SMTL ID : 5zha.2 (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

homo-dimer

Ligands

2 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 MN.25: 4 residues within 4Å: Chain B: H.39, H.106, E.172, D.247 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:H.39, B:E.172, B:E.172, B:D.247, B:D.247

16 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 3 residues within 4Å: Chain A: H.205, N.208, Q.209 Ligand excluded by PLIP GOL.3: 3 residues within 4Å: Chain A: Q.19, N.20, K.23 Ligand excluded by PLIP GOL.4: 5 residues within 4Å: Chain A: S.12, G.15, D.16, T.30, L.249 Ligand excluded by PLIP GOL.5: 3 residues within 4Å: Chain A: T.44, A.46 Ligands: ACT.22 Ligand excluded by PLIP GOL.6: 6 residues within 4Å: Chain A: I.91, G.92, S.94, V.176, S.186, Y.188 Ligand excluded by PLIP GOL.7: 4 residues within 4Å: Chain A: T.258, L.260, D.261 Ligands: ACT.15 Ligand excluded by PLIP GOL.8: 2 residues within 4Å: Chain A: S.94, D.100 Ligand excluded by PLIP GOL.9: 5 residues within 4Å: Chain A: E.119, R.122, K.123, T.126 Chain B: R.141 Ligand excluded by PLIP GOL.26: 3 residues within 4Å: Chain B: H.205, N.208, Q.209 Ligand excluded by PLIP GOL.27: 3 residues within 4Å: Chain B: Q.19, N.20, K.23 Ligand excluded by PLIP GOL.28: 5 residues within 4Å: Chain B: S.12, G.15, D.16, T.30, L.249 Ligand excluded by PLIP GOL.29: 3 residues within 4Å: Chain B: T.44, A.46 Ligands: ACT.46 Ligand excluded by PLIP GOL.30: 6 residues within 4Å: Chain B: I.91, G.92, S.94, V.176, S.186, Y.188 Ligand excluded by PLIP GOL.31: 4 residues within 4Å: Chain B: T.258, L.260, D.261 Ligands: ACT.39 Ligand excluded by PLIP GOL.32: 2 residues within 4Å: Chain B: S.94, D.100 Ligand excluded by PLIP GOL.33: 5 residues within 4Å: Chain A: R.141 Chain B: E.119, R.122, K.123, T.126 Ligand excluded by PLIP

28 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 Ligand excluded by PLIP ACT.11: 3 residues within 4Å: Chain A: G.87, I.88, N.89 Ligand excluded by PLIP ACT.12: 3 residues within 4Å: Chain A: S.186, L.187, Y.188 Ligand excluded by PLIP ACT.13: 3 residues within 4Å: Chain A: S.150, R.264 Ligands: ACT.15 Ligand excluded by PLIP ACT.14: 5 residues within 4Å: Chain A: V.28, T.29, T.30, E.33, K.50 Ligand excluded by PLIP ACT.15: 4 residues within 4Å: Chain A: D.261, R.264 Ligands: GOL.7, ACT.13 Ligand excluded by PLIP ACT.16: 2 residues within 4Å: Chain A: K.230, Y.240 Ligand excluded by PLIP ACT.17: 3 residues within 4Å: Chain A: S.199, P.200, S.201 Ligand excluded by PLIP ACT.18: 6 residues within 4Å: Chain A: S.38, H.39, H.63, L.64, E.66, I.192 Ligand excluded by PLIP ACT.19: 3 residues within 4Å: Chain A: K.70, Y.71 Ligands: ACT.10 Ligand excluded by PLIP ACT.20: 2 residues within 4Å: Chain A: N.74 Ligands: ACT.10 Ligand excluded by PLIP ACT.21: 2 residues within 4Å: Chain A: N.193, R.198 Ligand excluded by PLIP ACT.22: 3 residues within 4Å: Chain A: E.33, N.36 Ligands: GOL.5 Ligand excluded by PLIP ACT.23: 4 residues within 4Å: Chain A: Y.245, S.250, K.251, G.254 Ligand excluded by PLIP ACT.34: 5 residues within 4Å: Chain B: Q.52, T.73, N.74 Ligands: ACT.43, ACT.44 Ligand excluded by PLIP ACT.35: 3 residues within 4Å: Chain B: G.87, I.88, N.89 Ligand excluded by PLIP ACT.36: 3 residues within 4Å: Chain B: S.186, L.187, Y.188 Ligand excluded by PLIP ACT.37: 3 residues within 4Å: Chain B: S.150, R.264 Ligands: ACT.39 Ligand excluded by PLIP ACT.38: 5 residues within 4Å: Chain B: V.28, T.29, T.30, E.33, K.50 Ligand excluded by PLIP ACT.39: 4 residues within 4Å: Chain B: D.261, R.264 Ligands: GOL.31, ACT.37 Ligand excluded by PLIP ACT.40: 2 residues within 4Å: Chain B: K.230, Y.240 Ligand excluded by PLIP ACT.41: 3 residues within 4Å: Chain B: S.199, P.200, S.201 Ligand excluded by PLIP ACT.42: 6 residues within 4Å: Chain B: S.38, H.39, H.63, L.64, E.66, I.192 Ligand excluded by PLIP ACT.43: 3 residues within 4Å: Chain B: K.70, Y.71 Ligands: ACT.34 Ligand excluded by PLIP ACT.44: 2 residues within 4Å: Chain B: N.74 Ligands: ACT.34 Ligand excluded by PLIP ACT.45: 2 residues within 4Å: Chain B: N.193, R.198 Ligand excluded by PLIP ACT.46: 3 residues within 4Å: Chain B: E.33, N.36 Ligands: GOL.29 Ligand excluded by PLIP ACT.47: 4 residues within 4Å: Chain B: Y.245, S.250, K.251, G.254 Ligand excluded by PLIP

2 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 SO4.48: 2 residues within 4Å: Chain B: T.44, S.45 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B: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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Periplasmic solute binding protein

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