SMTL ID : 3tho.2 (2 other biounits)

Crystal structure of Mre11:Rad50 in its ATP/ADP bound state

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.61 Å

Oligo State

hetero-oligomer

Ligands

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

ADP.1: 24 residues within 4Å: Chain A: L.29, G.30, P.48, N.49, G.50, A.51, G.52, K.53, S.54, S.55, R.70, Y.71, D.76, V.78, N.79, R.80, E.328 Chain C: R.271, R.292, G.296, L.297, S.298, E.301 Ligands: MG.2 26 PLIP interactions: 18 interactions with chain A, 8 interactions with chain C Hydrogen bonds: A:G.50, A:G.50, A:A.51, A:G.52, A:K.53, A:S.54, A:S.55, A:Y.71, A:Y.71, A:R.80, C:R.271, C:R.292, C:S.298, C:S.298, C:E.301 Water bridges: A:N.49, A:K.53, A:S.54, A:S.54, A:R.80, A:N.81, C:R.271 Salt bridges: A:K.53, A:R.70 pi-Cation interactions: C:R.292, C:R.292 ADP.15: 24 residues within 4Å: Chain A: R.271, R.292, G.296, L.297, S.298, E.301 Chain C: L.29, G.30, P.48, N.49, G.50, A.51, G.52, K.53, S.54, S.55, R.70, Y.71, D.76, V.78, N.79, R.80, E.328 Ligands: MG.16 25 PLIP interactions: 17 interactions with chain C, 8 interactions with chain A Hydrogen bonds: C:G.50, C:G.50, C:A.51, C:G.52, C:K.53, C:S.54, C:S.55, C:Y.71, C:R.80, A:R.271, A:R.292, A:S.298, A:S.298, A:E.301 Water bridges: C:N.49, C:K.53, C:S.54, C:S.54, C:R.80, C:N.81, A:R.271 Salt bridges: C:K.53, C:R.70 pi-Cation interactions: A:R.292, A:R.292

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: S.54, E.328 Chain C: S.298, G.299 Ligands: ADP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.328 MG.16: 5 residues within 4Å: Chain A: S.298, G.299 Chain C: S.54, E.328 Ligands: ADP.15 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:E.328

18 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 2 residues within 4Å: Chain A: S.74, H.113 Ligand excluded by PLIP SO4.4: 3 residues within 4Å: Chain A: R.88, I.103, K.116 Ligand excluded by PLIP SO4.5: 3 residues within 4Å: Chain A: A.130, A.131, S.135 Ligand excluded by PLIP SO4.6: 10 residues within 4Å: Chain A: F.38, Q.39, S.40, G.41, I.42, T.43, V.354, I.355, V.356, R.370 Ligand excluded by PLIP SO4.7: 2 residues within 4Å: Chain A: S.183, R.320 Ligand excluded by PLIP SO4.11: 7 residues within 4Å: Chain B: M.1, R.122, Q.124, F.168, L.248, K.249 Ligands: SO4.12 Ligand excluded by PLIP SO4.12: 4 residues within 4Å: Chain B: R.122, E.247, K.249 Ligands: SO4.11 Ligand excluded by PLIP SO4.13: 5 residues within 4Å: Chain B: W.16, T.17, S.18, S.19, K.316 Ligand excluded by PLIP SO4.14: 3 residues within 4Å: Chain B: E.160, L.163, K.164 Ligand excluded by PLIP SO4.17: 2 residues within 4Å: Chain C: S.74, H.113 Ligand excluded by PLIP SO4.18: 3 residues within 4Å: Chain C: R.88, I.103, K.116 Ligand excluded by PLIP SO4.19: 3 residues within 4Å: Chain C: A.130, A.131, S.135 Ligand excluded by PLIP SO4.20: 10 residues within 4Å: Chain C: F.38, Q.39, S.40, G.41, I.42, T.43, V.354, I.355, V.356, R.370 Ligand excluded by PLIP SO4.21: 2 residues within 4Å: Chain C: S.183, R.320 Ligand excluded by PLIP SO4.25: 7 residues within 4Å: Chain D: M.1, R.122, Q.124, F.168, L.248, K.249 Ligands: SO4.26 Ligand excluded by PLIP SO4.26: 4 residues within 4Å: Chain D: R.122, E.247, K.249 Ligands: SO4.25 Ligand excluded by PLIP SO4.27: 5 residues within 4Å: Chain D: W.16, T.17, S.18, S.19, K.316 Ligand excluded by PLIP SO4.28: 3 residues within 4Å: Chain D: E.160, L.163, K.164 Ligand excluded by PLIP

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.8: 7 residues within 4Å: Chain A: E.328, F.330, S.331, I.358, T.359, C.360, D.361 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:E.328, A:F.330, A:S.331, A:S.331, A:I.358, A:C.360, A:D.361 PO4.22: 7 residues within 4Å: Chain C: E.328, F.330, S.331, I.358, T.359, C.360, D.361 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:E.328, C:E.328, C:F.330, C:S.331, C:S.331, C:I.358, C:T.359, C:C.360, C:D.361

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

MN.9: 7 residues within 4Å: Chain B: D.8, H.10, D.52, Q.88, H.210, H.212 Ligands: MN.10 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.8, B:H.10, B:D.52, B:H.212 MN.10: 6 residues within 4Å: Chain B: D.52, N.87, Q.88, H.174, H.210 Ligands: MN.9 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.52, B:H.174, B:H.210 MN.23: 7 residues within 4Å: Chain D: D.8, H.10, D.52, Q.88, H.210, H.212 Ligands: MN.24 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.8, D:H.10, D:D.52, D:H.212 MN.24: 6 residues within 4Å: Chain D: D.52, N.87, Q.88, H.174, H.210 Ligands: MN.23 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:D.52, D:H.174, D:H.210

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mockel, C. et al., ATP driven structural changes of the bacterial Mre11:Rad50 catalytic head complex. Nucleic Acids Res. (2012)

Release Date

2011-10-12

Peptides

Probable DNA double-strand break repair Rad50 ATPase: AC
Exonuclease, putative: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

B
B

D
B

Probable DNA double-strand break repair Rad50 ATPase

Exonuclease, putative

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