SMTL ID : 1twg.2 (2 other biounits)

RNA polymerase II complexed with CTP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.30 Å

Oligo State

hetero-4-4-4-4-4-4-4-4-4-4-mer

Ligands

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

MN.1: 5 residues within 4Å: Chain A: D.481, D.483, D.485 Ligands: MN.2, CTP.6 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.481, A:D.483, A:D.485 MN.2: 6 residues within 4Å: Chain A: D.481, D.483 Chain B: D.837, Q.986 Ligands: MN.1, CTP.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.12: 5 residues within 4Å: Chain K: D.481, D.483, D.485 Ligands: MN.13, CTP.17 3 PLIP interactions: 3 interactions with chain K Metal complexes: K:D.481, K:D.483, K:D.485 MN.13: 6 residues within 4Å: Chain K: D.481, D.483 Chain L: D.837, Q.986 Ligands: MN.12, CTP.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 MN.23: 5 residues within 4Å: Chain U: D.481, D.483, D.485 Ligands: MN.24, CTP.28 3 PLIP interactions: 3 interactions with chain U Metal complexes: U:D.481, U:D.483, U:D.485 MN.24: 6 residues within 4Å: Chain U: D.481, D.483 Chain V: D.837, Q.986 Ligands: MN.23, CTP.28 3 PLIP interactions: 1 interactions with chain V, 2 interactions with chain U Metal complexes: V:D.837, U:D.481, U:D.483 MN.34: 5 residues within 4Å: Chain 4: D.481, D.483, D.485 Ligands: MN.35, CTP.39 3 PLIP interactions: 3 interactions with chain 4 Metal complexes: 4:D.481, 4:D.483, 4:D.485 MN.35: 6 residues within 4Å: Chain 4: D.481, D.483 Chain 5: D.837, Q.986 Ligands: MN.34, CTP.39 3 PLIP interactions: 1 interactions with chain 5, 2 interactions with chain 4 Metal complexes: 5:D.837, 4:D.481, 4:D.483

32 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 3 PLIP interactions: 3 interactions with chain A Metal complexes: 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: 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: 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: 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 ZN.14: 5 residues within 4Å: Chain K: C.107, C.110, C.148, G.166, 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.15: 4 residues within 4Å: Chain K: C.67, C.70, C.77, H.80 3 PLIP interactions: 3 interactions with chain K Metal complexes: 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: 4 residues within 4Å: Chain M: C.86, C.88, 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: 4 residues within 4Å: Chain R: C.7, C.10, 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, S.36, C.48, C.51 4 PLIP interactions: 4 interactions with chain T Metal complexes: T:C.31, T:C.34, T:C.48, T:C.51 ZN.25: 5 residues within 4Å: Chain U: C.107, C.110, C.148, G.166, C.167 4 PLIP interactions: 4 interactions with chain U Metal complexes: U:C.107, U:C.110, U:C.148, U:C.167 ZN.26: 4 residues within 4Å: Chain U: C.67, C.70, C.77, H.80 3 PLIP interactions: 3 interactions with chain U Metal complexes: U:C.70, U:C.77, U:H.80 ZN.27: 4 residues within 4Å: Chain V: C.1163, C.1166, C.1182, C.1185 4 PLIP interactions: 4 interactions with chain V Metal complexes: V:C.1163, V:C.1166, V:C.1182, V:C.1185 ZN.29: 4 residues within 4Å: Chain W: C.86, C.88, C.92, C.95 4 PLIP interactions: 4 interactions with chain W Metal complexes: W:C.86, W:C.88, W:C.92, W:C.95 ZN.30: 5 residues within 4Å: Chain 0: C.7, C.10, C.29, T.31, C.32 4 PLIP interactions: 4 interactions with chain 0 Metal complexes: 0:C.7, 0:C.10, 0:C.29, 0:C.32 ZN.31: 6 residues within 4Å: Chain 0: C.75, K.77, C.78, C.103, C.106, H.108 4 PLIP interactions: 4 interactions with chain 0 Metal complexes: 0:C.75, 0:C.78, 0:C.103, 0:C.106 ZN.32: 4 residues within 4Å: Chain 1: C.7, C.10, C.45, C.46 4 PLIP interactions: 4 interactions with chain 1 Metal complexes: 1:C.7, 1:C.10, 1:C.45, 1:C.46 ZN.33: 5 residues within 4Å: Chain 3: C.31, C.34, S.36, C.48, C.51 4 PLIP interactions: 4 interactions with chain 3 Metal complexes: 3:C.31, 3:C.34, 3:C.48, 3:C.51 ZN.36: 5 residues within 4Å: Chain 4: C.107, C.110, C.148, G.166, C.167 4 PLIP interactions: 4 interactions with chain 4 Metal complexes: 4:C.107, 4:C.110, 4:C.148, 4:C.167 ZN.37: 4 residues within 4Å: Chain 4: C.67, C.70, C.77, H.80 3 PLIP interactions: 3 interactions with chain 4 Metal complexes: 4:C.70, 4:C.77, 4:H.80 ZN.38: 4 residues within 4Å: Chain 5: C.1163, C.1166, C.1182, C.1185 4 PLIP interactions: 4 interactions with chain 5 Metal complexes: 5:C.1163, 5:C.1166, 5:C.1182, 5:C.1185 ZN.40: 4 residues within 4Å: Chain 6: C.86, C.88, C.92, C.95 4 PLIP interactions: 4 interactions with chain 6 Metal complexes: 6:C.86, 6:C.88, 6:C.92, 6:C.95 ZN.41: 5 residues within 4Å: Chain a: C.7, C.10, C.29, T.31, C.32 4 PLIP interactions: 4 interactions with chain a Metal complexes: a:C.7, a:C.10, a:C.29, a:C.32 ZN.42: 6 residues within 4Å: Chain a: C.75, K.77, C.78, C.103, C.106, H.108 4 PLIP interactions: 4 interactions with chain a Metal complexes: a:C.75, a:C.78, a:C.103, a:C.106 ZN.43: 4 residues within 4Å: Chain b: C.7, C.10, C.45, C.46 4 PLIP interactions: 4 interactions with chain b Metal complexes: b:C.7, b:C.10, b:C.45, b:C.46 ZN.44: 5 residues within 4Å: Chain d: C.31, C.34, S.36, C.48, C.51 4 PLIP interactions: 4 interactions with chain d Metal complexes: d:C.31, d:C.34, d:C.48, d:C.51

4 x CTP: CYTIDINE-5'-TRIPHOSPHATE(Non-covalent)

CTP.6: 9 residues within 4Å: Chain A: D.481, D.483, D.485 Chain B: R.766, Q.986, K.987, R.1020 Ligands: MN.1, MN.2 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.766, B:Q.986 Salt bridges: B:R.766, B:K.987 CTP.17: 9 residues within 4Å: Chain K: D.481, D.483, D.485 Chain L: R.766, Q.986, K.987, R.1020 Ligands: MN.12, MN.13 5 PLIP interactions: 1 interactions with chain K, 4 interactions with chain L Hydrogen bonds: K:D.481, L:R.766, L:Q.986 Salt bridges: L:R.766, L:K.987 CTP.28: 9 residues within 4Å: Chain U: D.481, D.483, D.485 Chain V: R.766, Q.986, K.987, R.1020 Ligands: MN.23, MN.24 4 PLIP interactions: 4 interactions with chain V Hydrogen bonds: V:R.766, V:Q.986 Salt bridges: V:R.766, V:K.987 CTP.39: 9 residues within 4Å: Chain 4: D.481, D.483, D.485 Chain 5: R.766, Q.986, K.987, R.1020 Ligands: MN.34, MN.35 4 PLIP interactions: 4 interactions with chain 5 Hydrogen bonds: 5:R.766, 5:Q.986 Salt bridges: 5:R.766, 5:K.987

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: AKU4
DNA-directed RNA polymerase II 140 kDa polypeptide: BLV5
DNA-directed RNA polymerase II 45 kDa polypeptide: CMW6
DNA-directed RNA polymerases I, II, and III 27 kDa polypeptide: DNX7
DNA-directed RNA polymerases I, II, and III 23 kDa polypeptide: EOY8
DNA-directed RNA polymerases I, II, and III 14.5 kDa polypeptide: FPZ9
DNA-directed RNA polymerase II 14.2 kDa polypeptide: GQ0a
DNA-directed RNA polymerases I, II, and III 8.3 kDa polypeptide: HR1b
DNA-directed RNA polymerase II 13.6 kDa polypeptide: IS2c
DNA-directed RNA polymerases I, II, and III 7.7 kDa polypeptide: JT3d

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

K
A

U
A

4
A

B
B

L
B

V
B

5
B

C
C

M
C

W
C

6
C

D
E

N
E

X
E

7
E

E
F

O
F

Y
F

8
F

F
H

P
H

Z
H

9
H

G
I

Q
I

0
I

a
I

H
J

R
J

1
J

b
J

I
K

S
K

2
K

c
K

J
L

T
L

3
L

d
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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