SMTL ID : 4hov.1

DypB N246A in complex with manganese

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-hexamer

Ligands

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

HEM.1: 26 residues within 4Å: Chain A: D.150, L.152, F.154, V.155, D.156, G.157, T.158, E.159, Q.188, Y.190, H.192, I.209, R.211, H.229, V.230, N.233, R.247, T.262, F.264, T.274, M.277, L.278, M.281, V.293, S.297 Ligands: MN.4 25 PLIP interactions: 24 interactions with chain A, 1 Ligand-Water interactions Hydrophobic interactions: A:L.152, A:F.154, A:Y.190, A:Y.190, A:I.209, A:N.233, A:F.264, A:F.264, A:F.264, A:F.264, A:T.274, A:M.277, A:L.278, A:L.278, A:V.293 Hydrogen bonds: A:G.157, A:T.158, A:E.159 Water bridges: A:R.211 Salt bridges: A:R.247 pi-Stacking: A:H.229 pi-Cation interactions: A:H.229, A:R.247 Metal complexes: A:H.229, H2O.9 HEM.5: 26 residues within 4Å: Chain B: D.150, L.152, F.154, V.155, D.156, G.157, T.158, E.159, Q.188, Y.190, H.192, I.209, R.211, H.229, V.230, N.233, T.234, R.247, T.262, F.264, T.274, M.277, L.278, M.281, V.293, S.297 28 PLIP interactions: 27 interactions with chain B, 1 Ligand-Water interactions Hydrophobic interactions: B:L.152, B:F.154, B:Y.190, B:Y.190, B:Y.190, B:I.209, B:N.233, B:F.264, B:F.264, B:F.264, B:T.274, B:M.277, B:L.278, B:L.278, B:V.293 Hydrogen bonds: B:G.157, B:T.158, B:E.159 Water bridges: B:E.159, B:E.159, B:R.211, B:N.233 Salt bridges: B:R.247 pi-Stacking: B:H.229, B:F.264 pi-Cation interactions: B:R.247 Metal complexes: B:H.229, H2O.18 HEM.9: 26 residues within 4Å: Chain C: D.150, L.152, F.154, V.155, D.156, G.157, T.158, E.159, Q.188, Y.190, H.192, I.209, R.211, H.229, V.230, N.233, T.234, R.247, T.262, F.264, T.274, M.277, L.278, M.281, V.293, S.297 23 PLIP interactions: 22 interactions with chain C, 1 Ligand-Water interactions Hydrophobic interactions: C:L.152, C:F.154, C:Y.190, C:Y.190, C:I.209, C:N.233, C:F.264, C:F.264, C:T.274, C:M.277, C:L.278, C:L.278, C:V.293 Hydrogen bonds: C:G.157, C:T.158, C:E.159 Water bridges: C:D.244 Salt bridges: C:R.247 pi-Stacking: C:H.229, C:H.229 pi-Cation interactions: C:R.247 Metal complexes: C:H.229, H2O.26 HEM.12: 26 residues within 4Å: Chain D: D.150, L.152, F.154, V.155, D.156, G.157, T.158, E.159, Q.188, Y.190, H.192, I.209, R.211, H.229, V.230, N.233, R.247, T.262, F.264, T.274, M.277, L.278, M.281, V.293, S.297 Ligands: MN.15 27 PLIP interactions: 26 interactions with chain D, 1 Ligand-Water interactions Hydrophobic interactions: D:L.152, D:F.154, D:Y.190, D:Y.190, D:I.209, D:N.233, D:F.264, D:F.264, D:F.264, D:F.264, D:T.274, D:M.277, D:L.278, D:L.278, D:V.293 Hydrogen bonds: D:G.157, D:T.158, D:E.159 Water bridges: D:R.211, D:T.234, D:T.234 Salt bridges: D:R.247 pi-Stacking: D:H.229 pi-Cation interactions: D:H.229, D:R.247 Metal complexes: D:H.229, H2O.35 HEM.16: 26 residues within 4Å: Chain E: D.150, L.152, F.154, V.155, D.156, G.157, T.158, E.159, Q.188, Y.190, H.192, I.209, R.211, H.229, V.230, N.233, T.234, R.247, T.262, F.264, T.274, M.277, L.278, M.281, V.293, S.297 28 PLIP interactions: 27 interactions with chain E, 1 Ligand-Water interactions Hydrophobic interactions: E:L.152, E:F.154, E:Y.190, E:Y.190, E:Y.190, E:I.209, E:N.233, E:F.264, E:F.264, E:F.264, E:T.274, E:M.277, E:L.278, E:L.278, E:V.293 Hydrogen bonds: E:G.157, E:T.158, E:E.159 Water bridges: E:R.211, E:N.233, E:T.234, E:T.234 Salt bridges: E:R.247 pi-Stacking: E:H.229, E:F.264 pi-Cation interactions: E:R.247 Metal complexes: E:H.229, H2O.44 HEM.20: 26 residues within 4Å: Chain F: D.150, L.152, F.154, V.155, D.156, G.157, T.158, E.159, Q.188, Y.190, H.192, I.209, R.211, H.229, V.230, N.233, T.234, R.247, T.262, F.264, T.274, M.277, L.278, M.281, V.293, S.297 23 PLIP interactions: 22 interactions with chain F, 1 Ligand-Water interactions Hydrophobic interactions: F:L.152, F:F.154, F:Y.190, F:Y.190, F:I.209, F:N.233, F:F.264, F:F.264, F:T.274, F:M.277, F:L.278, F:L.278, F:V.293 Hydrogen bonds: F:G.157, F:T.158, F:E.159 Water bridges: F:D.244 Salt bridges: F:R.247 pi-Stacking: F:H.229, F:H.229 pi-Cation interactions: F:R.247 Metal complexes: F:H.229, H2O.51

6 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 4 residues within 4Å: Chain A: K.116, C.119, F.120, H.141 Ligand excluded by PLIP CL.6: 4 residues within 4Å: Chain B: K.116, C.119, F.120, H.141 Ligand excluded by PLIP CL.10: 4 residues within 4Å: Chain C: K.116, C.119, F.120, H.141 Ligand excluded by PLIP CL.13: 4 residues within 4Å: Chain D: K.116, C.119, F.120, H.141 Ligand excluded by PLIP CL.17: 4 residues within 4Å: Chain E: K.116, C.119, F.120, H.141 Ligand excluded by PLIP CL.21: 4 residues within 4Å: Chain F: K.116, C.119, F.120, H.141 Ligand excluded by PLIP

2 x FMT: FORMIC ACID(Non-functional Binders)

FMT.3: 6 residues within 4Å: Chain A: H.86, H.88, D.270, P.271, A.272, E.275 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.86, A:A.272 FMT.14: 6 residues within 4Å: Chain D: H.86, H.88, D.270, P.271, A.272, E.275 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:A.272 Water bridges: D:H.86, D:H.86

6 x MN: MANGANESE (II) ION(Non-covalent)(Non-functional Binders)

MN.4: 2 residues within 4Å: Chain A: E.218 Ligands: HEM.1 No protein-ligand interaction detected (PLIP) MN.7: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MN.11: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MN.15: 2 residues within 4Å: Chain D: E.218 Ligands: HEM.12 No protein-ligand interaction detected (PLIP) MN.18: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MN.22: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 7 residues within 4Å: Chain A: A.114, R.115, K.116 Chain B: A.22, A.114, R.115, K.116 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:K.116, B:A.114, B:K.116 Water bridges: A:D.117, A:R.144, B:D.117 GOL.19: 7 residues within 4Å: Chain D: A.114, R.115, K.116 Chain E: A.22, A.114, R.115, K.116 6 PLIP interactions: 3 interactions with chain E, 3 interactions with chain D Hydrogen bonds: E:A.114, E:K.116, D:K.116 Water bridges: E:D.117, D:D.117, D:R.144

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Singh, R. et al., Improved Manganese-Oxidizing Activity of DypB, a Peroxidase from a Lignolytic Bacterium. Acs Chem.Biol. (2013)

Release Date

2013-01-16

Peptides

DypB: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
A

E
B

F
C

DypB

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