SMTL ID : 6upy.1

RNA polymerase II elongation complex with 5-guanidinohydantoin lesion in state 2E

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.40 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: C.20, C.21, T.22, C.23, T.24, C.25, G.26, A.27, T.28 Chain C: K.323, R.350, R.446, Q.447, D.483, D.485 Chain D: Q.481, P.528, Q.776, K.979, K.987, H.1097, R.1124 Ligands: MG.4, APC.5 Protein-ligand interaction information (PLIP) not available

8 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain C: C.107, M.108, C.110, C.148, C.167 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:C.107, C:M.108, C:C.110, C:C.148, C:C.167 ZN.3: 5 residues within 4Å: Chain C: C.67, C.70, E.72, C.77, H.80 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.67, C:C.70, C:C.77, C:H.80 ZN.6: 4 residues within 4Å: Chain D: C.1163, C.1166, C.1182, C.1185 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.1163, D:C.1166, D:C.1182, D:C.1185 ZN.7: 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.8: 5 residues within 4Å: Chain I: C.7, C.10, C.29, T.31, 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.9: 5 residues within 4Å: Chain I: C.75, C.78, S.80, C.103, C.106 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.75, I:C.78, I:C.103, I:C.106 ZN.10: 4 residues within 4Å: Chain J: C.7, C.10, C.45, C.46 3 PLIP interactions: 3 interactions with chain J Metal complexes: J:C.7, J:C.45, J:C.46 ZN.11: 5 residues within 4Å: Chain L: C.31, C.34, S.36, C.48, C.51 5 PLIP interactions: 5 interactions with chain L Metal complexes: L:C.31, L:C.34, L:S.36, L:C.48, L:C.51

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 5 residues within 4Å: Chain C: R.446, D.481, D.483, D.485 Ligands: A-U-C-G-A-G-A-G-G.1 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.483, C:D.485, C:D.485

1 x APC: DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER(Non-covalent)

APC.5: 5 residues within 4Å: Chain C: N.479, K.752 Chain D: S.1019, R.1020 Ligands: A-U-C-G-A-G-A-G-G.1 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:Y.769, D:S.1019, D:R.1020, D:R.1020, C:N.479, C:K.752

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: 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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