SMTL ID : 1ii7.1

Crystal structure of P. furiosus Mre11 with manganese and dAMP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

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

MN.1: 6 residues within 4Å: Chain A: D.8, H.10, D.49, H.208 Ligands: MN.2, D5M.6 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.8, A:H.10, A:D.49, A:H.208, H2O.1 MN.2: 7 residues within 4Å: Chain A: D.8, D.49, N.84, H.173, H.206 Ligands: MN.1, D5M.6 5 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:D.49, A:H.173, A:H.206, H2O.1, D5M.6 MN.8: 7 residues within 4Å: Chain B: D.8, D.49, N.84, H.173, H.206 Ligands: PO4.7, MN.9 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.49, B:H.173, B:H.206, H2O.5 MN.9: 6 residues within 4Å: Chain B: D.8, H.10, D.49, H.208 Ligands: PO4.7, MN.8 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.8, B:H.10, B:D.49, B:H.208, H2O.5

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

SO4.3: 4 residues within 4Å: Chain A: S.53, S.54, R.55 Chain B: R.55 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Salt bridges: B:R.55 Hydrogen bonds: A:S.53, A:S.54, A:R.55 SO4.4: 4 residues within 4Å: Chain A: R.87, M.146, S.147, W.150 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.147, A:S.147 Salt bridges: A:R.87 SO4.5: 1 residues within 4Å: Chain A: R.160 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.160

1 x D5M: 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE(Non-covalent)

D5M.6: 10 residues within 4Å: Chain A: H.10, D.49, N.84, H.85, Y.187, H.206, I.207, H.208 Ligands: MN.1, MN.2 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.187 Hydrogen bonds: A:N.84, A:H.208 Salt bridges: A:H.10, A:H.85, A:H.206, A:H.208

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

PO4.7: 8 residues within 4Å: Chain B: H.10, D.49, N.84, H.85, H.206, H.208 Ligands: MN.8, MN.9 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:H.206 Salt bridges: B:H.10, B:H.85, B:H.206, B:H.208

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hopfner, K.P. et al., Structural biochemistry and interaction architecture of the DNA double-strand break repair Mre11 nuclease and Rad50-ATPase. Cell(Cambridge,Mass.) (2001)

Release Date

2001-05-30

Peptides

Mre11 nuclease: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Mre11 nuclease