, and III subunit RPABC5

DNA-directed RNA polymerase II subunit RPB11

DNA-directed RNA polymerases I, II, and III subunit RPABC4

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