Last updated on 2019-09-30 by Xiang-Jun Lu <xiangjun@x3dna.org>.
The block schematics were created with DSSR and
rendered using PyMOL.
- PDB-id
- 6C2F
- Class
- DNA binding protein-DNA
- Method
- X-ray (2.65 Å)
- Summary
- Mbd2 in complex with methylated DNA
List of 6 5mC-amino acid contacts:
-
B.5CM6: stacking-with-A.ARG188 is-WC-paired is-in-duplex [+]:CcG/CGG
-
E.5CM6: stacking-with-D.ARG188 is-WC-paired is-in-duplex [+]:CcG/CGG
-
H.5CM6: stacking-with-G.ARG188 is-WC-paired is-in-duplex [+]:CcG/CGG
-
K.5CM6: stacking-with-J.ARG188 is-WC-paired is-in-duplex [+]:CcG/CGG
-
N.5CM6: stacking-with-M.ARG188 is-WC-paired is-in-duplex [+]:CcG/CGG
-
Q.5CM6: stacking-with-P.ARG188 is-WC-paired is-in-duplex [+]:CcG/CGG
direct SNAP output · DNAproDB 2.0
- Reference
- Liu, K., Xu, C., Tempel, W., Arrowsmith, C.H., Bountra, C., Edwards, A.M., Min, J., Structural Genomics Consortium: "MBD2 in complex with methylated DNA." to be published
- Abstract
-
- The 5-methylcytosine group (PDB ligand '5CM') is shown in space-filling model,
with the methyl-carbon atom in black.
- Watson-Crick base pairs are represented as long rectangular blocks with the
minor-groove edge in black. Color code: A-T red, C-G yellow, G-C green, T-A blue.
- Protein is shown as cartoon in purple. DNA backbones are shown ribbon, colored code
by chain identifier.
- The block schematics were created with 3DNA-DSSR,
and images were rendered using PyMOL.
- Download the PyMOL session file corresponding to the top-left
image in the following panel.
- The contacts include paired nucleotides (mostly a G in G-C pairing), and
amino-acids within a 4.5-A distance cutoff to the base atoms of 5mC.
- The structure is oriented in the 'standard' base reference frame of 5mC, allowing for easy comparison
and direct superimposition between entries.
- The black sphere (•) denotes the 5-methyl carbon atom in 5mC.
 |
No. 1 B.5CM6: download PDB file
for the 5mC entry
stacking-with-A.ARG188 is-WC-paired is-in-duplex [+]:CcG/CGG
|
 |
No. 2 E.5CM6: download PDB file
for the 5mC entry
stacking-with-D.ARG188 is-WC-paired is-in-duplex [+]:CcG/CGG
|
 |
No. 3 H.5CM6: download PDB file
for the 5mC entry
stacking-with-G.ARG188 is-WC-paired is-in-duplex [+]:CcG/CGG
|
 |
No. 4 K.5CM6: download PDB file
for the 5mC entry
stacking-with-J.ARG188 is-WC-paired is-in-duplex [+]:CcG/CGG
|
 |
No. 5 N.5CM6: download PDB file
for the 5mC entry
stacking-with-M.ARG188 is-WC-paired is-in-duplex [+]:CcG/CGG
|
 |
No. 6 Q.5CM6: download PDB file
for the 5mC entry
stacking-with-P.ARG188 is-WC-paired is-in-duplex [+]:CcG/CGG
|
