SMTL ID : 3dj8.1 (1 other biounit)

Synthesis of (2S)-2-amino-7,8-epoxyoctanoic acid and structure of its metal-bridging complex with human arginase I

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.51 Å

Oligo State

homo-trimer

Ligands

6 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 6 residues within 4Å: Chain A: D.124, H.126, D.232, D.234 Ligands: MN.2, EXY.3 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.124, A:H.126, A:D.232, A:D.234, A:D.234 MN.2: 6 residues within 4Å: Chain A: H.101, D.124, D.128, D.232 Ligands: MN.1, EXY.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.101, A:D.124, A:D.128, A:D.232 MN.4: 6 residues within 4Å: Chain B: D.124, H.126, D.232, D.234 Ligands: MN.5, EXY.6 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.124, B:H.126, B:D.232, B:D.234, B:D.234 MN.5: 6 residues within 4Å: Chain B: H.101, D.124, D.128, D.232 Ligands: MN.4, EXY.6 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.101, B:D.124, B:D.128, B:D.232 MN.7: 6 residues within 4Å: Chain C: D.124, H.126, D.232, D.234 Ligands: MN.8, EXY.9 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.124, C:H.126, C:D.232, C:D.234, C:D.234 MN.8: 6 residues within 4Å: Chain C: H.101, D.124, D.128, D.232 Ligands: MN.7, EXY.9 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.101, C:D.124, C:D.128, C:D.232

3 x EXY: 6-[(2R)-oxiran-2-yl]-L-norleucine(Non-covalent)

EXY.3: 16 residues within 4Å: Chain A: H.101, D.124, H.126, D.128, N.130, S.137, H.141, G.142, D.183, E.186, D.232, D.234, T.246, E.277 Ligands: MN.1, MN.2 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:N.130, A:S.137, A:D.183, A:D.183 Water bridges: A:T.135, A:S.137, A:S.137, A:N.139, A:N.139 EXY.6: 16 residues within 4Å: Chain B: H.101, D.124, H.126, D.128, N.130, S.137, H.141, G.142, D.183, E.186, D.232, D.234, T.246, E.277 Ligands: MN.4, MN.5 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:N.130, B:S.137, B:D.183, B:D.183 Water bridges: B:T.135, B:S.137, B:S.137, B:N.139, B:N.139 EXY.9: 16 residues within 4Å: Chain C: H.101, D.124, H.126, D.128, N.130, S.137, H.141, G.142, D.183, E.186, D.232, D.234, T.246, E.277 Ligands: MN.7, MN.8 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:N.130, C:S.137, C:D.183, C:D.183 Water bridges: C:T.135, C:S.137, C:S.137, C:N.139, C:N.139

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zakharian, T.Y. et al., Synthesis of (2S)-2-amino-7,8-epoxyoctanoic acid and structure of its metal-bridging complex with human arginase I. Org.Biomol.Chem. (2008)

Release Date

2008-07-08

Peptides

Arginase-1: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Arginase-1

Related Entries With Identical Sequence