SMTL ID : 5w1f.2 (1 other biounit)

Crystal structure of Ni(II)- and Ca(II)-bound human calprotectin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

hetero-2-2-mer

Ligands

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

NA.1: 5 residues within 4Å: Chain A: S.20, K.23, N.25, A.28, Y.30 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.23 NA.4: 5 residues within 4Å: Chain B: S.23, L.26, H.28, T.31, E.36 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.26 Water bridges: B:N.33 NA.7: 5 residues within 4Å: Chain C: S.20, K.23, N.25, A.28, Y.30 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.23, C:K.23

5 x CA: CALCIUM ION(Non-covalent)

CA.2: 5 residues within 4Å: Chain A: D.59, N.61, D.63, A.65, E.70 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.59, A:D.63, A:A.65, A:E.70, H2O.1 CA.5: 5 residues within 4Å: Chain B: D.67, N.69, D.71, Q.73, E.78 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.67, B:D.71, B:Q.73, B:E.78, H2O.2 CA.8: 5 residues within 4Å: Chain C: D.59, N.61, D.63, A.65, E.70 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.59, C:D.63, C:A.65, C:E.70, H2O.2 CA.10: 5 residues within 4Å: Chain D: S.23, L.26, H.28, T.31, E.36 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:S.23, D:H.28, D:T.31, D:E.36, H2O.3 CA.11: 5 residues within 4Å: Chain D: D.67, N.69, D.71, Q.73, E.78 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.67, D:D.71, D:Q.73, D:E.78, H2O.3

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

NI.3: 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.6: 4 residues within 4Å: Chain C: H.83, H.87 Chain D: H.20, D.30 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain D Metal complexes: C:H.83, C:H.87, D:H.20, D:D.30 NI.9: 6 residues within 4Å: Chain C: H.17, H.27 Chain D: H.91, H.95, H.103, H.105 6 PLIP interactions: 2 interactions with chain C, 4 interactions with chain D Metal complexes: C:H.17, C:H.27, D:H.91, D:H.95, D:H.103, D:H.105

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nakashige, T.G. et al., Nickel Sequestration by the Host-Defense Protein Human Calprotectin. J. Am. Chem. Soc. (2017)

Release Date

2017-06-14

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

C
E

B
H

D
F

Protein S100-A8

Protein S100-A9

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