SMTL ID : 2e3a.1

Crystal structure of the NO-bound form of Arthromyces ramosus peroxidase at 1.3 Angstroms resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.30 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: 7 residues within 4Å: Chain A: A.82, R.104, I.108, G.111, V.112, F.114, N.143 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.104

1 x MAN: alpha-D-mannopyranose(Post Translational Modification)

MAN.2: 6 residues within 4Å: Chain A: P.238, G.239, S.339, L.340, A.341, P.342 4 PLIP interactions: 4 interactions with chain A Water bridges: A:G.239, A:L.340, A:A.341, A:A.341

2 x CA: CALCIUM ION(Non-covalent)

CA.3: 5 residues within 4Å: Chain A: D.57, G.75, D.77, S.79, I.80 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.57, A:D.77, A:S.79, H2O.3, H2O.3 CA.4: 7 residues within 4Å: Chain A: S.185, D.202, T.204, P.205, V.207, D.209, Q.211 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.202, A:D.202, A:T.204, A:V.207, A:D.209

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

HEM.5: 26 residues within 4Å: Chain A: R.48, K.49, L.51, R.52, F.55, P.154, G.155, P.156, I.163, L.180, L.181, A.183, H.184, L.186, A.187, S.188, Q.189, E.190, G.191, L.192, M.243, S.245, L.249, Y.273, M.277 Ligands: NO.6 30 PLIP interactions: 29 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:R.48, A:L.51, A:R.52, A:F.55, A:F.55, A:F.55, A:F.55, A:P.156, A:I.163, A:L.180, A:L.181, A:A.183, A:A.187, A:Q.189, A:L.192, A:L.249 Hydrogen bonds: A:S.188, A:E.190, A:G.191, A:L.192 Water bridges: A:R.48, A:R.48, A:K.49, A:K.49, A:R.52 Salt bridges: A:R.48, A:K.49, A:R.52 Metal complexes: A:H.184, NO.6

1 x NO: NITRIC OXIDE(Non-covalent)

NO.6: 4 residues within 4Å: Chain A: R.52, F.55, H.56 Ligands: HEM.5 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.52, A:R.52

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fukuyama, K. et al., Structures of cyanide, nitric oxide and hydroxylamine complexes of Arthromyces ramosusperoxidase at 100 K refined to 1.3 A resolution: coordination geometries of the ligands to the haem iron. ACTA CRYSTALLOGR.,SECT.D (2007)

Release Date

2007-03-20

Peptides

Peroxidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Peroxidase

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