SMTL ID : 2nvt.1

RNA Polymerase II Elongation Complex in 150 mM Mg+2 with GMPCPP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.36 Å

Oligo State

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

Ligands

1 x DG- DT- DA- DC- DT- DT- DG: 5'-D(*GP*TP*AP*CP*TP*TP*G)-3'(Non-covalent)

DG-DT-DA-DC-DT-DT-DG.1: 11 residues within 4Å: Chain B: C.1, A.2, A.3, G.4, A.6, T.8, T.9 Chain C: K.101, K.1102, K.1109, H.1387 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.1386, C:R.1386, C:E.1404, C:E.1404

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

G2P.2: 10 residues within 4Å: Chain A: C.10 Chain B: C.11, G.12 Chain C: R.446, P.448, N.479, D.483 Chain D: Y.769 Ligands: MG.5, MG.6 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:R.446, C:N.479, D:R.766, D:Y.769

8 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain C: C.107, 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: 5 residues within 4Å: Chain E: C.86, C.88, H.91, 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: 6 residues within 4Å: Chain J: C.7, S.9, C.10, R.43, 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: 2 residues within 4Å: Chain C: D.481 Ligands: G2P.2 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.481 MG.6: 5 residues within 4Å: Chain A: C.10 Chain C: D.481, D.483, D.485 Ligands: G2P.2 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.481, C:D.483, C:D.483, C:D.485

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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