SMTL ID : 6zfe.1

Crystal structure of murine S100A9 mutant C80A bound to calcium and zinc

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

homo-dimer

Ligands

4 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain A: S.26, E.29, H.31, T.34, E.39 6 PLIP interactions: 5 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:S.26, A:E.29, A:H.31, A:T.34, A:E.39, H2O.1 CA.2: 5 residues within 4Å: Chain A: D.70, N.72, D.74, Q.76, E.81 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.70, A:D.74, A:Q.76, A:E.81, A:E.81 CA.9: 5 residues within 4Å: Chain B: S.26, E.29, H.31, T.34, E.39 6 PLIP interactions: 5 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:S.26, B:E.29, B:H.31, B:T.34, B:E.39, H2O.1 CA.10: 5 residues within 4Å: Chain B: D.70, N.72, D.74, Q.76, E.81 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.70, B:D.74, B:Q.76, B:E.81, B:E.81

4 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: H.23, D.33 Chain B: H.94, H.98 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Metal complexes: A:H.23, A:D.33, A:D.33, B:H.94, B:H.98 ZN.4: 3 residues within 4Å: Chain A: H.105, H.107, H.109 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.105, A:H.107, A:H.109 ZN.11: 4 residues within 4Å: Chain A: H.94, H.98 Chain B: H.23, D.33 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Metal complexes: A:H.94, A:H.98, B:H.23, B:D.33, B:D.33 ZN.12: 3 residues within 4Å: Chain B: H.105, H.107, H.109 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.105, B:H.107, B:H.109

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

NA.5: 3 residues within 4Å: Chain A: D.33, E.80 Chain B: H.94 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.80 NA.13: 3 residues within 4Å: Chain A: H.94 Chain B: D.33, E.80 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.80

6 x SO4: SULFATE ION(Non-functional Binders)

SO4.6: 3 residues within 4Å: Chain A: K.37, R.41, N.63 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.37, A:R.41 SO4.7: 3 residues within 4Å: Chain A: R.13 Chain B: R.13 Ligands: SO4.15 No protein-ligand interaction detected (PLIP) SO4.8: 3 residues within 4Å: Chain A: H.98, N.101 Chain B: H.23 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Salt bridges: B:H.23, A:H.98 Hydrogen bonds: A:N.101 SO4.14: 3 residues within 4Å: Chain B: K.37, R.41, N.63 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:K.37, B:R.41 SO4.15: 3 residues within 4Å: Chain A: R.13 Chain B: R.13 Ligands: SO4.7 No protein-ligand interaction detected (PLIP) SO4.16: 3 residues within 4Å: Chain A: H.23 Chain B: H.98, N.101 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.101 Salt bridges: B:H.98, A:H.23

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Signor, L. et al., Divalent cations influence the dimerization mode of murine S100A9 protein by modulating its disulfide bond pattern. J.Struct.Biol. (2020)

Release Date

2021-01-13

Peptides

Protein S100-A9: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Protein S100-A9