SMTL ID : 1twh.1

RNA polymerase II complexed with 2'dATP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.40 Å

Oligo State

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

Ligands

2 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 5 residues within 4Å: Chain A: D.481, D.483, D.485 Ligands: MN.2, ATP.5 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.481, A:D.483, A:D.485 MN.2: 5 residues within 4Å: Chain A: D.481, D.483 Chain B: D.837 Ligands: MN.1, ATP.5 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Metal complexes: A:D.481, A:D.483, B:D.837

8 x ZN: ZINC ION(Non-covalent)

ZN.3: 5 residues within 4Å: Chain A: C.107, C.110, C.148, G.166, C.167 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.107, A:C.110, A:C.148, A:C.167 ZN.4: 4 residues within 4Å: Chain A: C.67, C.70, C.77, H.80 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.67, A:C.70, A:C.77, A:H.80 ZN.6: 4 residues within 4Å: Chain B: C.1163, C.1166, C.1182, C.1185 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.1163, B:C.1166, B:C.1182, B:C.1185 ZN.7: 4 residues within 4Å: Chain C: C.86, C.88, 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.8: 5 residues within 4Å: Chain G: C.7, C.10, C.29, T.31, C.32 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.7, G:C.10, G:C.29, G:C.32 ZN.9: 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.10: 4 residues within 4Å: Chain H: C.7, C.10, C.45, C.46 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:C.7, H:C.10, H:C.45, H:C.46 ZN.11: 5 residues within 4Å: Chain J: C.31, C.34, S.36, C.48, C.51 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:C.31, J:C.34, J:C.48, J:C.51

1 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.5: 10 residues within 4Å: Chain A: D.481, D.483, D.485 Chain B: R.766, D.837, Q.986, K.987, R.1020 Ligands: MN.1, MN.2 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.766, B:Q.986, A:D.481 Salt bridges: B:R.766, B:K.987, B:R.1020

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Westover, K.D. et al., Structural basis of transcription: nucleotide selection by rotation in the RNA polymerase II active center. Cell(Cambridge,Mass.) (2004)

Release Date

2004-11-16

Peptides

DNA-directed RNA polymerase II largest subunit: A
DNA-directed RNA polymerase II 140 kDa polypeptide: B
DNA-directed RNA polymerase II 45 kDa polypeptide: C
DNA-directed RNA polymerases I, II, and III 27 kDa polypeptide: D
DNA-directed RNA polymerases I, II, and III 23 kDa polypeptide: E
DNA-directed RNA polymerases I, II, and III 14.5 kDa polypeptide: F
DNA-directed RNA polymerase II 14.2 kDa polypeptide: G
DNA-directed RNA polymerases I, II, and III 8.3 kDa polypeptide: H
DNA-directed RNA polymerase II 13.6 kDa polypeptide: I
DNA-directed RNA polymerases I, II, and III 7.7 kDa polypeptide: 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 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 14.2 kDa polypeptide

DNA-directed RNA polymerases I, II, and III 8.3 kDa polypeptide

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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