SMTL ID : 3hk7.3 (3 other biounits)

Crystal structure of uronate isomerase from Bacillus halodurans complexed with zinc and D-Arabinarate, monoclinic crystal form

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-9-mer

Ligands

9 x RAT: D-arabinaric acid(Non-covalent)

RAT.1: 12 residues within 4Å: Chain A: H.26, H.28, H.49, Y.50, R.170, S.223, M.258, W.325, W.326, D.355, R.357 Ligands: ZN.2 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:H.28, A:Y.50, A:D.355, A:R.357 Salt bridges: A:H.26, A:H.28, A:H.28, A:H.49, A:R.170, A:R.357 RAT.4: 12 residues within 4Å: Chain B: H.26, H.28, H.49, Y.50, R.170, S.223, M.258, W.325, W.326, D.355, R.357 Ligands: ZN.6 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:H.28, B:Y.50, B:R.357 Water bridges: B:S.223 Salt bridges: B:H.26, B:H.28, B:H.49, B:R.170, B:R.357 RAT.7: 12 residues within 4Å: Chain C: H.26, H.28, H.49, Y.50, R.170, S.223, M.258, W.325, W.326, D.355, R.357 Ligands: ZN.10 13 PLIP interactions: 13 interactions with chain C Hydrogen bonds: C:H.28, C:Y.50, C:S.223, C:D.355, C:R.357 Water bridges: C:K.263, C:D.271 Salt bridges: C:H.26, C:H.28, C:H.28, C:H.49, C:R.170, C:R.357 RAT.12: 12 residues within 4Å: Chain D: H.26, H.28, H.49, Y.50, R.170, S.223, M.258, W.325, W.326, D.355, R.357 Ligands: ZN.13 14 PLIP interactions: 14 interactions with chain D Hydrogen bonds: D:H.28, D:Y.50, D:S.223, D:D.355, D:R.357 Water bridges: D:S.223, D:K.263, D:D.274 Salt bridges: D:H.26, D:H.28, D:H.28, D:H.49, D:R.170, D:R.357 RAT.14: 12 residues within 4Å: Chain E: H.26, H.28, H.49, Y.50, R.170, S.223, M.258, W.325, W.326, D.355, R.357 Ligands: ZN.16 12 PLIP interactions: 12 interactions with chain E Hydrogen bonds: E:H.28, E:S.223, E:W.325, E:R.357 Water bridges: E:D.355, E:D.355 Salt bridges: E:H.26, E:H.28, E:H.28, E:H.49, E:R.170, E:R.357 RAT.18: 12 residues within 4Å: Chain F: H.26, H.28, H.49, Y.50, R.170, S.223, M.258, W.325, W.326, D.355, R.357 Ligands: ZN.20 11 PLIP interactions: 11 interactions with chain F Hydrogen bonds: F:H.28, F:R.357 Water bridges: F:S.223, F:S.223, F:K.263, F:K.263 Salt bridges: F:H.26, F:H.28, F:H.49, F:R.170, F:R.357 RAT.22: 11 residues within 4Å: Chain G: H.26, H.28, H.49, Y.50, R.170, S.223, W.325, W.326, D.355, R.357 Ligands: ZN.24 10 PLIP interactions: 10 interactions with chain G Hydrogen bonds: G:S.223, G:D.355, G:R.357 Water bridges: G:H.49, G:S.223 Salt bridges: G:H.26, G:H.28, G:H.49, G:R.170, G:R.357 RAT.25: 12 residues within 4Å: Chain H: H.26, H.28, H.49, Y.50, R.170, S.223, M.258, W.325, W.326, D.355, R.357 Ligands: ZN.28 11 PLIP interactions: 11 interactions with chain H Hydrogen bonds: H:H.28, H:D.355, H:R.357 Water bridges: H:K.263, H:K.263, H:K.263 Salt bridges: H:H.26, H:H.28, H:H.49, H:R.170, H:R.357 RAT.29: 12 residues within 4Å: Chain I: H.26, H.28, H.49, Y.50, R.170, S.223, M.258, W.325, W.326, D.355, R.357 Ligands: ZN.30 11 PLIP interactions: 11 interactions with chain I Hydrogen bonds: I:S.223, I:W.325, I:D.355, I:R.357 Water bridges: I:H.49, I:S.223 Salt bridges: I:H.26, I:H.28, I:H.49, I:R.170, I:R.357

9 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: H.26, H.28, D.355 Ligands: RAT.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.26, A:H.28, A:D.355 ZN.6: 4 residues within 4Å: Chain B: H.26, H.28, D.355 Ligands: RAT.4 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.26, B:H.28, B:D.355 ZN.10: 4 residues within 4Å: Chain C: H.26, H.28, D.355 Ligands: RAT.7 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.26, C:H.28, C:D.355 ZN.13: 4 residues within 4Å: Chain D: H.26, H.28, D.355 Ligands: RAT.12 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:H.26, D:H.28, D:D.355 ZN.16: 4 residues within 4Å: Chain E: H.26, H.28, D.355 Ligands: RAT.14 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:H.26, E:H.28, E:D.355 ZN.20: 4 residues within 4Å: Chain F: H.26, H.28, D.355 Ligands: RAT.18 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:H.26, F:H.28, F:D.355 ZN.24: 4 residues within 4Å: Chain G: H.26, H.28, D.355 Ligands: RAT.22 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:H.26, G:H.28, G:D.355 ZN.28: 4 residues within 4Å: Chain H: H.26, H.28, D.355 Ligands: RAT.25 3 PLIP interactions: 3 interactions with chain H Metal complexes: H:H.26, H:H.28, H:D.355 ZN.30: 4 residues within 4Å: Chain I: H.26, H.28, D.355 Ligands: RAT.29 3 PLIP interactions: 3 interactions with chain I Metal complexes: I:H.26, I:H.28, I:D.355

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

CL.3: 4 residues within 4Å: Chain A: K.278, E.304 Chain B: K.278, E.304 Ligand excluded by PLIP CL.11: 4 residues within 4Å: Chain C: K.278, E.304 Chain D: K.278, E.304 Ligand excluded by PLIP CL.17: 6 residues within 4Å: Chain E: K.278, E.304 Chain F: K.278, E.304 Chain G: K.278, E.304 Ligand excluded by PLIP

8 x CO3: CARBONATE ION(Non-functional Binders)

CO3.5: 8 residues within 4Å: Chain A: H.49, Y.50, A.53, A.272, W.326, F.327 Chain B: R.314, K.315 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.314, B:K.315, A:H.49 CO3.8: 2 residues within 4Å: Chain C: R.314, K.315 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.314, C:K.315, C:K.315 CO3.9: 8 residues within 4Å: Chain C: H.49, Y.50, A.53, A.272, W.326, F.327 Chain D: R.314, K.315 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:H.49, D:R.314, D:K.315, D:K.315 CO3.15: 8 residues within 4Å: Chain E: R.314, K.315 Chain G: H.49, Y.50, A.53, A.272, W.326, F.327 4 PLIP interactions: 1 interactions with chain G, 3 interactions with chain E Hydrogen bonds: G:H.49, E:R.314, E:K.315, E:K.315 CO3.19: 8 residues within 4Å: Chain E: H.49, Y.50, A.53, A.272, W.326, F.327 Chain F: R.314, K.315 3 PLIP interactions: 2 interactions with chain F, 1 interactions with chain E Hydrogen bonds: F:R.314, F:K.315, E:H.49 CO3.23: 7 residues within 4Å: Chain F: H.49, Y.50, A.53, W.326, F.327 Chain G: R.314, K.315 4 PLIP interactions: 1 interactions with chain F, 3 interactions with chain G Hydrogen bonds: F:H.49, G:R.314, G:K.315, G:K.315 CO3.26: 2 residues within 4Å: Chain H: R.314, K.315 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:R.314, H:K.315 CO3.27: 8 residues within 4Å: Chain H: H.49, Y.50, A.53, A.272, W.326, F.327 Chain I: R.314, K.315 4 PLIP interactions: 3 interactions with chain I, 1 interactions with chain H Hydrogen bonds: I:R.314, I:K.315, I:K.315, H:H.49

2 x NA: SODIUM ION(Non-functional Binders)

NA.21: 2 residues within 4Å: Chain E: E.332 Chain F: E.332 3 PLIP interactions: 1 interactions with chain E, 2 interactions with chain F Hydrogen bonds: E:E.332 Water bridges: F:E.332, F:N.335 NA.31: 2 residues within 4Å: Chain H: E.332 Chain I: E.332 2 PLIP interactions: 2 interactions with chain I Water bridges: I:E.332, I:E.332

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nguyen, T.T. et al., The mechanism of the reaction catalyzed by uronate isomerase illustrates how an isomerase may have evolved from a hydrolase within the amidohydrolase superfamily. Biochemistry (2009)

Release Date

2009-08-25

Peptides

Uronate isomerase: ABCDEFGHI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

C
E

D
F

E
G

F
H

G
I

H
K

I
L

Uronate isomerase

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