SMTL ID : 6ixi.1

structure of Cd-bound periplasmic metal binding protein from candidatus liberibacter asiaticus

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.07 Å

Oligo State

monomer

Ligands

3 x CD: CADMIUM ION(Non-covalent)

CD.1: 5 residues within 4Å: Chain A: H.39, H.106, E.172, N.193, D.247 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:H.39, A:H.106, A:E.172, A:E.172, A:D.247 CD.2: 2 residues within 4Å: Chain A: E.66, E.102 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.66, A:E.102, A:E.102, H2O.1 CD.3: 1 residues within 4Å: Chain A: H.213 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.213, H2O.8

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 3 residues within 4Å: Chain A: Q.19, N.20, K.23 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.19, A:Q.19 Water bridges: A:N.20, A:K.23 GOL.5: 3 residues within 4Å: Chain A: A.46 Ligands: SO4.13, ACT.16 1 PLIP interactions: 1 interactions with chain A Water bridges: A:A.46 GOL.6: 6 residues within 4Å: Chain A: G.61, L.62, H.63, E.65, E.66, M.69 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.61, A:H.63, A:E.65 Water bridges: A:L.62, A:L.62, A:H.63 GOL.7: 3 residues within 4Å: Chain A: H.205, N.208, Q.209 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.208, A:Q.209 GOL.8: 6 residues within 4Å: Chain A: A.48, I.51, Q.52, Y.71, T.73, N.74 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.52, A:N.74 GOL.9: 3 residues within 4Å: Chain A: E.119, R.122, K.123 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.122 GOL.10: 1 residues within 4Å: Chain A: S.94 No protein-ligand interaction detected (PLIP)

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

SO4.11: 5 residues within 4Å: Chain A: V.28, T.29, T.30, E.33, K.50 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:V.28, A:T.30, A:E.33 Water bridges: A:T.30, A:T.30, A:K.50, A:K.50 Salt bridges: A:K.50 SO4.12: 4 residues within 4Å: Chain A: Y.245, S.250, K.251, G.254 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.245, A:K.251 Salt bridges: A:K.251 SO4.13: 5 residues within 4Å: Chain A: T.44, A.46, D.47 Ligands: GOL.5, SO4.15 3 PLIP interactions: 3 interactions with chain A Water bridges: A:S.45, A:A.46, A:D.47 SO4.14: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) SO4.15: 3 residues within 4Å: Chain A: T.44, S.45 Ligands: SO4.13 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.45 Water bridges: A:A.46

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

ACT.16: 1 residues within 4Å: Ligands: GOL.5 No protein-ligand interaction detected (PLIP) ACT.17: 4 residues within 4Å: Chain A: P.90, G.92, S.101, P.103 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.101 ACT.18: 7 residues within 4Å: Chain A: S.38, H.39, H.63, L.64, E.66, P.105, I.192 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:P.105, A:I.192 Hydrogen bonds: A:E.66 Salt bridges: A:H.39 ACT.19: 5 residues within 4Å: Chain A: S.186, L.187, Y.188, M.202, H.205 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.188 Salt bridges: A:H.205 ACT.20: 3 residues within 4Å: Chain A: Y.240, G.241, G.242 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.241 Salt bridges: A:K.269 ACT.21: 1 residues within 4Å: Chain A: N.237 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kumar, P. et al., Characterization of the heavy metal binding properties of periplasmic metal uptake protein CLas-ZnuA2. Metallomics (2020)

Release Date

2020-01-15

Peptides

Periplasmic solute binding protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Periplasmic solute binding protein

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