SMTL ID : 4gje.2 (1 other biounit)

Crystal structure of the refolded amino-terminal domain of human cardiac troponin C in complex with cadmium

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

14 x CD: CADMIUM ION(Non-covalent)

CD.1: 3 residues within 4Å: Chain A: D.33, C.35 Ligands: ACT.9 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.33, A:D.33, A:C.35, A:C.35, H2O.1 CD.2: 3 residues within 4Å: Chain A: D.65, T.71, E.76 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.65, A:E.76, H2O.1, H2O.2, H2O.2 CD.3: 2 residues within 4Å: Chain A: F.27, E.40 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:F.27, A:E.40, A:E.40, H2O.1, H2O.1 CD.4: 6 residues within 4Å: Chain A: P.52, E.56, C.84, D.87 Chain B: S.89 Ligands: CD.5 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Metal complexes: A:E.56, A:C.84, A:D.87, B:S.89, B:S.89 CD.5: 6 residues within 4Å: Chain A: Q.50, C.84, D.87 Chain B: D.88, S.89 Ligands: CD.4 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Metal complexes: B:D.88, B:S.89, A:C.84, A:C.84, A:D.87 CD.6: 3 residues within 4Å: Chain A: E.66, D.73, D.75 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.66, A:E.66, A:D.73, A:D.75, A:D.75 CD.7: 1 residues within 4Å: Chain A: E.59 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.59, H2O.2, H2O.2, H2O.2, H2O.2 CD.13: 3 residues within 4Å: Chain B: D.33, C.35 Ligands: ACT.21 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.33, B:D.33, B:C.35, B:C.35, H2O.4 CD.14: 3 residues within 4Å: Chain B: D.65, T.71, E.76 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.65, B:E.76, H2O.3, H2O.4, H2O.4 CD.15: 2 residues within 4Å: Chain B: F.27, E.40 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:F.27, B:E.40, B:E.40, H2O.4, H2O.4 CD.16: 6 residues within 4Å: Chain A: S.89 Chain B: P.52, E.56, C.84, D.87 Ligands: CD.17 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Metal complexes: B:E.56, B:C.84, B:D.87, A:S.89, A:S.89 CD.17: 6 residues within 4Å: Chain A: D.88, S.89 Chain B: Q.50, C.84, D.87 Ligands: CD.16 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Metal complexes: B:C.84, B:C.84, B:D.87, A:D.88, A:S.89 CD.18: 3 residues within 4Å: Chain B: E.66, D.73, D.75 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.66, B:E.66, B:D.73, B:D.75, B:D.75 CD.19: 1 residues within 4Å: Chain B: E.59 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:E.59, H2O.5, H2O.5, H2O.5, H2O.5

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

ACT.8: 6 residues within 4Å: Chain A: E.15 Chain B: E.15, E.19 Ligands: CA.11, CA.23, CA.24 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.15, B:E.15, B:E.19 ACT.9: 6 residues within 4Å: Chain A: D.33, C.35, I.36, S.37, T.71 Ligands: CD.1 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.71 Water bridges: A:S.37 ACT.10: 4 residues within 4Å: Chain A: E.10, Q.11, L.12, T.13 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.10 ACT.20: 6 residues within 4Å: Chain A: E.15, E.19 Chain B: E.15 Ligands: CA.11, CA.12, CA.23 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.15 ACT.21: 6 residues within 4Å: Chain B: D.33, C.35, I.36, S.37, T.71 Ligands: CD.13 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:T.71 Hydrogen bonds: B:C.35 Water bridges: B:S.37 ACT.22: 4 residues within 4Å: Chain B: E.10, Q.11, L.12, T.13 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.10

4 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)

CA.11: 7 residues within 4Å: Chain A: E.15, E.19 Chain B: E.15, E.19 Ligands: ACT.8, ACT.20, CA.23 5 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:E.15, A:E.19, B:E.19, H2O.3, H2O.5 CA.12: 1 residues within 4Å: Ligands: ACT.20 No protein-ligand interaction detected (PLIP) CA.23: 7 residues within 4Å: Chain A: E.15, E.19 Chain B: E.15, E.19 Ligands: ACT.8, CA.11, ACT.20 5 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:E.15, B:E.19, A:E.19, H2O.3, H2O.5 CA.24: 1 residues within 4Å: Ligands: ACT.8 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, X.L. et al., The structure of cardiac troponin C regulatory domain with bound Cd(2+) reveals a closed conformation and unique ion coordination. Acta Crystallogr.,Sect.D (2013)

Release Date

2013-02-06

Peptides

Troponin C, slow skeletal and cardiac muscles: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Troponin C, slow skeletal and cardiac muscles

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