SMTL ID : 2c4n.1

NagD from E.coli K-12 strain

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-tetramer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.9, D.11, D.201 Ligands: PO4.3 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.9, A:D.11, A:D.201, H2O.4, H2O.4 MG.4: 4 residues within 4Å: Chain B: D.9, D.11, D.201 Ligands: PO4.6 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.9, B:D.11, B:D.201, H2O.8, H2O.8 MG.7: 4 residues within 4Å: Chain C: D.9, D.11, D.201 Ligands: PO4.9 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.9, C:D.11, C:D.201, H2O.13, H2O.13 MG.10: 4 residues within 4Å: Chain D: D.9, D.11, D.201 Ligands: PO4.12 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.9, D:D.11, D:D.201, H2O.17, H2O.17

8 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 7 residues within 4Å: Chain A: N.43, Y.44, D.146, K.176, N.202, T.205 Ligands: PO4.3 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.43, A:D.146, A:D.146, A:N.202 Water bridges: A:D.9, A:Y.44, A:K.176 Salt bridges: A:K.176 PO4.3: 10 residues within 4Å: Chain A: D.9, I.10, D.11, L.41, T.42, N.43, Y.44, K.176 Ligands: MG.1, PO4.2 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:D.9, A:D.9, A:I.10, A:D.11, A:T.42, A:T.42, A:N.43 Water bridges: A:Y.44 Salt bridges: A:K.176 PO4.5: 7 residues within 4Å: Chain B: N.43, Y.44, D.146, K.176, N.202, T.205 Ligands: PO4.6 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:N.43, B:D.146, B:D.146, B:N.202, B:T.205 Water bridges: B:D.9, B:K.176 Salt bridges: B:K.176 PO4.6: 10 residues within 4Å: Chain B: D.9, I.10, D.11, L.41, T.42, N.43, Y.44, K.176 Ligands: MG.4, PO4.5 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:D.9, B:D.9, B:I.10, B:D.11, B:D.11, B:T.42, B:N.43 Salt bridges: B:K.176 PO4.8: 7 residues within 4Å: Chain C: N.43, Y.44, D.146, K.176, N.202, T.205 Ligands: PO4.9 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:N.43, C:D.146, C:D.146, C:N.202 Water bridges: C:D.9, C:Y.44, C:K.176 Salt bridges: C:K.176 PO4.9: 10 residues within 4Å: Chain C: D.9, I.10, D.11, L.41, T.42, N.43, Y.44, K.176 Ligands: MG.7, PO4.8 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:D.9, C:D.9, C:I.10, C:D.11, C:T.42, C:T.42, C:N.43 Water bridges: C:Y.44 Salt bridges: C:K.176 PO4.11: 7 residues within 4Å: Chain D: N.43, Y.44, D.146, K.176, N.202, T.205 Ligands: PO4.12 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:N.43, D:D.146, D:D.146, D:N.202, D:T.205 Water bridges: D:D.9, D:K.176 Salt bridges: D:K.176 PO4.12: 10 residues within 4Å: Chain D: D.9, I.10, D.11, L.41, T.42, N.43, Y.44, K.176 Ligands: MG.10, PO4.11 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:D.9, D:D.9, D:I.10, D:D.11, D:D.11, D:T.42, D:N.43 Salt bridges: D:K.176

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tremblay, L.W. et al., Structure and Activity Analyses of Escherichia Coli K-12 Nagd Provide Insight Into the Evolution of Biochemical Function in the Haloalkanoic Acid Dehalogenase Superfamily. Biochemistry (2006)

Release Date

2006-01-26

Peptides

PROTEIN NAGD: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

PROTEIN NAGD