SMTL ID : 7c75.1

Crystal structure of yak lactoperoxidase with partially coordinated Na ion in the distal heme cavity

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

monomer

Ligands

4 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.1: 3 residues within 4Å: Chain A: N.95, R.96, Q.568 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.96 Water bridges: A:N.95 NAG.2: 7 residues within 4Å: Chain A: N.205, S.208, L.210, L.212, A.214, V.215, Q.217 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.208, A:V.215, A:Q.217, A:Q.217 Water bridges: A:N.205 NAG.3: 3 residues within 4Å: Chain A: N.241, A.244, W.384 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.385 NAG.4: 3 residues within 4Å: Chain A: N.332, S.334, V.335 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.332

1 x CA: CALCIUM ION(Non-covalent)

CA.5: 5 residues within 4Å: Chain A: D.110, T.184, F.186, D.188, S.190 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.110, A:T.184, A:T.184, A:F.186, A:S.190

1 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)

HEM.6: 22 residues within 4Å: Chain A: M.101, G.104, Q.105, D.108, H.109, D.112, R.255, E.258, Q.259, T.344, F.347, R.348, G.350, H.351, V.354, F.380, L.417, Q.423, L.433, I.436, R.440 Ligands: NA.9 23 PLIP interactions: 22 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: A:Q.105, A:E.258, A:Q.259, A:F.347, A:F.347, A:F.347, A:R.348, A:V.354, A:F.380, A:L.417, A:L.433, A:L.433, A:I.436 Water bridges: A:E.116, A:R.255, A:R.348 Salt bridges: A:H.109, A:R.255, A:R.348, A:R.440 pi-Cation interactions: A:H.109 Metal complexes: A:H.351, H2O.2

1 x K: POTASSIUM ION(Non-covalent)

K.7: 6 residues within 4Å: Chain A: A.44, R.45, W.46, N.341, V.342, W.452 No protein-ligand interaction detected (PLIP)

1 x ZN: ZINC ION(Non-covalent)

ZN.8: 2 residues within 4Å: Chain A: H.222, H.558 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.222, A:H.558

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

NA.9: 3 residues within 4Å: Chain A: H.109, R.255 Ligands: HEM.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.255

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Singh, P.K. et al., Potassium-induced partial inhibition of lactoperoxidase: structure of the complex of lactoperoxidase with potassium ion at 2.20 angstrom resolution. J.Biol.Inorg.Chem. (2021)

Release Date

2020-06-24

Peptides

Lactoperoxidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lactoperoxidase

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