SMTL ID : 7asb.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

homo-dimer

Ligands

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 6 residues within 4Å: Chain A: W.103, R.139 Chain B: N.9, A.62, S.63, N.64 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.139, A:R.139 Water bridges: A:W.103, B:S.63, B:I.65 GOL.2: 7 residues within 4Å: Chain A: Y.11, F.13, W.21, I.42, L.83, R.134, W.150 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.21, A:R.134, A:R.134 Water bridges: A:E.152 GOL.5: 7 residues within 4Å: Chain A: I.65, L.73, L.76, Q.77, E.80, R.133 Ligands: MES.3 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:L.73, A:Q.77, A:E.80, A:R.133, A:R.133 GOL.6: 4 residues within 4Å: Chain A: I.26, R.27, N.28, L.36 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:I.26 Water bridges: A:I.26, A:I.26, A:I.26, A:N.28, A:L.36 GOL.11: 8 residues within 4Å: Chain B: Y.11, F.13, W.21, I.42, L.83, R.134, L.136, W.150 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:W.21, B:R.134, B:R.134 Water bridges: B:N.84, B:N.84, B:R.187, B:R.187 GOL.13: 5 residues within 4Å: Chain B: I.65, R.133, R.134, L.135 Ligands: HEM.12 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:L.135, B:L.135 Water bridges: B:R.133, B:R.133, B:R.133, B:R.133

1 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.3: 8 residues within 4Å: Chain A: E.80, P.81, M.82, L.83, R.133, R.134, L.135 Ligands: GOL.5 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:L.135 Water bridges: A:S.63, A:E.80, A:L.83, A:R.133, A:R.133, A:R.133 Salt bridges: A:E.80, A:R.133

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

HEM.4: 30 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, F.147, T.149, F.151, F.161, L.164, L.165, M.168, R.169, E.173, W.174, E.180 24 PLIP interactions: 23 interactions with chain A, 1 Ligand-Water interactions Hydrophobic interactions: A:I.65, A:L.76, A:L.76, A:I.94, A:F.114, A:F.114, A:V.131, A:L.135, A:L.135, A:F.147, A:F.147, A:F.151, A:F.151, 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, A:H.137 Salt bridges: A:K.98 Metal complexes: A:H.120, H2O.5 HEM.12: 30 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, F.147, T.149, F.151, F.161, L.164, L.165, M.168, E.173, W.174, E.180 Ligands: GOL.13 25 PLIP interactions: 24 interactions with chain B, 1 Ligand-Water interactions, Hydrophobic interactions: B:I.65, B:L.76, B:L.76, B:I.94, B:F.114, B:F.114, B:V.131, B:L.135, B:L.135, B:F.147, B:F.147, B:T.149, B:F.151, B:F.151, 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:H.137 Salt bridges: B:K.98 Metal complexes: B:H.120, H2O.10

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

PEG.7: 4 residues within 4Å: Chain A: R.57, G.142, E.143, E.144 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.144, A:E.144 PEG.9: 3 residues within 4Å: Chain A: R.10 Chain B: L.141 Ligands: SO4.8 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:L.141, A:R.10 Water bridges: A:R.10 PEG.10: 6 residues within 4Å: Chain A: N.9, A.62, S.63, N.64 Chain B: W.103, R.139 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:R.139, B:R.139 Water bridges: A:N.9, A:N.9, A:S.63, A:I.65 PEG.14: 4 residues within 4Å: Chain B: T.18, G.19, Q.20, K.39 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.19, B:K.39

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

SO4.8: 5 residues within 4Å: Chain A: R.10, L.141 Chain B: R.10, L.141 Ligands: PEG.9 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

Schmidt, D. et al., Arresting the Catalytic Arginine in Chlorite Dismutases: Impact on Heme Coordination, Thermal Stability, and Catalysis. Biochemistry (2021)

Release Date

2021-02-17

Peptides

Chlorite dismutase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Chlorite dismutase

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