SMTL ID : 1w15.1

rat synaptotagmin 4 C2B domain in the presence of calcium

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.93 Å

Oligo State

homo-trimer

Ligands

9 x CA: CALCIUM ION(Non-covalent)

CA.1: 4 residues within 4Å: Chain A: D.52, D.106, S.107, E.108 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.52, A:D.106, A:S.107, A:E.108, H2O.2 CA.2: 1 residues within 4Å: Chain A: E.93 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.93, H2O.1, H2O.2 CA.3: 2 residues within 4Å: Chain A: D.152, G.153 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.152, H2O.3 CA.15: 4 residues within 4Å: Chain B: D.52, D.106, S.107, E.108 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.52, B:D.106, B:S.107, B:E.108, H2O.6 CA.16: 1 residues within 4Å: Chain B: E.93 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.93, H2O.4, H2O.6 CA.17: 2 residues within 4Å: Chain B: D.152, G.153 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.152, H2O.6 CA.29: 4 residues within 4Å: Chain C: D.52, D.106, S.107, E.108 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.52, C:D.106, C:S.107, C:E.108, H2O.10 CA.30: 1 residues within 4Å: Chain C: E.93 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.93, H2O.8, H2O.9 CA.31: 2 residues within 4Å: Chain C: D.152, G.153 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.152, H2O.10

6 x NA: SODIUM ION(Non-functional Binders)

NA.4: 3 residues within 4Å: Chain A: S.67, F.88, D.89 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.67, A:D.89 Water bridges: A:D.89 NA.5: 3 residues within 4Å: Chain A: E.108, S.111, N.113 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.108, A:E.108 Water bridges: A:G.110, A:N.113 NA.18: 3 residues within 4Å: Chain B: S.67, F.88, D.89 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.67, B:D.89 Water bridges: B:I.66, B:D.89 NA.19: 3 residues within 4Å: Chain B: E.108, S.111, N.113 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.108, B:N.113 Water bridges: B:G.110, B:N.113 NA.32: 3 residues within 4Å: Chain C: S.67, F.88, D.89 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.67, C:S.67, C:D.89 NA.33: 3 residues within 4Å: Chain C: E.108, S.111, N.113 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:E.108, C:E.108 Water bridges: C:G.110, C:N.113

27 x CL: CHLORIDE ION(Non-functional Binders)

CL.6: 5 residues within 4Å: Chain A: N.83 Chain B: N.83 Chain C: N.83 Ligands: CL.20, CL.34 Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain A: K.146, W.147 Chain B: V.87 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain A: Y.54, K.56, L.105 Ligand excluded by PLIP CL.9: 5 residues within 4Å: Chain A: K.69, F.86, V.87 Chain C: R.40, W.147 Ligand excluded by PLIP CL.10: 4 residues within 4Å: Chain A: K.56, N.58, R.65, L.103 Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain A: K.56, R.65, K.68 Ligand excluded by PLIP CL.12: 2 residues within 4Å: Chain A: R.40, H.41 Ligand excluded by PLIP CL.13: 3 residues within 4Å: Chain A: R.65, I.66, S.67 Ligand excluded by PLIP CL.14: 4 residues within 4Å: Chain A: Y.25, S.94, L.95, C.137 Ligand excluded by PLIP CL.20: 5 residues within 4Å: Chain A: N.83 Chain B: N.83 Chain C: N.83 Ligands: CL.6, CL.34 Ligand excluded by PLIP CL.21: 3 residues within 4Å: Chain B: K.146, W.147 Chain C: V.87 Ligand excluded by PLIP CL.22: 3 residues within 4Å: Chain B: Y.54, K.56, L.105 Ligand excluded by PLIP CL.23: 5 residues within 4Å: Chain A: R.40, W.147 Chain B: K.69, F.86, V.87 Ligand excluded by PLIP CL.24: 4 residues within 4Å: Chain B: K.56, N.58, R.65, L.103 Ligand excluded by PLIP CL.25: 3 residues within 4Å: Chain B: K.56, R.65, K.68 Ligand excluded by PLIP CL.26: 2 residues within 4Å: Chain B: R.40, H.41 Ligand excluded by PLIP CL.27: 3 residues within 4Å: Chain B: R.65, I.66, S.67 Ligand excluded by PLIP CL.28: 4 residues within 4Å: Chain B: Y.25, S.94, L.95, C.137 Ligand excluded by PLIP CL.34: 5 residues within 4Å: Chain A: N.83 Chain B: N.83 Chain C: N.83 Ligands: CL.6, CL.20 Ligand excluded by PLIP CL.35: 3 residues within 4Å: Chain A: V.87 Chain C: K.146, W.147 Ligand excluded by PLIP CL.36: 3 residues within 4Å: Chain C: Y.54, K.56, L.105 Ligand excluded by PLIP CL.37: 5 residues within 4Å: Chain B: R.40, W.147 Chain C: K.69, F.86, V.87 Ligand excluded by PLIP CL.38: 4 residues within 4Å: Chain C: K.56, N.58, R.65, L.103 Ligand excluded by PLIP CL.39: 3 residues within 4Å: Chain C: K.56, R.65, K.68 Ligand excluded by PLIP CL.40: 2 residues within 4Å: Chain C: R.40, H.41 Ligand excluded by PLIP CL.41: 3 residues within 4Å: Chain C: R.65, I.66, S.67 Ligand excluded by PLIP CL.42: 4 residues within 4Å: Chain C: Y.25, S.94, L.95, C.137 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dai, H. et al., Structural Basis for the Evolutionary Inactivation of Ca2+ Binding to Synaptotagmin 4. Nat.Struct.Mol.Biol. (2004)

Release Date

2004-08-13

Peptides

SYNAPTOTAGMIN IV: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

SYNAPTOTAGMIN IV

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