SMTL ID : 3ucy.1

Structure of Mg2+ bound N-terminal domain of calmodulin in the presence of Zn2+

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

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

NA.1: 6 residues within 4Å: Chain A: D.20, D.22, D.24, T.26 Ligands: ZN.3, CAC.5 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.20, A:D.22, A:T.26, A:T.26 NA.6: 6 residues within 4Å: Chain B: D.20, D.22, D.24, T.26 Ligands: ZN.8, CAC.10 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.20, B:T.26

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: D.56, D.58, N.60, T.62 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.56, A:D.58, A:T.62, H2O.1, H2O.1 MG.7: 4 residues within 4Å: Chain B: D.56, D.58, N.60, T.62 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.56, B:D.58, B:T.62, H2O.3, H2O.4

4 x ZN: ZINC ION(Non-covalent)

ZN.3: 7 residues within 4Å: Chain A: D.22, D.24 Chain B: D.22 Ligands: NA.1, CAC.5, ZN.8, CAC.10 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.22, A:D.22, A:D.24 ZN.4: 2 residues within 4Å: Chain A: D.64, E.67 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.64, A:D.64, A:E.67, H2O.3 ZN.8: 7 residues within 4Å: Chain A: D.22 Chain B: D.22, D.24 Ligands: ZN.3, CAC.5, NA.6, CAC.10 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.22, B:D.22, B:D.24 ZN.9: 2 residues within 4Å: Chain B: D.64, E.67 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.64, B:D.64, B:E.67, H2O.5

2 x CAC: CACODYLATE ION(Non-covalent)

CAC.5: 12 residues within 4Å: Chain A: D.22, D.24, T.26, I.27, T.28, T.62 Chain B: D.22, D.24 Ligands: NA.1, ZN.3, ZN.8, CAC.10 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.26 Water bridges: A:D.20 CAC.10: 12 residues within 4Å: Chain A: D.22, D.24 Chain B: D.22, D.24, T.26, I.27, T.28, T.62 Ligands: ZN.3, CAC.5, NA.6, ZN.8 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Senguen, F.T. et al., X-ray Structures of Magnesium and Manganese Complexes with the N-Terminal Domain of Calmodulin: Insights into the Mechanism and Specificity of Metal Ion Binding to an EF-Hand. Biochemistry (2012)

Release Date

2012-08-08

Peptides

Calmodulin: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Calmodulin

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