SMTL ID : 7ou5.1

Crystal structure of dimeric chlorite dismutase from Cyanothece sp. PCC7425 in complex with nitrite

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 x NO2: NITRITE ION(Non-covalent)

NO2.1: 7 residues within 4Å: Chain A: R.133, R.134, L.135, T.149, W.150, F.151 Ligands: HEM.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.133, A:R.133 NO2.4: 7 residues within 4Å: Chain B: R.133, R.134, L.135, T.149, W.150, F.151 Ligands: HEM.5 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.133, B:R.133

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

HEM.2: 32 residues within 4Å: Chain A: I.65, R.66, Y.67, A.68, L.76, I.94, I.96, K.98, W.102, F.114, H.120, T.121, G.124, L.125, Y.127, L.128, V.131, R.133, L.135, H.137, F.147, T.149, F.151, F.161, L.164, L.165, M.168, R.169, E.173, W.174, E.180 Ligands: NO2.1 22 PLIP interactions: 22 interactions with chain A, Hydrophobic interactions: A:I.65, A:L.76, A:L.76, A:I.94, A:F.114, A:V.131, A:L.135, A:F.147, A:F.147, A:T.149, A:F.151, A:F.151, A:L.164, A:W.174 Hydrogen bonds: A:R.66, A:Y.67, A:A.68, A:W.102 Water bridges: A:Y.67, A:Y.67 Salt bridges: A:K.98 Metal complexes: A:H.120 HEM.5: 32 residues within 4Å: Chain B: I.65, R.66, Y.67, A.68, L.76, I.94, I.96, K.98, W.102, F.114, H.120, T.121, G.124, L.125, Y.127, L.128, V.131, R.133, L.135, H.137, F.147, T.149, F.151, F.161, L.164, L.165, M.168, R.169, E.173, W.174, E.180 Ligands: NO2.4 26 PLIP interactions: 26 interactions with chain B, Hydrophobic interactions: B:I.65, B:L.76, B:L.76, B:I.94, B:F.114, B:F.114, B:L.128, B:L.128, B:V.131, B:L.135, B:F.147, B:F.147, B:T.149, B:F.151, B:F.151, B:L.164, B:W.174 Hydrogen bonds: B:R.66, B:Y.67, B:A.68, B:W.102 Water bridges: B:Y.67, B:Y.67 Salt bridges: B:K.98 pi-Cation interactions: B:H.120 Metal complexes: B:H.120

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: A.62, S.63, N.64 Chain B: W.103, R.139 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.139, B:R.139, A:S.63 Water bridges: A:S.63

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

SO4.6: 5 residues within 4Å: Chain A: R.10, Q.59, L.141 Chain B: R.10, L.141 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Salt bridges: B:R.10, A:R.10

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Serra, I. et al., Impact of the dynamics of the catalytic arginine on nitrite and chlorite binding by dimeric chlorite dismutase. J.Inorg.Biochem. (2021)

Release Date

2021-12-22

Peptides

Chlorite Dismutase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Chlorite Dismutase

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