SMTL ID : 3m4o.1

RNA polymerase II elongation complex B

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.57 Å

Oligo State

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

Ligands

8 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.110, C.148, G.166, C.167 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:C.148 ZN.2: 4 residues within 4Å: Chain A: C.67, C.70, C.77, H.80 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.67, A:C.70, A:C.77 ZN.4: 5 residues within 4Å: Chain B: C.1163, I.1165, C.1166, C.1182, C.1185 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.1163, B:C.1166, B:C.1185 ZN.5: 5 residues within 4Å: Chain C: C.86, C.88, H.91, C.92, C.95 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.86, C:C.88, C:C.92, C:C.95 ZN.6: 4 residues within 4Å: Chain G: C.10, C.29, T.31, C.32 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:C.10, G:C.29, G:C.32 ZN.7: 4 residues within 4Å: Chain G: C.75, C.78, C.103, C.106 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.75, G:C.78, G:C.103, G:C.106 ZN.8: 5 residues within 4Å: Chain H: C.7, C.10, R.43, C.45, C.46 3 PLIP interactions: 3 interactions with chain H Metal complexes: H:C.10, H:C.45, H:C.46 ZN.9: 5 residues within 4Å: Chain J: C.31, C.34, S.36, C.48, C.51 3 PLIP interactions: 3 interactions with chain J Metal complexes: J:C.34, J:C.48, J:C.51

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: D.481, D.483, D.485 Chain K: A.10 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.481, A:D.481, A:D.483, A:D.483, A:D.485

1 x C7P: cis-diammine(pyridine)chloroplatinum(II)(Non-covalent)

C7P.10: 5 residues within 4Å: Chain A: A.828, V.829, A.832 Chain B: R.512 Chain L: G.18 1 PLIP interactions: 1 interactions with chain A, Hydrophobic interactions: A:V.829

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, D. et al., X-ray structure and mechanism of RNA polymerase II stalled at an antineoplastic monofunctional platinum-DNA adduct. Proc.Natl.Acad.Sci.USA (2010)

Release Date

2010-05-12

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
E

E
F

F
H

G
I

H
J

I
K

J
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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