SMTL ID : 5a6t.1

1.65 A resolution Sulphite inhibited Sporosarcina pasteurii urease

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

hetero-3-3-3-mer

Ligands

21 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 9 residues within 4Å: Chain A: G.50, K.51, T.52, F.86, P.87, D.88 Chain I: V.309, N.310, K.559 Ligand excluded by PLIP EDO.2: 6 residues within 4Å: Chain A: N.4, A.6, E.7, K.10 Chain I: F.568, F.570 Ligand excluded by PLIP EDO.3: 6 residues within 4Å: Chain B: Q.41 Chain C: G.46 Chain I: L.253, L.325, D.332, F.335 Ligand excluded by PLIP EDO.8: 4 residues within 4Å: Chain C: V.16, D.34, T.36, Y.38 Ligand excluded by PLIP EDO.9: 6 residues within 4Å: Chain C: D.286, A.289, I.537, D.538, I.539 Chain E: R.38 Ligand excluded by PLIP EDO.10: 4 residues within 4Å: Chain C: Y.35, Y.83, I.97, E.429 Ligand excluded by PLIP EDO.11: 3 residues within 4Å: Chain C: P.229, D.233 Chain E: D.101 Ligand excluded by PLIP EDO.12: 9 residues within 4Å: Chain C: V.309, N.310, K.559 Chain D: G.50, K.51, T.52, F.86, P.87, D.88 Ligand excluded by PLIP EDO.13: 6 residues within 4Å: Chain C: F.568, F.570 Chain D: N.4, A.6, E.7, K.10 Ligand excluded by PLIP EDO.14: 6 residues within 4Å: Chain C: L.253, L.325, D.332, F.335 Chain E: Q.41 Chain F: G.46 Ligand excluded by PLIP EDO.19: 4 residues within 4Å: Chain F: V.16, D.34, T.36, Y.38 Ligand excluded by PLIP EDO.20: 6 residues within 4Å: Chain F: D.286, A.289, I.537, D.538, I.539 Chain H: R.38 Ligand excluded by PLIP EDO.21: 4 residues within 4Å: Chain F: Y.35, Y.83, I.97, E.429 Ligand excluded by PLIP EDO.22: 3 residues within 4Å: Chain F: P.229, D.233 Chain H: D.101 Ligand excluded by PLIP EDO.23: 9 residues within 4Å: Chain F: V.309, N.310, K.559 Chain G: G.50, K.51, T.52, F.86, P.87, D.88 Ligand excluded by PLIP EDO.24: 6 residues within 4Å: Chain F: F.568, F.570 Chain G: N.4, A.6, E.7, K.10 Ligand excluded by PLIP EDO.25: 6 residues within 4Å: Chain F: L.253, L.325, D.332, F.335 Chain H: Q.41 Chain I: G.46 Ligand excluded by PLIP EDO.30: 4 residues within 4Å: Chain I: V.16, D.34, T.36, Y.38 Ligand excluded by PLIP EDO.31: 6 residues within 4Å: Chain B: R.38 Chain I: D.286, A.289, I.537, D.538, I.539 Ligand excluded by PLIP EDO.32: 4 residues within 4Å: Chain I: Y.35, Y.83, I.97, E.429 Ligand excluded by PLIP EDO.33: 3 residues within 4Å: Chain B: D.101 Chain I: P.229, D.233 Ligand excluded by PLIP

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

SO4.4: 2 residues within 4Å: Chain B: L.112, R.116 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.116 SO4.15: 2 residues within 4Å: Chain E: L.112, R.116 1 PLIP interactions: 1 interactions with chain E Salt bridges: E:R.116 SO4.26: 2 residues within 4Å: Chain H: L.112, R.116 1 PLIP interactions: 1 interactions with chain H Salt bridges: H:R.116

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

NI.5: 8 residues within 4Å: Chain C: H.137, K.220, H.222, H.249, H.275, G.280 Ligands: NI.6, SO3.7 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:H.249, C:H.275 NI.6: 6 residues within 4Å: Chain C: H.137, H.139, K.220, D.363 Ligands: NI.5, SO3.7 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.137, C:H.139, C:D.363 NI.16: 8 residues within 4Å: Chain F: H.137, K.220, H.222, H.249, H.275, G.280 Ligands: NI.17, SO3.18 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:H.249, F:H.275 NI.17: 6 residues within 4Å: Chain F: H.137, H.139, K.220, D.363 Ligands: NI.16, SO3.18 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:H.137, F:H.139, F:D.363 NI.27: 8 residues within 4Å: Chain I: H.137, K.220, H.222, H.249, H.275, G.280 Ligands: NI.28, SO3.29 2 PLIP interactions: 2 interactions with chain I Metal complexes: I:H.249, I:H.275 NI.28: 6 residues within 4Å: Chain I: H.137, H.139, K.220, D.363 Ligands: NI.27, SO3.29 3 PLIP interactions: 3 interactions with chain I Metal complexes: I:H.137, I:H.139, I:D.363

3 x SO3: SULFITE ION(Non-covalent)

SO3.7: 12 residues within 4Å: Chain C: H.137, H.139, A.170, K.220, H.222, H.249, H.275, G.280, D.363, A.366 Ligands: NI.5, NI.6 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:D.363 SO3.18: 12 residues within 4Å: Chain F: H.137, H.139, A.170, K.220, H.222, H.249, H.275, G.280, D.363, A.366 Ligands: NI.16, NI.17 1 PLIP interactions: 1 interactions with chain F Salt bridges: F:D.363 SO3.29: 12 residues within 4Å: Chain I: H.137, H.139, A.170, K.220, H.222, H.249, H.275, G.280, D.363, A.366 Ligands: NI.27, NI.28 1 PLIP interactions: 1 interactions with chain I Salt bridges: I:D.363

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mazzei, L. et al., Kinetic and Structural Studies Reveal a Unique Binding Mode of Sulfite to the Nickel Center in Urease. J.Inorg.Biochem. (2015)

Release Date

2015-12-02

Peptides

UREASE SUBUNIT GAMMA: ADG
UREASE SUBUNIT BETA: BEH
UREASE SUBUNIT ALPHA: 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

UREASE SUBUNIT GAMMA

UREASE SUBUNIT BETA

UREASE SUBUNIT ALPHA

Related Entries With Identical Sequence