SMTL ID : 7owi.1 (1 other biounit)

Crystal structure of dimeric chlorite dismutase variant R127A (CCld R127A) from Cyanothece sp. PCC7425

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

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

HEM.1: 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, A.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: MPD.3 25 PLIP interactions: 24 interactions with chain A, 1 Ligand-Water interactions Hydrophobic interactions: A:L.76, A:L.76, A:I.94, A:F.114, A:F.114, A:T.121, A:L.128, A:A.133, A:L.135, A:F.147, A:F.147, A:T.149, A:F.151, A:F.151, A:W.174, A:W.174 Hydrogen bonds: A:R.66, A:Y.67, A:A.68, A:W.102 Water bridges: A:N.64, A:Y.67 Salt bridges: A:K.98 Metal complexes: A:H.120, H2O.4 HEM.6: 31 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, A.133, L.135, F.147, T.149, F.151, F.161, L.164, L.165, M.168, R.169, E.173, W.174, E.180 Ligands: MPD.7 25 PLIP interactions: 25 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:L.135, B:F.147, B:F.147, B:F.151, B:F.151, B:L.164, B:W.174, 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 Metal complexes: B:H.120

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.2: 5 residues within 4Å: Chain A: R.57, L.58, G.142, E.143, E.144 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.143, A:E.144 Water bridges: A:E.143

2 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.3: 7 residues within 4Å: Chain A: I.65, L.76, Q.80, A.133, R.134, L.135 Ligands: HEM.1 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.65, A:A.133 Hydrogen bonds: A:L.135 MPD.7: 9 residues within 4Å: Chain B: L.76, Q.80, A.133, R.134, L.135, T.149, W.150, F.151 Ligands: HEM.6 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:A.133, B:L.135, B:F.151

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 7 residues within 4Å: Chain B: Y.11, F.13, I.42, L.83, R.134, L.136, W.150 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.134 Water bridges: B:W.150 GOL.5: 4 residues within 4Å: Chain B: R.57, G.142, E.143, E.144 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.142, B:E.143, B:E.144

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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