SMTL ID : 2nvz.1

RNA Polymerase II elongation complex with UTP, updated 11/2006

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 4.30 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: 3 residues within 4Å: Chain D: M.108, C.110, C.167 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:C.110, D:C.167 ZN.2: 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: 4 residues within 4Å: Chain E: C.1163, C.1166, C.1182, C.1185 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:C.1166, E:C.1182, E:C.1185 ZN.7: 5 residues within 4Å: Chain F: C.86, C.88, H.91, 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.8: 5 residues within 4Å: Chain J: C.7, C.10, C.29, R.30, C.32 3 PLIP interactions: 3 interactions with chain J Metal complexes: J:C.10, J:C.29, J:C.32 ZN.9: 5 residues within 4Å: Chain J: C.75, C.78, S.80, C.103, C.106 5 PLIP interactions: 5 interactions with chain J Metal complexes: J:C.75, J:C.78, J:C.78, J:S.80, J:C.103 ZN.10: 5 residues within 4Å: Chain K: C.7, S.9, 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.11: 4 residues within 4Å: Chain M: C.31, C.34, C.48, C.51 3 PLIP interactions: 3 interactions with chain M Metal complexes: M:C.34, M:C.48, M:C.51

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 6 residues within 4Å: Chain A: A.10 Chain D: D.481, D.483, D.485 Ligands: MG.4, UTP.6 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:D.483, D:D.483, D:D.485 MG.4: 6 residues within 4Å: Chain D: D.481, D.483 Chain E: D.837, R.1020 Ligands: MG.3, UTP.6 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain E Metal complexes: D:D.481, D:D.483, E:D.837

1 x UTP: URIDINE 5'-TRIPHOSPHATE(Non-covalent)

UTP.6: 18 residues within 4Å: Chain A: A.10 Chain B: A.18 Chain D: R.446, N.479, D.481, D.483, D.485, T.827, Q.1078, N.1082, H.1085 Chain E: R.766, Y.769, D.837, K.987, R.1020 Ligands: MG.3, MG.4 10 PLIP interactions: 7 interactions with chain D, 3 interactions with chain E Hydrophobic interactions: D:T.827 Hydrogen bonds: D:R.446, D:R.446, D:N.479, D:D.481, D:D.481 Salt bridges: D:H.1085, E:R.766, E:R.1020, E:R.1020

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, D. et al., Structural basis of transcription: role of the trigger loop in substrate specificity and catalysis. Cell(Cambridge,Mass.) (2006)

Release Date

2006-12-19

Peptides

DNA-directed RNA polymerase II largest subunit: D
DNA-directed RNA polymerase II 140 kDa polypeptide: E
DNA-directed RNA polymerase II 45 kDa polypeptide: F
DNA-directed RNA polymerases I, II, and III 27 kDa polypeptide: G
DNA-directed RNA polymerases I, II, and III 23 kDa polypeptide: H
DNA-directed RNA polymerases I, II, and III 14.5 kDa polypeptide: I
DNA-directed RNA polymerase II subunit 9: J
DNA-directed RNA polymerases I/II/III subunit 10: K
DNA-directed RNA polymerase II 13.6 kDa polypeptide: L
DNA-directed RNA polymerases I, II, and III 7.7 kDa polypeptide: 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 largest subunit

DNA-directed RNA polymerase II 140 kDa polypeptide

DNA-directed RNA polymerase II 45 kDa polypeptide

DNA-directed RNA polymerases I, II, and III 27 kDa polypeptide

DNA-directed RNA polymerases I, II, and III 23 kDa polypeptide

DNA-directed RNA polymerases I, II, and III 14.5 kDa polypeptide

DNA-directed RNA polymerase II subunit 9

DNA-directed RNA polymerases I/II/III subunit 10

DNA-directed RNA polymerase II 13.6 kDa polypeptide

DNA-directed RNA polymerases I, II, and III 7.7 kDa polypeptide

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