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

Crystal structure of calcium and zinc-bound human S100A8 in space group C2221

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

4 x CA: CALCIUM ION(Non-covalent)

CA.1: 6 residues within 4Å: Chain A: S.21, K.24, N.26, F.27, A.29, Y.31 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:S.21, A:K.24, A:N.26, A:A.29, H2O.1 CA.2: 5 residues within 4Å: Chain A: D.60, N.62, D.64, A.66, E.71 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.60, A:D.64, A:A.66, A:E.71, H2O.1 CA.11: 5 residues within 4Å: Chain B: S.21, K.24, N.26, A.29, Y.31 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:S.21, B:K.24, B:N.26, B:A.29, H2O.3 CA.12: 5 residues within 4Å: Chain B: D.60, N.62, D.64, A.66, E.71 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.60, B:D.64, B:A.66, B:E.71, H2O.3

4 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: H.18 Chain B: H.84 Ligands: CAC.10, CL.14 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Metal complexes: A:H.18, B:H.84 ZN.4: 5 residues within 4Å: Chain A: H.28 Chain B: H.88, H.92 Ligands: CL.7, CAC.10 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Metal complexes: A:H.28, B:H.92 ZN.5: 4 residues within 4Å: Chain A: H.84, H.88 Chain B: H.18, H.28 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Metal complexes: A:H.84, A:H.88, B:H.18, B:H.28 ZN.13: 2 residues within 4Å: Chain B: H.88, E.94 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.88, B:E.94, B:E.94

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.6: 2 residues within 4Å: Chain A: H.88 Chain B: H.28 Ligand excluded by PLIP CL.7: 4 residues within 4Å: Chain A: H.28 Chain B: H.92 Ligands: ZN.4, CAC.10 Ligand excluded by PLIP CL.14: 6 residues within 4Å: Chain A: Y.17, H.18, H.28 Chain B: H.84 Ligands: ZN.3, CAC.10 Ligand excluded by PLIP CL.15: 3 residues within 4Å: Chain B: K.50, W.55, E.58 Ligand excluded by PLIP

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

ACT.8: 6 residues within 4Å: Chain A: K.8, A.9, S.12 Chain B: K.8, A.9, S.12 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:S.12, B:S.12, B:S.12 Water bridges: A:A.9 Hydrophobic interactions: B:K.8 ACT.9: 4 residues within 4Å: Chain A: I.47, K.50, K.78, A.82 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.47, A:A.82 Water bridges: A:K.78 Salt bridges: A:K.50, A:K.78 ACT.16: 2 residues within 4Å: Chain B: N.62, T.63 No protein-ligand interaction detected (PLIP)

1 x CAC: CACODYLATE ION(Non-covalent)

CAC.10: 11 residues within 4Å: Chain A: H.18, F.27, H.28 Chain B: H.84, H.88, S.91, H.92 Ligands: ZN.3, ZN.4, CL.7, CL.14 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lin, H. et al., Crystal structure of human S100A8 in complex with zinc and calcium. Bmc Struct.Biol. (2016)

Release Date

2016-06-08

Peptides

Protein S100-A8: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
D

Protein S100-A8

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