SMTL ID : 7oua.1

Crystal structure of dimeric chlorite dismutase variant R127K (CCld R127K) from Cyanothece sp. PCC7425

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.09 Å

Oligo State

homo-dimer

Ligands

2 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)(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, K.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: MES.3 26 PLIP interactions: 26 interactions with chain A, Hydrophobic interactions: A:L.76, A:I.94, A:F.114, A:F.114, A:T.121, A:L.128, A:L.128, A:K.133, A:L.135, 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, A:W.174 Hydrogen bonds: A:R.66, A:Y.67, A:Y.67, A:A.68, A:W.102 Salt bridges: A:K.98 Metal complexes: A:H.120 HEM.7: 33 residues within 4Å: Chain B: 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, K.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: MES.10 20 PLIP interactions: 20 interactions with chain B, Hydrophobic interactions: B:L.76, B:I.94, B:F.114, B:F.114, B:L.128, B:L.135, B:F.147, B:F.147, B:T.149, B:F.151, B:F.151, B:W.174 Hydrogen bonds: B:R.66, B:Y.67, B:Y.67, B:A.68, B:W.102 Salt bridges: B:K.98 pi-Cation interactions: B:H.120 Metal complexes: B:H.120

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 4 residues within 4Å: Chain A: R.10, A.46 Chain B: R.10, L.141 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.10, B:R.10, B:R.10

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

MES.3: 9 residues within 4Å: Chain A: I.65, L.73, L.76, Q.77, Q.80, K.133, R.134, L.135 Ligands: HEM.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.77, A:K.133 MES.10: 9 residues within 4Å: Chain B: I.65, L.73, L.76, Q.77, Q.80, K.133, R.134, L.135 Ligands: HEM.7 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.77, B:Q.80, B:K.133

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

PGE.4: 9 residues within 4Å: Chain A: Y.11, F.13, I.42, A.62, L.83, R.134, L.135, L.136, W.150 No protein-ligand interaction detected (PLIP) PGE.5: 9 residues within 4Å: Chain A: W.103, E.104, R.139, G.142 Chain B: N.8, N.9, A.62, S.63, N.64 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.103, A:R.139 PGE.9: 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 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.139, B:R.139

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

SO4.6: 3 residues within 4Å: Chain A: M.82, L.83, R.134 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.83 Salt bridges: A:R.134

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

PEG.8: 8 residues within 4Å: Chain B: Y.11, F.13, I.42, A.62, L.83, R.134, L.136, W.150 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