SMTL ID : 7ou9.1

Crystal structure of dimeric chlorite dismutase variant Q74E (CCld Q74E) from Cyanothece sp. PCC7425 in complex with nitrite

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.42 Å

Oligo State

homo-dimer

Ligands

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

HEM.1: 33 residues within 4Å: Chain A: N.64, 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: NO2.2 24 PLIP interactions: 24 interactions with chain A, Hydrophobic interactions: A:L.76, A:I.94, A:F.114, A:L.128, A:L.135, A:F.147, A:F.147, A:F.147, A:T.149, A:F.151, A:F.151, A:L.165, A:W.174 Hydrogen bonds: A:R.66, A:Y.67, A:Y.67, A:A.68, A:W.102 Water bridges: A:N.64, A:H.137, A:H.137 Salt bridges: A:K.98 pi-Cation interactions: A:H.120 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: NO2.6 32 PLIP interactions: 32 interactions with chain B, Hydrophobic interactions: B:L.76, B:L.76, B:I.94, B:F.114, B:F.114, B:T.121, 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:L.165, B:W.174, B:W.174 Hydrogen bonds: B:R.66, B:Y.67, B:A.68, B:W.102 Water bridges: B:N.64, B:Y.67, B:Y.67, B:Y.67, B:Y.67, B:H.137, B:H.137 Salt bridges: B:K.98 pi-Stacking: B:H.120 Metal complexes: B:H.120

2 x NO2: NITRITE ION(Non-covalent)

NO2.2: 7 residues within 4Å: Chain A: R.133, R.134, L.135, T.149, W.150, F.151 Ligands: HEM.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.133, A:R.133 NO2.6: 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

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

SO4.3: 4 residues within 4Å: Chain A: R.10, L.141 Chain B: R.10, L.141 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Salt bridges: A:R.10, B:R.10 Water bridges: B:Q.59, B:Q.59

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 6 residues within 4Å: Chain B: F.13, W.21, I.42, N.84, R.134, W.150 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:W.21, B:R.134 Water bridges: B:R.187

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.7: 9 residues within 4Å: Chain A: N.9, A.62, S.63, N.64 Chain B: W.103, E.104, R.139, D.140, G.142 No protein-ligand interaction detected (PLIP)

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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