SMTL ID : 2e2j.1

RNA polymerase II elongation complex in 5 mM Mg+2 with GMPCPP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.50 Å

Oligo State

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

Ligands

1 x A- U- C- G- A- G- A- G- G: 5'-R(P*AP*UP*CP*GP*AP*GP*AP*GP*G)-3'(Non-covalent)

A-U-C-G-A-G-A-G-G.1: 29 residues within 4Å: Chain A: C.19, C.20, T.21, C.22, T.23, C.24, G.25, A.26, T.27 Chain C: K.323, R.350, R.446, Q.447, D.481, D.483, D.485 Chain D: A.477, G.478, Q.481, Q.531, A.772, Q.776, K.979, K.987, H.1097, Q.1112, R.1124 Ligands: G2P.2, MG.5 Protein-ligand interaction information (PLIP) not available

1 x G2P: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER(Non-covalent)

G2P.2: 11 residues within 4Å: Chain A: C.18, C.19 Chain C: R.446, P.448, N.479, D.481 Chain D: R.766, R.1020 Ligands: A-U-C-G-A-G-A-G-G.1, MG.5, MG.6 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:R.766, C:R.446, C:D.481 Salt bridges: D:R.1020

8 x ZN: ZINC ION(Non-covalent)

ZN.3: 5 residues within 4Å: Chain C: C.107, M.108, C.110, C.148, C.167 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.107, C:C.110, C:C.148, C:C.167 ZN.4: 5 residues within 4Å: Chain C: C.67, Q.68, C.70, C.77, H.80 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.67, C:C.70, C:C.77, C:H.80 ZN.7: 4 residues within 4Å: Chain D: C.1163, C.1166, C.1182, C.1185 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.1163, D:C.1166, D:C.1182, D:C.1185 ZN.8: 4 residues within 4Å: Chain E: C.86, C.88, C.92, C.95 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.86, E:C.88, E:C.92, E:C.95 ZN.9: 5 residues within 4Å: Chain I: C.7, C.10, C.29, T.31, C.32 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.7, I:C.10, I:C.29, I:C.32 ZN.10: 4 residues within 4Å: Chain I: C.75, C.78, C.103, C.106 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.75, I:C.78, I:C.103, I:C.106 ZN.11: 4 residues within 4Å: Chain J: C.7, C.10, C.45, C.46 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:C.7, J:C.10, J:C.45, J:C.46 ZN.12: 4 residues within 4Å: Chain L: C.31, C.34, C.48, C.51 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:C.31, L:C.34, L:C.48, L:C.51

2 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 6 residues within 4Å: Chain C: D.481, D.483, D.485 Ligands: A-U-C-G-A-G-A-G-G.1, G2P.2, MG.6 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.481, C:D.481, C:D.483, C:D.483, C:D.485 MG.6: 5 residues within 4Å: Chain C: D.481, D.483 Chain D: D.837 Ligands: G2P.2, MG.5 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.483

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

2006-12-12

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
A

D
B

E
C

F
E

G
F

H
H

I
I

J
J

K
K

L
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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