SMTL ID : 2r7z.1

Cisplatin lesion containing RNA polymerase II elongation complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.80 Å

Oligo State

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

Ligands

1 x DC- DA- DA- DG- DT- DA- DG: 5'-D(*CP*AP*AP*GP*TP*AP*G)-3'(Non-covalent)

DC-DA-DA-DG-DT-DA-DG.1: 13 residues within 4Å: Chain A: T.1, A.2, C.3, T.4, T.5, G.6, G.7 Chain C: K.100, K.101, K.1109, N.1110, H.1387 Chain D: K.507 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:T.831 Hydrogen bonds: C:R.350, C:Q.447, C:Y.836, C:R.1386, C:E.1403 Salt bridges: C:K.330, C:K.332, C:K.332, C:R.337

1 x CPT: Cisplatin(Non-functional Binders)

CPT.2: 3 residues within 4Å: Chain A: T.5, G.6, G.7 No protein-ligand interaction detected (PLIP)

8 x ZN: ZINC ION(Non-covalent)

ZN.3: 5 residues within 4Å: Chain C: M.108, C.110, C.148, G.166, C.167 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:C.110, C:C.148, C:C.167 ZN.4: 4 residues within 4Å: Chain C: C.67, C.70, 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: 4 residues within 4Å: Chain K: C.7, C.10, C.29, C.32 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:C.7, K:C.10, K:C.29, K:C.32 ZN.9: 5 residues within 4Å: Chain K: C.75, C.78, C.103, C.106, H.108 2 PLIP interactions: 2 interactions with chain K Metal complexes: K:C.78, K:C.106 ZN.10: 5 residues within 4Å: Chain L: C.7, C.10, R.43, C.45, C.46 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:C.7, L:C.10, L:C.45, L:C.46 ZN.11: 4 residues within 4Å: Chain N: C.31, C.34, C.48, C.51 3 PLIP interactions: 3 interactions with chain N Metal complexes: N:C.31, N:C.34, N:C.48

1 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 4 residues within 4Å: Chain B: G.10 Chain C: D.481, D.483, D.485 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.481, C:D.481, C:D.483, C:D.483

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Damsma, G.E. et al., Mechanism of transcriptional stalling at cisplatin-damaged DNA. Nat.Struct.Mol.Biol. (2007)

Release Date

2007-11-20

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 polymerase II subunit RPB4: 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 polymerase II subunit RPB7: I
DNA-directed RNA polymerases I, II, and III subunit RPABC3: J
DNA-directed RNA polymerase II subunit RPB9: K
DNA-directed RNA polymerases I, II, and III subunit RPABC5: L
DNA-directed RNA polymerase II subunit RPB11: M
DNA-directed RNA polymerases I, II, and III subunit RPABC4: N

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
A

D
B

E
C

F
D

G
E

H
F

I
G

J
H

K
I

L
J

M
K

N
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

Related Entries With Identical Sequence