SMTL ID : 8ukq.1

RNA polymerase II elongation complex with Fapy-dG lesion in apo state

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.50 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: 20 residues within 4Å: Chain A: C.20, C.21, T.22, C.23, T.24, C.25, G.26, A.27, T.28 Chain C: R.350, Q.447, D.483, D.485 Chain D: G.478, Q.481, Q.776, K.979, K.987, H.1097 Ligands: MG.4 Protein-ligand interaction information (PLIP) not available

8 x ZN: ZINC ION(Non-covalent)

ZN.2: 6 residues within 4Å: Chain C: C.107, H.109, C.110, K.112, C.167, N.169 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.107, C:H.109, C:C.110, C:C.167 ZN.3: 3 residues within 4Å: Chain C: C.67, C.70, C.77 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:C.67, C:C.70, C:C.77 ZN.5: 6 residues within 4Å: Chain D: C.1163, C.1166, T.1170, C.1182, C.1185, N.1187 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:C.1163, D:C.1166, D:T.1170, D:C.1182, D:C.1185 ZN.6: 5 residues within 4Å: Chain E: C.86, C.88, H.91, C.92, C.95 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.86, E:C.88, E:C.92, E:C.95 ZN.7: 4 residues within 4Å: Chain I: C.7, C.10, C.29, C.32 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.7, I:C.10, I:C.29, I:C.32 ZN.8: 5 residues within 4Å: Chain I: C.75, C.78, C.103, C.106, F.110 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.75, I:C.78, I:C.103, I:C.106 ZN.9: 5 residues within 4Å: Chain J: C.7, C.10, R.43, C.45, C.46 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:C.7, J:C.10, J:C.45, J:C.46 ZN.10: 4 residues within 4Å: Chain L: C.31, C.34, C.48, C.51 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:C.31, L:C.34, L:C.48, L:C.51

1 x MG: MAGNESIUM ION(Non-covalent)

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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gao, S. et al., Molecular Mechanism of RNA Polymerase II Transcriptional Mutagenesis by the Epimerizable DNA Lesion, Fapy·dG. J.Am.Chem.Soc. (2024)

Release Date

2024-04-24

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
A

D
B

E
C

F
E

G
F

H
H

I
I

J
J

K
K

L
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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