SMTL ID : 2r93.1

Elongation complex of RNA polymerase II with a hepatitis delta virus-derived RNA stem loop

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 4.00 Å

Oligo State

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

Ligands

8 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain B: C.107, M.108, C.110, C.148, C.167 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:C.110, B:C.148 ZN.2: 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.4: 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.5: 5 residues within 4Å: Chain D: C.86, C.88, H.91, 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.6: 5 residues within 4Å: Chain J: C.7, R.8, 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.7: 5 residues within 4Å: Chain J: C.75, C.78, C.103, C.106, H.108 2 PLIP interactions: 2 interactions with chain J Metal complexes: J:C.75, J:C.106 ZN.8: 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.9: 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 MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: C.18 Chain B: D.481, D.483, D.485 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.481, B:D.481, B:D.483, B:D.483, B:D.485

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lehmann, E. et al., Molecular basis of RNA-dependent RNA polymerase II activity. Nature (2007)

Release Date

2007-11-27

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 polymerase II subunit RPB4: 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 polymerase II subunit RPB7: 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:

B
A

C
B

D
C

E
D

F
E

G
F

H
G

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 polymerase II subunit RPB4

DNA-directed RNA polymerases I, II, and III subunit RPABC1

DNA-directed RNA polymerases I, II, and III subunit RPABC2

DNA-directed RNA polymerase II subunit RPB7

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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