SMTL ID : 6s85.1

Cutting state of the E. coli Mre11-Rad50 (SbcCD) head complex bound to ADP and dsDNA.

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-mer

Ligands

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 18 residues within 4Å: Chain A: N.12, S.13, G.40, A.41, G.42, K.43, T.44, T.45, D.70, T.73, Q.155 Chain B: R.921, Y.922, R.946, T.950, S.952, G.953 Ligands: MG.2 16 PLIP interactions: 5 interactions with chain B, 11 interactions with chain A Hydrogen bonds: B:R.921, B:Y.922, B:R.946, B:G.953, A:S.13, A:G.40, A:G.40, A:G.42, A:K.43, A:T.44, A:T.44, A:T.45, A:T.45, A:D.70, A:Q.155 pi-Cation interactions: B:R.946 ADP.3: 20 residues within 4Å: Chain A: R.921, Y.922, R.946, S.952, G.953, E.955 Chain B: N.12, S.13, G.40, G.42, K.43, T.44, T.45, R.60, D.70, L.71, M.72, R.74, Q.155 Ligands: MG.4 20 PLIP interactions: 8 interactions with chain A, 12 interactions with chain B Hydrogen bonds: A:R.921, A:R.921, A:R.946, A:R.946, A:G.953, A:E.955, B:G.40, B:G.40, B:G.42, B:K.43, B:T.44, B:T.44, B:T.44, B:T.45, B:D.70, B:R.74 pi-Cation interactions: A:R.946, A:R.946 Salt bridges: B:K.43, B:R.60

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: K.43, T.44, Q.155 Ligands: ADP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.44 MG.4: 5 residues within 4Å: Chain B: T.44, Q.155, D.983, E.984 Ligands: ADP.3 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:T.44, B:E.984

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

MN.5: 7 residues within 4Å: Chain C: D.8, H.10, D.48, H.224 Chain F: A.57, G.58 Ligands: MN.6 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.8, C:H.10, C:D.48 MN.6: 7 residues within 4Å: Chain C: D.48, N.83, H.184, H.222 Chain F: A.57, G.58 Ligands: MN.5 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.48, C:H.184, C:H.222 MN.7: 5 residues within 4Å: Chain D: D.8, H.10, D.48, H.224 Ligands: MN.8 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:H.10, D:D.48, D:H.224 MN.8: 5 residues within 4Å: Chain D: D.48, N.83, H.184, H.222 Ligands: MN.7 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.48, D:D.48, D:H.184, D:H.222

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kashammer, L. et al., Mechanism of DNA End Sensing and Processing by the Mre11-Rad50 Complex. Mol.Cell (2019)

Release Date

2019-09-04

Peptides

Nuclease SbcCD subunit C: AB
Nuclease SbcCD subunit D: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

C
A

D
B

Nuclease SbcCD subunit C

Nuclease SbcCD subunit D

Related Entries With Identical Sequence