SMTL ID : 5zha.1 (1 other biounit)

Structure of Y68F mutant Mn-Bound periplasmic metal binding protein from candidatus liberibacter asiaticus

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.84 Å

Oligo State

monomer

Ligands

1 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 4 residues within 4Å: Chain A: H.39, H.106, E.172, D.247 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:H.39, A:E.172, A:E.172, A:D.247, A:D.247

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 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.3: 3 residues within 4Å: Chain A: Q.19, N.20, K.23 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Q.19 Water bridges: A:N.20, A:N.20, A:K.23, A:K.23, A:D.24, A:D.24 GOL.4: 5 residues within 4Å: Chain A: S.12, G.15, D.16, T.30, L.249 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.16, A:T.30 Water bridges: A:T.30, A:E.33 GOL.5: 3 residues within 4Å: Chain A: T.44, A.46 Ligands: ACT.22 2 PLIP interactions: 2 interactions with chain A Water bridges: A:A.46, A:A.46 GOL.6: 6 residues within 4Å: Chain A: I.91, G.92, S.94, V.176, S.186, Y.188 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:S.94, A:S.186, A:Y.188 Water bridges: A:G.92, A:S.186, A:S.186, A:S.186, A:S.186 GOL.7: 4 residues within 4Å: Chain A: T.258, L.260, D.261 Ligands: ACT.15 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.258, A:D.261, A:D.261 Water bridges: A:S.150 GOL.8: 2 residues within 4Å: Chain A: S.94, D.100 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.94, A:S.94, A:D.100 GOL.9: 4 residues within 4Å: Chain A: E.119, R.122, K.123, T.126 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.122, A:R.122 Water bridges: A:K.123

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

ACT.10: 5 residues within 4Å: Chain A: Q.52, T.73, N.74 Ligands: ACT.19, ACT.20 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.52, A:N.74 ACT.11: 3 residues within 4Å: Chain A: G.87, I.88, N.89 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:N.89 Water bridges: A:G.87, A:I.88 ACT.12: 3 residues within 4Å: Chain A: S.186, L.187, Y.188 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.188 Hydrogen bonds: A:Y.188 Salt bridges: A:H.205 ACT.13: 3 residues within 4Å: Chain A: S.150, R.264 Ligands: ACT.15 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.264 ACT.14: 5 residues within 4Å: Chain A: V.28, T.29, T.30, E.33, K.50 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.30 Water bridges: A:T.30, A:T.30, A:K.50, A:K.50 Salt bridges: A:K.50 ACT.15: 4 residues within 4Å: Chain A: D.261, R.264 Ligands: GOL.7, ACT.13 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.264 ACT.16: 2 residues within 4Å: Chain A: K.230, Y.240 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.226 Salt bridges: A:K.230 ACT.17: 3 residues within 4Å: Chain A: S.199, P.200, S.201 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.201 ACT.18: 6 residues within 4Å: Chain A: S.38, H.39, H.63, L.64, E.66, I.192 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.192 Hydrogen bonds: A:E.66, A:E.66 Water bridges: A:T.67 Salt bridges: A:H.39 ACT.19: 3 residues within 4Å: Chain A: K.70, Y.71 Ligands: ACT.10 No protein-ligand interaction detected (PLIP) ACT.20: 2 residues within 4Å: Chain A: N.74 Ligands: ACT.10 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:N.74 ACT.21: 2 residues within 4Å: Chain A: N.193, R.198 3 PLIP interactions: 3 interactions with chain A Water bridges: A:I.192, A:R.198 Salt bridges: A:R.198 ACT.22: 3 residues within 4Å: Chain A: E.33, N.36 Ligands: GOL.5 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:E.33 Hydrogen bonds: A:N.36 Water bridges: A:E.33, A:Y.41 ACT.23: 4 residues within 4Å: Chain A: Y.245, S.250, K.251, G.254 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.245 Hydrogen bonds: A:Y.245, A:K.251 Water bridges: A:K.251 Salt bridges: A:K.251

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

SO4.24: 2 residues within 4Å: Chain A: T.44, S.45 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.45

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Saini, G. et al., The analysis of subtle internal communications through mutation studies in periplasmic metal uptake protein CLas-ZnuA2. J. Struct. Biol. (2018)

Release Date

2018-10-03

Peptides

Periplasmic solute binding protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Periplasmic solute binding protein

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