SMTL ID : 3n0q.1

Crystal structure of a Putative aromatic-ring hydroxylating dioxygenase (TM1040_3219) from SILICIBACTER SP. TM1040 at 1.80 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-trimer

Ligands

3 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)

FES.1: 9 residues within 4Å: Chain A: C.84, H.86, R.87, S.89, C.104, Y.106, H.107, Q.108, W.109 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.84, A:H.86, A:C.104, A:H.107 FES.9: 9 residues within 4Å: Chain B: C.84, H.86, R.87, S.89, C.104, Y.106, H.107, Q.108, W.109 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.84, B:H.86, B:C.104, B:H.107 FES.17: 9 residues within 4Å: Chain C: C.84, H.86, R.87, S.89, C.104, Y.106, H.107, Q.108, W.109 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.84, C:H.86, C:C.104, C:H.107

6 x NI: NICKEL (II) ION(Non-covalent)

NI.2: 5 residues within 4Å: Chain A: N.196, H.202, H.207, D.357 Ligands: TRS.5 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.202, A:H.207, A:D.357 NI.3: 2 residues within 4Å: Chain A: H.17 Ligands: TRS.6 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.17, H2O.4, H2O.6 NI.10: 5 residues within 4Å: Chain B: N.196, H.202, H.207, D.357 Ligands: TRS.13 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.202, B:H.207, B:D.357 NI.11: 2 residues within 4Å: Chain B: H.17 Ligands: TRS.14 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.17, H2O.22, H2O.25 NI.18: 5 residues within 4Å: Chain C: N.196, H.202, H.207, D.357 Ligands: TRS.21 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.202, C:H.207, C:D.357 NI.19: 2 residues within 4Å: Chain C: H.17 Ligands: TRS.22 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:H.17, H2O.40, H2O.43

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 4 residues within 4Å: Chain A: N.197, W.302, H.304 Ligands: TRS.5 Ligand excluded by PLIP CL.12: 4 residues within 4Å: Chain B: N.197, W.302, H.304 Ligands: TRS.13 Ligand excluded by PLIP CL.20: 4 residues within 4Å: Chain C: N.197, W.302, H.304 Ligands: TRS.21 Ligand excluded by PLIP

6 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.5: 15 residues within 4Å: Chain A: N.196, N.197, E.199, C.200, H.202, C.203, H.207, L.210, F.214, T.221, W.350, T.353, D.357 Ligands: NI.2, CL.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.199 Water bridges: A:N.197 TRS.6: 10 residues within 4Å: Chain A: R.14, H.17, E.374, P.375, G.376, P.377 Chain B: R.85, R.131, H.132 Ligands: NI.3 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.85, A:E.374 Water bridges: A:R.14 TRS.13: 15 residues within 4Å: Chain B: N.196, N.197, E.199, C.200, H.202, C.203, H.207, L.210, F.214, T.221, W.350, T.353, D.357 Ligands: NI.10, CL.12 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.199 Water bridges: B:N.197 TRS.14: 10 residues within 4Å: Chain B: R.14, H.17, E.374, P.375, G.376, P.377 Chain C: R.85, R.131, H.132 Ligands: NI.11 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:R.85, B:E.374 Water bridges: B:R.14 TRS.21: 15 residues within 4Å: Chain C: N.196, N.197, E.199, C.200, H.202, C.203, H.207, L.210, F.214, T.221, W.350, T.353, D.357 Ligands: NI.18, CL.20 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.199 Water bridges: C:N.197 TRS.22: 10 residues within 4Å: Chain A: R.85, R.131, H.132 Chain C: R.14, H.17, E.374, P.375, G.376, P.377 Ligands: NI.19 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:R.85, C:E.374 Water bridges: C:R.14

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 7 residues within 4Å: Chain A: G.72, A.73, D.74, R.78, E.112, L.113, D.114 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.73, A:D.74 GOL.8: 4 residues within 4Å: Chain A: H.13, A.15, E.391, L.394 3 PLIP interactions: 3 interactions with chain A Water bridges: A:H.13, A:E.391, A:E.391 GOL.15: 7 residues within 4Å: Chain B: G.72, A.73, D.74, R.78, E.112, L.113, D.114 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.73, B:D.74 GOL.16: 4 residues within 4Å: Chain B: H.13, A.15, E.391, L.394 3 PLIP interactions: 3 interactions with chain B Water bridges: B:H.13, B:E.391, B:E.391 GOL.23: 7 residues within 4Å: Chain C: G.72, A.73, D.74, R.78, E.112, L.113, D.114 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:A.73, C:D.74 GOL.24: 4 residues within 4Å: Chain C: H.13, A.15, E.391, L.394 3 PLIP interactions: 3 interactions with chain C Water bridges: C:H.13, C:E.391, C:E.391

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Joint Center for Structural Genomics (JCSG), Crystal structure of a Putative aromatic-ring hydroxylating dioxygenase (TM1040_3219) from SILICIBACTER SP. TM1040 at 1.80 A resolution. To be published

Release Date

2010-06-09

Peptides

Putative aromatic-ring hydroxylating dioxygenase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Putative aromatic-ring hydroxylating dioxygenase