SMTL ID : 3tho.1 (2 other biounits)

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.61 Å

Oligo State

hetero-oligomer

Ligands

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

ADP.1: 18 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 Ligands: MG.2 17 PLIP interactions: 17 interactions with chain A 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 Water bridges: A:N.49, A:K.53, A:S.54, A:S.54, A:N.81 Salt bridges: A:K.53, A:R.70

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: S.54, E.328 Ligands: ADP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.328

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

SO4.3: 2 residues within 4Å: Chain A: S.74, H.113 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.74, A:S.74, A:S.74 Salt bridges: A:H.113 SO4.4: 3 residues within 4Å: Chain A: R.88, I.103, K.116 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.88, A:K.116 SO4.5: 3 residues within 4Å: Chain A: A.130, A.131, S.135 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.131, A:S.135, A:S.135 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 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Q.39, A:Q.39, A:T.43, A:T.43, A:I.355, A:I.355 Salt bridges: A:R.370 SO4.7: 2 residues within 4Å: Chain A: S.183, R.320 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.95, A:R.320 SO4.11: 7 residues within 4Å: Chain B: M.1, R.122, Q.124, F.168, L.248, K.249 Ligands: SO4.12 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:M.1, B:M.1, B:Q.124 Salt bridges: B:R.122, B:K.249 SO4.12: 4 residues within 4Å: Chain B: R.122, E.247, K.249 Ligands: SO4.11 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.247 Salt bridges: B:R.122, B:K.249 SO4.13: 5 residues within 4Å: Chain B: W.16, T.17, S.18, S.19, K.316 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:T.17, B:S.18, B:S.18, B:S.19 Salt bridges: B:K.316, A:K.340 SO4.14: 3 residues within 4Å: Chain B: E.160, L.163, K.164 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:K.164

1 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

2 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

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: A
Exonuclease, putative: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Probable DNA double-strand break repair Rad50 ATPase

Exonuclease, putative

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