SMTL ID : 4uob.1

Crystal structure of Deinococcus radiodurans Endonuclease III-3

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.31 Å

Oligo State

monomer

Ligands

1 x SF4: IRON/SULFUR CLUSTER(Non-covalent)

SF4.1: 16 residues within 4Å: Chain A: A.195, R.198, L.199, H.236, T.240, C.241, P.246, L.247, C.248, C.251, L.253, R.254, C.257, S.259, A.260, F.263 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.241, A:C.248, A:C.251, A:C.257

1 x CO: COBALT (II) ION(Non-covalent)

CO.2: 2 residues within 4Å: Chain A: H.245, E.267 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.245, A:E.267, H2O.16, H2O.17

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

SO4.3: 4 residues within 4Å: Chain A: T.78, R.79, R.80, R.238 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.79 Water bridges: A:R.79, A:R.80, A:R.80 Salt bridges: A:R.79 SO4.4: 5 residues within 4Å: Chain A: R.79, I.231, V.234, R.235, R.238 6 PLIP interactions: 6 interactions with chain A Water bridges: A:R.235, A:R.235, A:R.238 Salt bridges: A:R.79, A:R.235, A:R.238

4 x ACT: ACETATE ION(Non-functional Binders)

ACT.5: 7 residues within 4Å: Chain A: F.61, P.62, D.63, L.65, G.66, W.86, W.96 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.86 Hydrogen bonds: A:D.63, A:G.66, A:W.96 ACT.6: 5 residues within 4Å: Chain A: R.48, P.53, E.54, L.55, E.224 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:P.53, A:L.55 Water bridges: A:R.48 ACT.7: 7 residues within 4Å: Chain A: Q.75, Y.125, G.167, V.168, G.169, K.171, T.172 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Y.125, A:G.169, A:K.171, A:T.172, A:T.172 Water bridges: A:Q.75, A:Q.75 ACT.8: 3 residues within 4Å: Chain A: L.30, K.210, R.213 3 PLIP interactions: 3 interactions with chain A Water bridges: A:K.210 Salt bridges: A:K.210, A:R.213

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sarre, A. et al., Structural and Functional Characterization of Two Unusual Endonuclease III Enzymes from Deinococcus Radiodurans. J.Struct.Biol. (2015)

Release Date

2015-06-10

Peptides

ENDONUCLEASE III-3: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

ENDONUCLEASE III-3