SMTL ID : 6uq3.1

RNA polymerase II elongation complex with 5-guanidinohydantoin lesion in state 5

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.47 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: 6 residues within 4Å: Chain A: A.10, U.11 Chain D: R.446, D.481, D.483, D.485 3 PLIP interactions: 3 interactions with chain D Metal complexes: 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, M.108, C.110, C.148, C.167 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, Q.68, C.70, C.77, 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.5: 5 residues within 4Å: Chain E: C.1163, I.1165, 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: 4 residues within 4Å: Chain F: C.86, C.88, C.92, C.95 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.86, F:C.88, F:C.92, F:C.95 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: 6 residues within 4Å: Chain J: C.75, C.78, S.80, C.103, C.106, H.108 3 PLIP interactions: 3 interactions with chain J Metal complexes: J:C.75, J:C.78, J:C.103 ZN.9: 4 residues within 4Å: Chain K: C.7, C.10, 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: 4 residues within 4Å: Chain M: C.31, C.34, 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 PPV: PYROPHOSPHATE(Non-covalent)

PPV.4: 3 residues within 4Å: Chain D: K.752 Chain E: S.1019, R.1020 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain E Salt bridges: D:K.752, E:R.1020 Hydrogen bonds: E:S.1019

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Oh, J. et al., RNA polymerase II stalls on oxidative DNA damage via a torsion-latch mechanism involving lone pair-pi and CH-pi interactions. Proc.Natl.Acad.Sci.USA (2020)

Release Date

2020-06-10

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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