SMTL ID : 3m5q.1

0.93 A Structure of Manganese-Bound Manganese Peroxidase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 0.93 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: 8 residues within 4Å: Chain A: L.69, M.94, Q.95, N.98, T.99, I.100, S.101, N.131 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.98 Water bridges: A:Q.95

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

MAN.2: 7 residues within 4Å: Chain A: A.308, P.331, G.332, A.333, S.334, Q.335, S.336 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:P.331, A:S.334 Water bridges: A:L.337, A:L.337

2 x CA: CALCIUM ION(Non-covalent)

CA.3: 5 residues within 4Å: Chain A: S.174, D.191, T.193, T.196, D.198 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.191, A:D.191, A:T.193, A:T.196, A:D.198 CA.4: 4 residues within 4Å: Chain A: D.47, G.62, D.64, S.66 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.47, A:D.64, A:S.66, H2O.4, H2O.5

1 x MN: MANGANESE (II) ION(Non-covalent)

MN.5: 4 residues within 4Å: Chain A: E.35, E.39, D.179 Ligands: HEM.7 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.35, A:E.39, A:D.179, H2O.2, H2O.5

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 6 residues within 4Å: Chain A: D.23, T.27, P.92, F.93, K.96, F.353 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.27, A:K.96

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

HEM.7: 27 residues within 4Å: Chain A: E.35, H.38, E.39, I.41, R.42, F.45, P.142, E.143, P.144, I.151, L.169, L.170, S.172, H.173, V.175, A.176, R.177, A.178, D.179, K.180, V.181, F.190, L.239, S.241, F.269, M.273 Ligands: MN.5 32 PLIP interactions: 31 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: A:H.38, A:I.41, A:R.42, A:F.45, A:F.45, A:F.45, A:F.45, A:P.142, A:P.144, A:I.151, A:L.169, A:L.170, A:A.176, A:A.178, A:V.181, A:F.190, A:F.190, A:L.239, A:F.269 Hydrogen bonds: A:R.177, A:D.179, A:K.180, A:V.181 Water bridges: A:R.42, A:R.177, A:D.179 Salt bridges: A:H.38, A:R.42 pi-Stacking: A:F.190 pi-Cation interactions: A:R.42 Metal complexes: A:H.173, H2O.6

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sundaramoorthy, M. et al., Ultrahigh (0.93A) resolution structure of manganese peroxidase from Phanerochaete chrysosporium: implications for the catalytic mechanism. J.Inorg.Biochem. (2010)

Release Date

2010-04-14

Peptides

Manganese peroxidase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Manganese peroxidase 1

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