SMTL ID : 7yzp.1

Hairpin-bound state of the E. coli Mre11-Rad50 (SbcCD) head complex bound to ADP and a DNA hairpin

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-mer

Ligands

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

MN.1: 4 residues within 4Å: Chain B: D.8, H.10, D.48, H.224 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:H.10, B:H.224 MN.2: 4 residues within 4Å: Chain B: D.48, N.83, H.184, H.222 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:H.184, B:H.222 MN.3: 4 residues within 4Å: Chain C: D.8, H.10, D.48, H.224 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.8, C:D.8, C:H.10, C:H.224 MN.4: 5 residues within 4Å: Chain C: D.48, G.82, N.83, Q.84, H.184 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.48, C:D.48, C:H.184

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

ADP.5: 19 residues within 4Å: Chain D: N.12, S.13, T.39, G.40, A.41, G.42, K.43, T.44, T.45, D.70, M.72, T.73, R.74, Q.155 Chain E: R.946, T.950, S.952, G.953 Ligands: MG.6 17 PLIP interactions: 5 interactions with chain E, 12 interactions with chain D Hydrogen bonds: E:R.946, E:S.952, E:S.952, E:G.953, D:G.40, D:G.42, D:K.43, D:T.44, D:T.44, D:T.45, D:T.45, D:R.74, D:R.74, D:R.74, D:Q.155, D:Q.155 pi-Cation interactions: E:R.946 ADP.7: 20 residues within 4Å: Chain D: Y.922, Q.941, R.946, T.950, S.952, G.953, E.955 Chain E: N.12, S.13, T.39, G.40, G.42, K.43, T.44, T.45, R.60, D.70, M.72, R.74 Ligands: MG.8 19 PLIP interactions: 12 interactions with chain E, 7 interactions with chain D Hydrogen bonds: E:S.13, E:G.40, E:G.40, E:G.42, E:K.43, E:T.44, E:T.45, E:D.70, E:R.74, E:R.74, D:Y.922, D:Q.941, D:R.946, D:R.946, D:G.953, D:E.955 Salt bridges: E:K.43, E:R.60 pi-Cation interactions: D:R.946

2 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 4 residues within 4Å: Chain D: T.44, Q.155, D.983 Ligands: ADP.5 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.44 MG.8: 3 residues within 4Å: Chain E: T.44, D.983 Ligands: ADP.7 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.44

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gut, F. et al., Structural mechanism of endonucleolytic processing of blocked DNA ends and hairpins by Mre11-Rad50. Mol.Cell (2022)

Release Date

2022-08-17

Peptides

Nuclease SbcCD subunit D: BC
Nuclease SbcCD subunit C: DE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

B
A

C
B

D
C

E
D

Nuclease SbcCD subunit D

Nuclease SbcCD subunit C

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