SMTL ID : 2itb.1

CRYSTAL STRUCTURE OF A PUTATIVE TRNA-(MS(2)IO(6)A)-HYDROXYLASE (PP_2188) FROM PSEUDOMONAS PUTIDA KT2440 AT 2.05 A RESOLUTION

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-dimer

Ligands

4 x FE: FE (III) ION(Non-covalent)

FE.1: 6 residues within 4Å: Chain A: E.39, E.70, H.73, E.152 Ligands: FE.2, PER.3 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.39, A:E.70, A:H.73, H2O.1, H2O.1 FE.2: 6 residues within 4Å: Chain A: E.70, E.123, E.152, H.155 Ligands: FE.1, PER.3 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.70, A:E.123, A:E.123, A:H.155, H2O.1 FE.11: 6 residues within 4Å: Chain B: E.39, E.70, H.73, E.152 Ligands: FE.12, UNL.13 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.39, B:E.70, B:H.73, H2O.4 FE.12: 6 residues within 4Å: Chain B: E.70, E.123, E.152, H.155 Ligands: FE.11, UNL.13 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.70, B:E.123, B:E.123, B:E.152, B:H.155

1 x PER: PEROXIDE ION(Non-covalent)

PER.3: 7 residues within 4Å: Chain A: E.39, E.70, E.123, E.152 Ligands: FE.1, FE.2, EDO.10 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.70 Water bridges: A:H.73, A:H.73, A:H.73

17 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 4 residues within 4Å: Chain A: L.103, R.105, D.114, C.175 Ligand excluded by PLIP EDO.5: 3 residues within 4Å: Chain A: H.56, L.112, Y.166 Ligand excluded by PLIP EDO.6: 9 residues within 4Å: Chain A: T.45, L.49, R.101, T.115, V.118, G.119, I.122, Y.159 Ligands: EDO.10 Ligand excluded by PLIP EDO.7: 5 residues within 4Å: Chain A: D.34, N.37, C.38, A.93, G.94 Ligand excluded by PLIP EDO.8: 7 residues within 4Å: Chain A: K.36, N.37, F.40, H.74 Chain B: I.50, N.54, I.60 Ligand excluded by PLIP EDO.9: 2 residues within 4Å: Chain A: D.171, R.174 Ligand excluded by PLIP EDO.10: 8 residues within 4Å: Chain A: A.42, T.45, E.70, I.122, E.123, Y.159 Ligands: PER.3, EDO.6 Ligand excluded by PLIP EDO.14: 4 residues within 4Å: Chain B: C.38, H.197 Ligands: UNL.13, EDO.20 Ligand excluded by PLIP EDO.15: 3 residues within 4Å: Chain B: G.13, R.180, M.184 Ligand excluded by PLIP EDO.16: 6 residues within 4Å: Chain A: A.51, N.54 Chain B: N.37, F.40 Ligands: EDO.19, EDO.23 Ligand excluded by PLIP EDO.17: 4 residues within 4Å: Chain B: H.164, N.165, G.167, D.168 Ligand excluded by PLIP EDO.18: 5 residues within 4Å: Chain B: L.103, R.105, D.114, C.175, L.178 Ligand excluded by PLIP EDO.19: 7 residues within 4Å: Chain B: D.34, N.37, C.38, K.41, A.93, G.94 Ligands: EDO.16 Ligand excluded by PLIP EDO.20: 9 residues within 4Å: Chain B: A.42, T.45, E.70, R.101, I.122, E.123, Y.159 Ligands: UNL.13, EDO.14 Ligand excluded by PLIP EDO.21: 5 residues within 4Å: Chain B: H.73, Q.76, F.144, G.147, L.148 Ligand excluded by PLIP EDO.22: 1 residues within 4Å: Chain B: R.83 Ligand excluded by PLIP EDO.23: 6 residues within 4Å: Chain A: I.50, N.54, I.60 Chain B: K.36, H.74 Ligands: EDO.16 Ligand excluded by PLIP

1 x UNL: UNKNOWN LIGAND(Non-functional Binders)

UNL.13: 11 residues within 4Å: Chain B: C.38, E.39, A.42, E.70, E.123, S.126, E.152 Ligands: FE.11, FE.12, EDO.14, EDO.20 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.39, B:E.123, B:S.126, B:E.152

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Joint Center for Structural Genomics (JCSG), Crystal structure of putative tRNA-(ms(2)io(6)a)-hydroxylase (NP_744337.1) from Pseudomonas Putida KT2440 at 2.05 A resolution. To be published

Release Date

2006-11-07

Peptides

TRNA-(Ms(2)io(6)a)-hydroxylase, putative: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

TRNA-(Ms(2)io(6)a)-hydroxylase, putative