SMTL ID : 2nvx.1

RNA polymerase II elongation complex in 5 mM Mg+2 with 2'-dUTP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.60 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 D: C.107, C.110, C.148, C.167 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:C.107, D:C.148 ZN.2: 4 residues within 4Å: Chain D: C.67, C.70, C.77, H.80 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:C.67, D:C.70, D:C.77 ZN.4: 6 residues within 4Å: Chain E: C.1163, C.1166, G.1167, T.1170, C.1182, C.1185 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:C.1166 ZN.6: 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.7: 5 residues within 4Å: Chain J: C.7, C.10, C.29, T.31, C.32 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:C.10, J:C.10, J:C.29, J:C.32 ZN.8: 5 residues within 4Å: Chain J: C.75, C.78, S.80, C.103, C.106 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:C.75, J:C.78, J:C.103, J:C.106 ZN.9: 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.10: 5 residues within 4Å: Chain M: C.31, C.34, S.36, C.48, C.51 3 PLIP interactions: 3 interactions with chain M Metal complexes: M:C.31, M:C.34, M:C.51

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain D: D.481, D.483 Ligands: DUT.5 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.483

1 x DUT: DEOXYURIDINE-5'-TRIPHOSPHATE(Non-covalent)

DUT.5: 8 residues within 4Å: Chain A: A.10 Chain D: D.481, D.483, D.485, K.752 Chain E: S.1019, R.1020 Ligands: MG.3 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain E Hydrogen bonds: D:D.481, D:D.481, E:R.766, E:S.1019, 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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