SMTL ID : 6ds2.2 (1 other biounit)

Crystal structure of Ni(II)-bound human calprotectin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

hetero-2-2-mer

Ligands

3 x NI: NICKEL (II) ION(Non-covalent)

NI.1: 4 residues within 4Å: Chain A: H.83, H.87 Chain B: H.20, D.30 5 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: A:H.83, A:H.87, B:H.20, B:D.30, H2O.4 NI.4: 6 residues within 4Å: Chain A: H.17, H.27 Chain B: H.91, H.95, H.103, H.105 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Metal complexes: A:H.17, A:H.27, B:H.91, B:H.95, B:H.103, B:H.105 NI.8: 6 residues within 4Å: Chain C: H.17, H.27 Chain D: H.91, H.95, H.103, H.105 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain C Metal complexes: D:H.91, D:H.95, D:H.103, D:H.105, C:H.17, C:H.27

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

NA.2: 5 residues within 4Å: Chain A: S.20, K.23, N.25, A.28, Y.30 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.23, A:K.23, A:A.28 NA.3: 5 residues within 4Å: Chain A: D.59, N.61, D.63, A.65, E.70 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.59, A:D.63 Water bridges: A:N.61 NA.5: 5 residues within 4Å: Chain B: S.23, L.26, H.28, T.31, N.33 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.23, B:H.28, B:N.33 NA.6: 5 residues within 4Å: Chain C: S.20, K.23, N.25, A.28, Y.30 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:K.23, C:A.28, C:A.28 Water bridges: C:I.22 NA.7: 5 residues within 4Å: Chain C: D.59, N.61, D.63, A.65, E.70 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.63 Water bridges: C:N.67

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nakashige, T.G. et al., Biophysical Examination of the Calcium-Modulated Nickel-Binding Properties of Human Calprotectin Reveals Conformational Change in the EF-Hand Domains and His3Asp Site. Biochemistry (2018)

Release Date

2018-07-04

Peptides

Protein S100-A8: AC
Protein S100-A9: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

C
G

B
F

D
H

Protein S100-A8

Protein S100-A9

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