SMTL ID : 1twf.2 (1 other biounit)

RNA polymerase II complexed with UTP at 2.3 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

hetero-2-2-2-2-2-2-2-2-2-2-mer

Ligands

16 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.107, C.110, C.148, 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.2: 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.5: 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: 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.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: 6 residues within 4Å: Chain G: C.75, K.77, C.78, C.103, C.106, H.108 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.75, G:C.78, G:C.103, G:C.106 ZN.10: 5 residues within 4Å: Chain H: C.7, C.10, R.43, 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, C.48, K.49, C.51 3 PLIP interactions: 3 interactions with chain J Metal complexes: J:C.31, J:C.34, J:C.48 ZN.12: 4 residues within 4Å: Chain K: C.107, C.110, C.148, C.167 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:C.107, K:C.110, K:C.148, K:C.167 ZN.13: 4 residues within 4Å: Chain K: C.67, C.70, C.77, H.80 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:C.67, K:C.70, K:C.77, K:H.80 ZN.16: 4 residues within 4Å: Chain L: C.1163, C.1166, C.1182, C.1185 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:C.1163, L:C.1166, L:C.1182, L:C.1185 ZN.18: 5 residues within 4Å: Chain M: C.86, C.88, H.91, C.92, C.95 4 PLIP interactions: 4 interactions with chain M Metal complexes: M:C.86, M:C.88, M:C.92, M:C.95 ZN.19: 5 residues within 4Å: Chain Q: C.7, C.10, C.29, T.31, C.32 4 PLIP interactions: 4 interactions with chain Q Metal complexes: Q:C.7, Q:C.10, Q:C.29, Q:C.32 ZN.20: 6 residues within 4Å: Chain Q: C.75, K.77, C.78, C.103, C.106, H.108 4 PLIP interactions: 4 interactions with chain Q Metal complexes: Q:C.75, Q:C.78, Q:C.103, Q:C.106 ZN.21: 5 residues within 4Å: Chain R: C.7, C.10, R.43, C.45, C.46 4 PLIP interactions: 4 interactions with chain R Metal complexes: R:C.7, R:C.10, R:C.45, R:C.46 ZN.22: 5 residues within 4Å: Chain T: C.31, C.34, C.48, K.49, C.51 3 PLIP interactions: 3 interactions with chain T Metal complexes: T:C.31, T:C.34, T:C.48

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

MN.3: 5 residues within 4Å: Chain A: D.481, D.483, D.485 Ligands: MN.4, UTP.6 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.481, A:D.483, A:D.485 MN.4: 6 residues within 4Å: Chain A: D.481, D.483 Chain B: D.837, R.1020 Ligands: MN.3, UTP.6 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Metal complexes: B:D.837, A:D.481, A:D.483 MN.14: 5 residues within 4Å: Chain K: D.481, D.483, D.485 Ligands: MN.15, UTP.17 3 PLIP interactions: 3 interactions with chain K Metal complexes: K:D.481, K:D.483, K:D.485 MN.15: 6 residues within 4Å: Chain K: D.481, D.483 Chain L: D.837, R.1020 Ligands: MN.14, UTP.17 3 PLIP interactions: 2 interactions with chain K, 1 interactions with chain L Metal complexes: K:D.481, K:D.483, L:D.837

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

UTP.6: 10 residues within 4Å: Chain A: D.481, D.483, D.485 Chain B: R.766, E.836, Q.986, K.987, R.1020 Ligands: MN.3, MN.4 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Q.986, B:R.1020, A:D.483 Salt bridges: B:R.766, B:K.987, B:R.1020 pi-Cation interactions: A:K.752 UTP.17: 10 residues within 4Å: Chain K: D.481, D.483, D.485 Chain L: R.766, E.836, Q.986, K.987, R.1020 Ligands: MN.14, MN.15 7 PLIP interactions: 2 interactions with chain K, 5 interactions with chain L Hydrogen bonds: K:D.483, L:Q.986, L:R.1020 pi-Cation interactions: K:K.752 Salt bridges: L:R.766, L:K.987, L: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: AK
DNA-directed RNA polymerase II 140 kDa polypeptide: BL
DNA-directed RNA polymerase II 45 kDa polypeptide: CM
DNA-directed RNA polymerases I, II, and III 27 kDa polypeptide: DN
DNA-directed RNA polymerases I, II, and III 23 kDa polypeptide: EO
DNA-directed RNA polymerases I, II, and III 14.5 kDa polypeptide: FP
DNA-directed RNA polymerase II 14.2 kDa polypeptide: GQ
DNA-directed RNA polymerases I, II, and III 8.3 kDa polypeptide: HR
DNA-directed RNA polymerase II 13.6 kDa polypeptide: IS
DNA-directed RNA polymerases I, II, and III 7.7 kDa polypeptide: JT

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

K
A

B
B

L
B

C
C

M
C

D
E

N
E

E
F

O
F

F
H

P
H

G
I

Q
I

H
J

R
J

I
K

S
K

J
L

T
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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