SMTL ID : 4y7n.1

The Structure Insight into 5-Carboxycytosine Recognition by RNA Polymerase II during Transcription Elongation.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.30 Å

Oligo State

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

Ligands

1 x A- U- G- G- A- G- A- G- G: RNA (5'-D(*AP*UP*GP*GP*AP*GP*AP*GP*G)-3')(Non-covalent)

A-U-G-G-A-G-A-G-G.1: 25 residues within 4Å: Chain A: I.250, R.350, R.446, Q.447, P.448, D.483, D.485 Chain B: A.477, Q.481, Q.776, K.979, K.987, H.1097 Chain K: C.20, C.21, T.22, C.23, T.24, C.25, C.26, A.27, T.28, G.29 Ligands: MG.4, G2P.12 Protein-ligand interaction information (PLIP) not available

8 x ZN: ZINC ION(Non-covalent)

ZN.2: 6 residues within 4Å: Chain A: C.107, H.109, C.110, G.111, 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.3: 5 residues within 4Å: Chain A: C.67, Q.68, 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: 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: 4 residues within 4Å: Chain G: C.7, C.10, C.29, 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, C.48, K.49, C.51 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:C.31, J:C.34, J:C.48, J:C.51

2 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.4: 5 residues within 4Å: Chain A: D.481, D.483, D.485 Ligands: A-U-G-G-A-G-A-G-G.1, G2P.12 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.481, A:D.481, A:D.483, A:D.485, A:D.485 MG.5: 1 residues within 4Å: Ligands: G2P.12 No protein-ligand interaction detected (PLIP)

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

G2P.12: 12 residues within 4Å: Chain A: R.446, P.448, N.479, T.831 Chain B: R.766, Y.769, R.1020 Chain K: X.19, C.20 Ligands: A-U-G-G-A-G-A-G-G.1, MG.4, MG.5 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:R.446, A:R.446, A:N.479, B:R.766, B:Y.769, B:R.1020

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, L. et al., Molecular basis for 5-carboxycytosine recognition by RNA polymerase II elongation complex. Nature (2015)

Release Date

2015-07-15

Peptides

DNA-directed RNA polymerase II subunit RPB1: A
DNA-directed RNA polymerase II subunit RPB2,DNA-directed RNA polymerase II subunit RPB2: B
DNA-directed RNA polymerase II subunit RPB3: C
DNA-directed RNA polymerases I, II, and III subunit RPABC1: D
DNA-directed RNA polymerases I, II, and III subunit RPABC2: E
DNA-directed RNA polymerases I, II, and III subunit RPABC3: F
DNA-directed RNA polymerase II subunit RPB9: G
DNA-directed RNA polymerases I, II, and III subunit RPABC5: H
DNA-directed RNA polymerase II subunit RPB11: I
DNA-directed RNA polymerases I, II, and III subunit RPABC4: 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 subunit RPB1

DNA-directed RNA polymerase II subunit RPB2,DNA-directed RNA polymerase II subunit RPB2

DNA-directed RNA polymerase II subunit RPB3

DNA-directed RNA polymerases I, II, and III subunit RPABC1

DNA-directed RNA polymerases I, II, and III subunit RPABC2

DNA-directed RNA polymerases I, II, and III subunit RPABC3

DNA-directed RNA polymerase II subunit RPB9

DNA-directed RNA polymerases I, II, and III subunit RPABC5

DNA-directed RNA polymerase II subunit RPB11

DNA-directed RNA polymerases I, II, and III subunit RPABC4

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