SMTL ID : 7wyj.1

Structure of the complex of lactoperoxidase with nitric oxide catalytic product nitrite at 1.89 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

monomer

Ligands

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 6 residues within 4Å: Chain A: N.205, S.208, A.214, V.215, Q.217, W.220 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.217 Water bridges: A:Q.217

1 x CA: CALCIUM ION(Non-covalent)

CA.2: 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:D.110, A:T.184, A:F.186, A:S.190

22 x IOD: IODIDE ION(Non-functional Binders)

IOD.3: 2 residues within 4Å: Chain A: N.80, P.145 Ligand excluded by PLIP IOD.4: 1 residues within 4Å: Chain A: W.530 Ligand excluded by PLIP IOD.5: 1 residues within 4Å: Chain A: R.31 Ligand excluded by PLIP IOD.6: 2 residues within 4Å: Chain A: S.359, K.402 Ligand excluded by PLIP IOD.7: 1 residues within 4Å: Chain A: G.466 Ligand excluded by PLIP IOD.8: 1 residues within 4Å: Chain A: P.375 Ligand excluded by PLIP IOD.9: 3 residues within 4Å: Chain A: E.218, F.229, N.231 Ligand excluded by PLIP IOD.10: 2 residues within 4Å: Chain A: P.236, T.425 Ligand excluded by PLIP IOD.11: 3 residues within 4Å: Chain A: R.76, P.149, N.419 Ligand excluded by PLIP IOD.20: 5 residues within 4Å: Chain A: H.109, R.255, E.258 Ligands: NO2.15, HEM.17 Ligand excluded by PLIP IOD.21: 1 residues within 4Å: Chain A: S.198 Ligand excluded by PLIP IOD.22: 4 residues within 4Å: Chain A: K.150, N.419, H.429, G.430 Ligand excluded by PLIP IOD.23: 1 residues within 4Å: Chain A: R.202 Ligand excluded by PLIP IOD.24: 6 residues within 4Å: Chain A: A.44, R.45, W.46, N.341, V.342, W.452 Ligand excluded by PLIP IOD.25: 3 residues within 4Å: Chain A: S.33, P.34, A.35 Ligand excluded by PLIP IOD.26: 2 residues within 4Å: Chain A: L.86, D.87 Ligand excluded by PLIP IOD.27: 2 residues within 4Å: Chain A: H.222, H.558 Ligand excluded by PLIP IOD.28: 5 residues within 4Å: Chain A: E.363, Y.365, I.559, T.560, K.561 Ligand excluded by PLIP IOD.29: 1 residues within 4Å: Chain A: R.506 Ligand excluded by PLIP IOD.30: 4 residues within 4Å: Chain A: C.15, E.17, C.28, R.31 Ligand excluded by PLIP IOD.31: 3 residues within 4Å: Chain A: H.377, H.429 Ligands: SCN.19 Ligand excluded by PLIP IOD.32: 4 residues within 4Å: Chain A: D.311, H.565, A.566, F.567 Ligand excluded by PLIP

3 x SCN: THIOCYANATE ION(Non-functional Binders)

SCN.12: 5 residues within 4Å: Chain A: N.230, P.236, C.248, F.254, F.381 No protein-ligand interaction detected (PLIP) SCN.18: 4 residues within 4Å: Chain A: I.24, P.197, R.204 Ligands: EDO.16 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.204 SCN.19: 3 residues within 4Å: Chain A: H.377, T.378 Ligands: IOD.31 No protein-ligand interaction detected (PLIP)

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.13: 5 residues within 4Å: Chain A: L.224, A.225, R.271, N.274, R.278 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.274, A:R.278, A:R.278 Water bridges: A:R.275 EDO.14: 4 residues within 4Å: Chain A: N.450, S.451, Q.460, D.488 4 PLIP interactions: 4 interactions with chain A Water bridges: A:N.68, A:S.451, A:S.451, A:D.488 EDO.16: 6 residues within 4Å: Chain A: V.13, T.23, I.24, T.25, P.197 Ligands: SCN.18 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.24, A:T.25

1 x NO2: NITRITE ION(Non-covalent)

NO2.15: 6 residues within 4Å: Chain A: Q.105, D.108, H.109, R.255 Ligands: HEM.17, IOD.20 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.105 Water bridges: A:R.255

1 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)

HEM.17: 23 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: NO2.15, IOD.20 24 PLIP interactions: 24 interactions with chain A, Hydrophobic interactions: A:Q.105, A:D.108, A:E.258, A:Q.259, A:F.347, A:F.347, A:R.348, A:V.354, 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, A:Q.423, A:R.440 Salt bridges: A:H.109, A:R.255, A:R.348, A:R.440 Metal complexes: A:H.351

1 x ZN: ZINC ION(Non-covalent)

ZN.33: 3 residues within 4Å: Chain A: E.130, H.426, K.427 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.130, H2O.2, H2O.2

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

NAG.34: 4 residues within 4Å: Chain A: N.95, R.96, I.315, Q.568 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.96 Water bridges: A:N.95 NAG.35: 4 residues within 4Å: Chain A: N.241, A.244, W.384, K.388 No protein-ligand interaction detected (PLIP) NAG.36: 3 residues within 4Å: Chain A: N.332, S.334, V.335 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.332 Water bridges: A:N.332

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Viswanathan, V. et al., Structural evidence of the conversion of nitric oxide (NO) to nitrite ion (NO2-) by lactoperoxidase (LPO): Structure of the complex of LPO with NO2- at 1.89 angstrom resolution. J.Inorg.Biochem. (2023)

Release Date

2023-01-11

Peptides

Lactoperoxidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lactoperoxidase

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