SMTL ID : 3q08.2 (3 other biounits)

Crystal Structure of Chlorite Dismutase from D. Aromatica at pH 6.5

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.05 Å

Oligo State

homo-pentamer

Ligands

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

HEM.1: 22 residues within 4Å: Chain A: L.116, N.117, Y.118, I.119, L.131, V.149, K.151, M.167, H.170, T.171, T.174, Y.177, L.178, R.183, L.185, F.196, T.198, F.200, L.211, M.212, L.215 Ligands: NO2.2 20 PLIP interactions: 20 interactions with chain A, Hydrophobic interactions: A:L.116, A:I.119, A:V.149, A:T.174, A:Y.177, A:L.178, A:L.185, A:L.185, A:F.196, A:F.196, A:F.196, A:F.200, A:F.200, A:L.211, A:L.211, A:L.215 Hydrogen bonds: A:N.117, A:Y.118 Salt bridges: A:K.151 Metal complexes: A:H.170 HEM.5: 24 residues within 4Å: Chain B: L.116, N.117, Y.118, I.119, L.131, I.147, V.149, K.151, W.155, M.167, H.170, T.171, T.174, Y.177, L.178, R.183, L.185, F.196, T.198, F.200, L.211, M.212, L.215 Ligands: NO2.6 21 PLIP interactions: 21 interactions with chain B, Hydrophobic interactions: B:L.116, B:L.131, B:I.147, B:V.149, B:Y.177, B:L.178, B:L.185, B:F.196, B:F.196, B:F.196, B:F.200, B:F.200, B:F.200, B:L.211, B:L.211, B:L.215 Hydrogen bonds: B:N.117, B:Y.118 Salt bridges: B:K.151 pi-Cation interactions: B:R.183 Metal complexes: B:H.170 HEM.9: 24 residues within 4Å: Chain C: P.115, L.116, N.117, Y.118, I.119, L.131, V.149, K.151, W.156, M.167, H.170, T.171, T.174, L.175, L.178, R.183, L.185, F.196, T.198, F.200, L.211, M.212, L.215 Ligands: NO2.10 22 PLIP interactions: 22 interactions with chain C, Hydrophobic interactions: C:L.116, C:L.131, C:V.149, C:V.149, C:T.174, C:L.175, C:L.178, C:L.178, C:L.185, C:F.196, C:F.196, C:F.196, C:F.200, C:F.200, C:F.200, C:L.211, C:L.211, C:L.215 Hydrogen bonds: C:N.117, C:Y.118 Salt bridges: C:K.151 Metal complexes: C:H.170 HEM.13: 23 residues within 4Å: Chain D: L.116, N.117, Y.118, I.119, L.131, V.149, K.151, W.155, M.167, H.170, T.171, T.174, L.175, Y.177, L.178, R.183, F.196, T.198, F.200, L.211, M.212, L.215 Ligands: NO2.14 20 PLIP interactions: 20 interactions with chain D, Hydrophobic interactions: D:L.116, D:L.131, D:V.149, D:V.149, D:T.171, D:Y.177, D:L.178, D:F.196, D:F.196, D:F.200, D:F.200, D:F.200, D:L.211, D:L.211, D:L.215 Hydrogen bonds: D:N.117, D:Y.118, D:I.119 Salt bridges: D:K.151 Metal complexes: D:H.170 HEM.18: 22 residues within 4Å: Chain E: L.116, N.117, Y.118, I.119, I.147, V.149, K.151, M.167, H.170, T.171, T.174, Y.177, L.178, R.183, L.185, F.196, T.198, F.200, L.211, M.212, L.215 Ligands: NO2.19 22 PLIP interactions: 22 interactions with chain E, Hydrophobic interactions: E:L.116, E:I.119, E:I.147, E:V.149, E:V.149, E:T.174, E:Y.177, E:L.178, E:L.185, E:F.196, E:F.196, E:F.196, E:F.200, E:F.200, E:F.200, E:L.211, E:L.215 Hydrogen bonds: E:N.117, E:Y.118 Salt bridges: E:K.151 pi-Stacking: E:H.170 Metal complexes: E:H.170

5 x NO2: NITRITE ION(Non-covalent)

NO2.2: 5 residues within 4Å: Chain A: R.183, K.184, L.185, T.198 Ligands: HEM.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.183 NO2.6: 7 residues within 4Å: Chain B: H.170, R.183, K.184, L.185, T.198, F.200 Ligands: HEM.5 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.183 NO2.10: 6 residues within 4Å: Chain C: H.170, R.183, L.185, T.198, F.200 Ligands: HEM.9 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.183 NO2.14: 6 residues within 4Å: Chain D: R.183, K.184, L.185, T.198, F.200 Ligands: HEM.13 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.183 NO2.19: 7 residues within 4Å: Chain E: H.170, R.183, K.184, L.185, T.198, F.200 Ligands: HEM.18 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:R.183

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

MES.3: 8 residues within 4Å: Chain A: Q.17, P.18, T.113, K.114, P.115, L.116, L.131, R.183 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.183 MES.7: 9 residues within 4Å: Chain B: T.16, Q.17, P.18, T.113, K.114, L.116, L.131, R.183, K.184 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.183 MES.11: 9 residues within 4Å: Chain C: T.16, Q.17, P.18, T.113, K.114, L.116, L.131, R.183, K.184 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:R.183 MES.15: 9 residues within 4Å: Chain D: T.16, Q.17, P.18, T.113, K.114, L.116, L.131, R.183, K.184 1 PLIP interactions: 1 interactions with chain D Salt bridges: D:R.183 MES.20: 9 residues within 4Å: Chain E: T.16, Q.17, P.18, T.113, K.114, L.116, L.131, R.183, K.184 1 PLIP interactions: 1 interactions with chain E Salt bridges: E:R.183

5 x CA: CALCIUM ION(Non-covalent)

CA.4: 3 residues within 4Å: Chain A: E.70, T.231 Chain B: D.192 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Metal complexes: A:E.70, A:E.70, A:T.231, B:D.192 CA.8: 3 residues within 4Å: Chain B: E.70, T.231 Chain C: D.192 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain B Metal complexes: C:D.192, B:E.70, B:E.70, B:T.231 CA.12: 3 residues within 4Å: Chain C: E.70, T.231 Chain D: D.192 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain D Metal complexes: C:E.70, C:E.70, C:T.231, D:D.192 CA.16: 3 residues within 4Å: Chain D: E.70, T.231 Chain E: D.192 4 PLIP interactions: 1 interactions with chain E, 3 interactions with chain D Metal complexes: E:D.192, D:E.70, D:E.70, D:T.231 CA.17: 3 residues within 4Å: Chain A: D.192 Chain E: E.70, T.231 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain A Metal complexes: E:E.70, E:E.70, E:T.231, A:D.192

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Goblirsch, B.R. et al., Structural features promoting dioxygen production by Dechloromonas aromatica chlorite dismutase. J.Biol.Inorg.Chem. (2010)

Release Date

2011-01-05

Peptides

Chlorite dismutase: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
F

B
G

C
H

D
I

E
J

Chlorite dismutase

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