SMTL ID : 6s6v.1

Resting state of the E. coli Mre11-Rad50 (SbcCD) head complex bound to ATPgS

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-mer

Ligands

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

MN.1: 7 residues within 4Å: Chain A: D.8, H.10, D.48, H.184, H.222, H.224 Ligands: MN.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.8, A:H.10, A:D.48, A:H.224 MN.2: 6 residues within 4Å: Chain A: D.8, D.48, N.83, H.184, H.222 Ligands: MN.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.48, A:H.184, A:H.222 MN.3: 7 residues within 4Å: Chain B: D.8, H.10, D.48, H.184, H.222, H.224 Ligands: MN.4 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.8, B:H.10, B:D.48, B:H.224 MN.4: 6 residues within 4Å: Chain B: D.8, D.48, N.83, H.184, H.222 Ligands: MN.3 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.48, B:H.184, B:H.222

2 x AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER(Covalent)

AGS.5: 24 residues within 4Å: Chain C: Y.922, Q.941, R.946, T.950, S.952, G.954, E.955 Chain D: N.12, S.13, P.38, G.40, A.41, G.42, K.43, T.44, T.45, R.60, D.70, L.71, M.72, T.73, R.74, Q.155 Ligands: MG.8 19 PLIP interactions: 14 interactions with chain D, 5 interactions with chain C Hydrogen bonds: D:S.13, D:G.40, D:A.41, D:G.42, D:K.43, D:K.43, D:T.44, D:T.45, D:D.70, D:R.74, D:Q.155, D:Q.155, C:Y.922, C:S.952, C:G.953, C:G.954, C:E.955 Salt bridges: D:K.43, D:R.60 AGS.7: 24 residues within 4Å: Chain C: N.12, S.13, G.40, A.41, G.42, K.43, T.44, T.45, R.60, L.71, M.72, T.73, R.74, Q.155, H.1016 Chain D: Y.922, Q.941, R.946, T.950, S.952, G.953, G.954, E.955 Ligands: MG.6 23 PLIP interactions: 16 interactions with chain C, 7 interactions with chain D Hydrogen bonds: C:S.13, C:G.40, C:G.40, C:A.41, C:G.42, C:K.43, C:K.43, C:T.44, C:T.44, C:T.45, C:D.70, C:R.74, C:Q.155, C:Q.155, D:Y.922, D:R.946, D:T.950, D:S.952, D:G.953, D:G.954 Salt bridges: C:K.43, C:R.60 pi-Cation interactions: D:R.946

2 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 3 residues within 4Å: Chain C: T.44, Q.155 Ligands: AGS.7 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.44 MG.8: 3 residues within 4Å: Chain D: T.44, Q.155 Ligands: AGS.5 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.44

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 D: AB
Nuclease SbcCD subunit C: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Nuclease SbcCD subunit D

Nuclease SbcCD subunit C

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