SMTL ID : 5z2j.2 (1 other biounit)

structure of S38A mutant metal-free periplasmic metal binding protein from candidatus liberibacter asiaticus

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.87 Å

Oligo State

homo-dimer

Ligands

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

ACT.1: 2 residues within 4Å: Chain A: T.44, S.45 Ligand excluded by PLIP ACT.2: 3 residues within 4Å: Chain A: G.87, I.88, N.89 Ligand excluded by PLIP ACT.3: 3 residues within 4Å: Chain A: R.198, N.224, S.225 Ligand excluded by PLIP ACT.4: 2 residues within 4Å: Chain A: S.150, R.264 Ligand excluded by PLIP ACT.5: 3 residues within 4Å: Chain A: Q.52, T.73, N.74 Ligand excluded by PLIP ACT.6: 1 residues within 4Å: Chain A: R.211 Ligand excluded by PLIP ACT.7: 6 residues within 4Å: Chain A: D.86, G.87, I.116, E.119, N.120, K.123 Ligand excluded by PLIP ACT.8: 1 residues within 4Å: Ligands: GOL.13 Ligand excluded by PLIP ACT.19: 2 residues within 4Å: Chain B: T.44, S.45 Ligand excluded by PLIP ACT.20: 3 residues within 4Å: Chain B: G.87, I.88, N.89 Ligand excluded by PLIP ACT.21: 3 residues within 4Å: Chain B: R.198, N.224, S.225 Ligand excluded by PLIP ACT.22: 2 residues within 4Å: Chain B: S.150, R.264 Ligand excluded by PLIP ACT.23: 3 residues within 4Å: Chain B: Q.52, T.73, N.74 Ligand excluded by PLIP ACT.24: 1 residues within 4Å: Chain B: R.211 Ligand excluded by PLIP ACT.25: 6 residues within 4Å: Chain B: D.86, G.87, I.116, E.119, N.120, K.123 Ligand excluded by PLIP ACT.26: 1 residues within 4Å: Ligands: GOL.31 Ligand excluded by PLIP

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

SO4.9: 2 residues within 4Å: Chain A: E.33, N.36 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.36 Water bridges: A:E.33 SO4.10: 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 SO4.11: 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 SO4.27: 2 residues within 4Å: Chain B: E.33, N.36 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:N.36 Water bridges: B:E.33, B:E.33, B:Y.41, B:Y.41, B:Y.41, B:Y.41 SO4.28: 4 residues within 4Å: Chain B: Y.245, S.250, K.251, G.254 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.251 Salt bridges: B:K.251 SO4.29: 5 residues within 4Å: Chain B: V.28, T.29, T.30, E.33, K.50 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:V.28, B:T.30, B:E.33 Water bridges: B:T.30, B:T.30, B:E.33, B:K.50 Salt bridges: B:K.50

14 x GOL: GLYCEROL(Non-functional Binders)

GOL.12: 7 residues within 4Å: Chain A: K.4, K.5, L.25, V.26, D.129, S.131, N.132 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.4, A:K.5, A:S.131, A:N.132 GOL.13: 5 residues within 4Å: Chain A: S.199, P.200, S.201, R.204 Ligands: ACT.8 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.201, A:R.204, A:R.204 GOL.14: 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:N.20 Water bridges: A:D.16, A:N.20 GOL.15: 6 residues within 4Å: Chain A: S.12, G.15, D.16, Q.19, T.30, E.33 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.33 Water bridges: A:T.30, A:E.33 GOL.16: 4 residues within 4Å: Chain A: Y.41, T.44, A.46, D.47 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.41, A:D.47 Water bridges: A:D.47 GOL.17: 3 residues within 4Å: Chain A: T.73, N.74, L.75 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.74, A:L.75 Water bridges: A:F.72 GOL.18: 3 residues within 4Å: Chain A: H.205, N.208, Q.209 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.209 Water bridges: A:H.205 GOL.30: 7 residues within 4Å: Chain B: K.4, K.5, L.25, V.26, D.129, S.131, N.132 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.5, B:S.131, B:N.132 GOL.31: 5 residues within 4Å: Chain B: S.199, P.200, S.201, R.204 Ligands: ACT.26 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.201, B:R.204, B:R.204 GOL.32: 3 residues within 4Å: Chain B: Q.19, N.20, K.23 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.19, B:N.20 Water bridges: B:D.16, B:N.20 GOL.33: 6 residues within 4Å: Chain B: S.12, G.15, D.16, Q.19, T.30, E.33 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.30, B:E.33 Water bridges: B:D.16 GOL.34: 4 residues within 4Å: Chain B: Y.41, T.44, A.46, D.47 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.41, B:T.44, B:D.47 GOL.35: 3 residues within 4Å: Chain B: T.73, N.74, L.75 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.74, B:L.75 Water bridges: B:F.72 GOL.36: 3 residues within 4Å: Chain B: H.205, N.208, Q.209 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.205, B:Q.209 Water bridges: B:H.205

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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Periplasmic solute binding protein

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