SMTL ID : 8ukt.1

RNA polymerase II elongation complex with Fapy-dG lesion with AMP added

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.60 Å

Oligo State

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

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: G.9, A.10 Chain D: D.483, D.485 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.483, D:D.483, D:D.485, D:D.485

8 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain D: C.107, H.109, C.110, C.167, N.169 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:C.107, D:C.110, D:C.167 ZN.3: 5 residues within 4Å: Chain D: C.67, C.70, C.77, G.79, H.80 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.67, D:C.70, D:C.77, D:H.80 ZN.4: 4 residues within 4Å: Chain E: C.1163, C.1166, C.1182, C.1185 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.1163, E:C.1166, E:C.1182, E:C.1185 ZN.6: 5 residues within 4Å: Chain F: C.86, C.88, H.91, C.92, C.95 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:C.86, F:C.88, F:C.92 ZN.7: 4 residues within 4Å: Chain J: C.7, C.10, C.29, C.32 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:C.7, J:C.10, J:C.29, J:C.32 ZN.8: 5 residues within 4Å: Chain J: C.75, C.78, C.103, C.106, F.110 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:C.75, J:C.78, J:C.103, J:C.106 ZN.9: 5 residues within 4Å: Chain K: C.7, C.10, R.43, C.45, C.46 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:C.7, K:C.10, K:C.45, K:C.46 ZN.10: 5 residues within 4Å: Chain M: C.31, C.34, L.38, C.48, C.51 4 PLIP interactions: 4 interactions with chain M Metal complexes: M:C.31, M:C.34, M:C.48, M:C.51

1 x POP: PYROPHOSPHATE 2-(Non-covalent)

POP.5: 3 residues within 4Å: Chain D: K.752 Chain E: S.1019, R.1020 6 PLIP interactions: 2 interactions with chain D, 4 interactions with chain E Salt bridges: D:K.752, D:K.752, E:R.1020, E:R.1020 Hydrogen bonds: E:S.1019, E:S.1019

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

D
A

E
B

F
C

G
E

H
F

I
H

J
I

K
J

L
K

M
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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