SMTL ID : 2ubp.2 (1 other biounit)

STRUCTURE OF NATIVE UREASE FROM BACILLUS PASTEURII

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

hetero-3-3-3-mer

Ligands

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

SO4.1: 8 residues within 4Å: Chain C: A.170, H.222, E.223, D.224, H.249, G.280, H.323, R.339 9 PLIP interactions: 8 interactions with chain C, 1 interactions with chain I Hydrogen bonds: C:E.223 Water bridges: C:A.170, C:G.280, C:R.339, I:G.46 Salt bridges: C:H.222, C:H.249, C:H.323, C:R.339 SO4.4: 8 residues within 4Å: Chain F: A.170, H.222, E.223, D.224, H.249, G.280, H.323, R.339 9 PLIP interactions: 8 interactions with chain F, 1 interactions with chain C Hydrogen bonds: F:E.223 Water bridges: F:A.170, F:G.280, F:R.339, C:G.46 Salt bridges: F:H.222, F:H.249, F:H.323, F:R.339 SO4.7: 8 residues within 4Å: Chain I: A.170, H.222, E.223, D.224, H.249, G.280, H.323, R.339 9 PLIP interactions: 8 interactions with chain I, 1 interactions with chain F Hydrogen bonds: I:E.223 Water bridges: I:A.170, I:G.280, I:R.339, F:G.46 Salt bridges: I:H.222, I:H.249, I:H.323, I:R.339

6 x NI: NICKEL (II) ION(Non-covalent)

NI.2: 6 residues within 4Å: Chain C: K.220, H.222, H.249, H.275, G.280 Ligands: NI.3 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:H.249, C:H.275, H2O.15, H2O.16 NI.3: 6 residues within 4Å: Chain C: H.137, H.139, T.172, K.220, D.363 Ligands: NI.2 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:H.137, C:H.139, C:D.363, H2O.16, H2O.18 NI.5: 6 residues within 4Å: Chain F: K.220, H.222, H.249, H.275, G.280 Ligands: NI.6 4 PLIP interactions: 2 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:H.249, F:H.275, H2O.49, H2O.49 NI.6: 6 residues within 4Å: Chain F: H.137, H.139, T.172, K.220, D.363 Ligands: NI.5 5 PLIP interactions: 3 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:H.137, F:H.139, F:D.363, H2O.49, H2O.51 NI.8: 6 residues within 4Å: Chain I: K.220, H.222, H.249, H.275, G.280 Ligands: NI.9 4 PLIP interactions: 2 interactions with chain I, 2 Ligand-Water interactions Metal complexes: I:H.249, I:H.275, H2O.83, H2O.83 NI.9: 6 residues within 4Å: Chain I: H.137, H.139, T.172, K.220, D.363 Ligands: NI.8 5 PLIP interactions: 3 interactions with chain I, 2 Ligand-Water interactions Metal complexes: I:H.137, I:H.139, I:D.363, H2O.83, H2O.85

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Benini, S. et al., A new proposal for urease mechanism based on the crystal structures of the native and inhibited enzyme from Bacillus pasteurii: why urea hydrolysis costs two nickels. Structure Fold.Des. (1999)

Release Date

1999-11-08

Peptides

PROTEIN (UREASE GAMMA SUBUNIT): ADG
PROTEIN (UREASE BETA SUBUNIT): BEH
PROTEIN (UREASE ALPHA SUBUNIT): CFI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
A

G
A

B
B

E
B

H
B

C
C

F
C

I
C

PROTEIN (UREASE GAMMA SUBUNIT)

PROTEIN (UREASE BETA SUBUNIT)

PROTEIN (UREASE ALPHA SUBUNIT)

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