SMTL ID : 5jpr.1

Neutron Structure of Compound II of Ascorbate Peroxidase

Coordinates

PDB Format

Method

NEUTRON DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

1 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.1: 29 residues within 4Å: Chain A: P.45, L.46, L.48, R.49, W.52, P.143, D.144, A.145, L.152, F.156, I.167, L.170, S.171, G.173, H.174, I.176, G.177, A.178, A.179, H.180, R.183, S.184, G.185, F.186, W.190, L.216, S.218, Y.246, L.253 33 PLIP interactions: 31 interactions with chain A, 2 Ligand-Water interactions Hydrophobic interactions: A:L.48, A:R.49, A:W.52, A:W.52, A:W.52, A:P.143, A:P.143, A:A.145, A:L.152, A:F.156, A:L.170, A:L.170, A:A.179, A:W.190, A:L.216, A:S.218 Hydrogen bonds: A:A.178, A:A.178, A:H.180, A:R.183, A:S.184 Water bridges: A:R.49, A:H.180, A:H.180, A:H.180, A:H.180, A:H.180 Salt bridges: A:R.49, A:H.180, A:H.180 Metal complexes: A:H.174, H2O.2, H2O.2

1 x K: POTASSIUM ION(Non-covalent)

K.2: 7 residues within 4Å: Chain A: T.175, T.191, N.193, P.194, I.196, D.198, S.200 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:T.175, A:T.191, A:N.193, A:I.196, A:D.198

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

SO4.3: 2 residues within 4Å: Chain A: P.138, R.141 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.141, A:R.141, A:R.141 Salt bridges: A:R.141 SO4.4: 5 residues within 4Å: Chain A: K.147, G.148, S.149, D.150, H.151 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.148, A:D.150, A:D.150, A:H.151 Water bridges: A:S.149

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kwon, H. et al., Direct visualization of a Fe(IV)-OH intermediate in a heme enzyme. Nat Commun (2016)

Release Date

2016-12-21

Peptides

Ascorbate peroxidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Ascorbate peroxidase

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