SMTL ID : 7riq.1

RNA polymerase II elongation complex scaffold 1 without polyamide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

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

Ligands

1 x A- U- C- G- A- G- A- G- G: RNA(Non-covalent)

A-U-C-G-A-G-A-G-G.1: 24 residues within 4Å: Chain A: G.20, C.21, C.22, T.23, C.24, T.25, C.26, G.27, A.28, T.29 Chain B: R.350, R.446, Q.447, P.448, D.483, D.485 Chain C: G.478, Q.481, E.529, Q.776, K.979, K.987, H.1097 Ligands: MG.2 Protein-ligand interaction information (PLIP) not available

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain B: D.483, D.485 Ligands: A-U-C-G-A-G-A-G-G.1 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.483, B:D.483

8 x ZN: ZINC ION(Non-covalent)

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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Oh, J. et al., RNA polymerase II trapped on a molecular treadmill: Structural basis of persistent transcriptional arrest by a minor groove DNA binder. Proc.Natl.Acad.Sci.USA (2022)

Release Date

2022-01-12

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

B
A

C
B

D
C

E
E

F
F

G
H

H
I

I
J

J
K

K
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

Related Entries With Identical Sequence