SMTL ID : 5z2k.2 (1 other biounit)

Structure of S38A mutant Mn-bound periplasmic metal binding protein from candidatus liberibacter asiaticus

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

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

MN.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 MN.16: 5 residues within 4Å: Chain B: H.39, H.106, E.172, N.193, D.247 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:H.39, B:H.106, B:E.172, B:E.172, B:D.247

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

SO4.2: 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 SO4.17: 5 residues within 4Å: Chain B: V.28, T.29, T.30, E.33, K.50 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:V.28, B:T.30, B:E.33 Water bridges: B:E.33, B:K.50 Salt bridges: B:K.50

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

ACT.3: 1 residues within 4Å: Chain A: R.211 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.211 ACT.4: 4 residues within 4Å: Chain A: R.198, T.223, N.224, S.225 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.225 Water bridges: A:R.198, A:T.223 Salt bridges: A:R.198 ACT.5: 3 residues within 4Å: Chain B: Q.209, S.212, H.213 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.209 Salt bridges: B:H.213 ACT.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) ACT.7: 3 residues within 4Å: Chain A: G.87, N.89, P.90 1 PLIP interactions: 1 interactions with chain B Water bridges: B:T.156 ACT.8: 1 residues within 4Å: Chain A: N.74 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Q.52, A:Y.71 ACT.18: 1 residues within 4Å: Chain B: R.211 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.211 ACT.19: 4 residues within 4Å: Chain B: R.198, T.223, N.224, S.225 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.225 Water bridges: B:R.198, B:T.223 Salt bridges: B:R.198 ACT.20: 3 residues within 4Å: Chain A: Q.209, S.212, H.213 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.209 Salt bridges: A:H.213 ACT.21: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) ACT.22: 3 residues within 4Å: Chain B: G.87, N.89, P.90 No protein-ligand interaction detected (PLIP) ACT.23: 1 residues within 4Å: Chain B: N.74 2 PLIP interactions: 2 interactions with chain B Water bridges: B:Q.52, B:Y.71

14 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 5 residues within 4Å: Chain A: R.141 Chain B: E.119, R.122, K.123, T.126 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:R.122, B:R.122, A:R.141, A:R.141 Water bridges: A:E.142 GOL.10: 5 residues within 4Å: Chain A: S.12, G.15, D.16, V.28, T.30 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.12 Water bridges: A:T.30, A:T.30, A:E.33 GOL.11: 3 residues within 4Å: Chain A: H.205, N.208, Q.209 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.205, A:N.208, A:Q.209 Water bridges: A:H.205 GOL.12: 2 residues within 4Å: Chain A: Q.19, N.20 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.19, A:N.20, A:N.20 Water bridges: A:K.146 GOL.13: 4 residues within 4Å: Chain A: S.199, P.200, S.201, R.204 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.201, A:S.201, A:R.204, A:R.204 GOL.14: 3 residues within 4Å: Chain A: T.44, A.46, D.47 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.44 Water bridges: A:S.45, A:D.47 GOL.15: 4 residues within 4Å: Chain A: Y.245, S.250, K.251, G.254 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.245, A:K.251 Water bridges: A:S.222, A:S.222, A:Y.245 GOL.24: 5 residues within 4Å: Chain A: E.119, R.122, K.123, T.126 Chain B: R.141 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.122, A:R.122, B:R.141, B:R.141 GOL.25: 5 residues within 4Å: Chain B: S.12, G.15, D.16, V.28, T.30 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.12, B:T.30 GOL.26: 3 residues within 4Å: Chain B: H.205, N.208, Q.209 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.205, B:N.208, B:Q.209 Water bridges: B:H.205 GOL.27: 2 residues within 4Å: Chain B: Q.19, N.20 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.19, B:N.20, B:N.20 Water bridges: B:K.146 GOL.28: 4 residues within 4Å: Chain B: S.199, P.200, S.201, R.204 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.201, B:S.201, B:R.204, B:R.204 GOL.29: 3 residues within 4Å: Chain B: T.44, A.46, D.47 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.44, B:T.44 Water bridges: B:S.45 GOL.30: 4 residues within 4Å: Chain B: Y.245, S.250, K.251, G.254 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.251 Water bridges: B:S.222, B:S.222, B:Y.245

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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