SMTL ID : 4inf.2 (1 other biounit)

Crystal structure of amidohydrolase saro_0799 (target efi-505250) from novosphingobium aromaticivorans dsm 12444 with bound calcium

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.48 Å

Oligo State

homo-dimer

Ligands

2 x CA: CALCIUM ION(Non-covalent)

CA.1: 4 residues within 4Å: Chain A: E.41, H.210, D.336 Ligands: OXD.6 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.41, A:H.210, A:D.336, H2O.1, H2O.3, H2O.22 CA.7: 4 residues within 4Å: Chain B: E.41, H.210, D.336 Ligands: OXD.10 6 PLIP interactions: 3 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.41, B:H.210, B:D.336, H2O.22, H2O.25, H2O.40

6 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 6 residues within 4Å: Chain A: L.69, Y.73, G.229, A.230 Chain B: R.287 Ligands: OXD.6 Ligand excluded by PLIP CL.3: 4 residues within 4Å: Chain A: S.78, E.79, R.80 Chain B: S.285 Ligand excluded by PLIP CL.4: 3 residues within 4Å: Chain A: E.190, E.191, R.290 Ligand excluded by PLIP CL.5: 2 residues within 4Å: Chain A: Q.280, R.284 Ligand excluded by PLIP CL.8: 6 residues within 4Å: Chain A: R.287 Chain B: L.69, Y.73, G.229, A.230 Ligands: OXD.10 Ligand excluded by PLIP CL.9: 4 residues within 4Å: Chain B: Y.143, P.144, D.145, R.146 Ligand excluded by PLIP

2 x OXD: OXALIC ACID(Non-covalent)

OXD.6: 7 residues within 4Å: Chain A: L.69, Y.73, H.210, F.234, Y.339 Ligands: CA.1, CL.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.73 Water bridges: A:Y.73, A:T.112, A:D.336 Salt bridges: A:H.210 OXD.10: 7 residues within 4Å: Chain B: L.69, Y.73, H.210, F.234, Y.339 Ligands: CA.7, CL.8 4 PLIP interactions: 4 interactions with chain B Water bridges: B:R.80, B:T.112, B:S.113 Salt bridges: B:H.210

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Patskovsky, Y. et al., Crystal structure of amidohydrolase sarp_0799 (target efi-505250) from novosphingobium aromaticivorans. To be Published

Release Date

2013-01-16

Peptides

METAL-DEPENDENT HYDROLASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

METAL-DEPENDENT HYDROLASE

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