SMTL ID : 2pau.2 (1 other biounit)

Crystal structure of the 5'-deoxynucleotidase YfbR mutant E72A complexed with Co(2+) and dAMP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-hexamer

Ligands

6 x CO: COBALT (II) ION(Non-covalent)

CO.1: 5 residues within 4Å: Chain A: H.35, H.70, D.71, D.139 Ligands: D5M.2 6 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:H.35, A:H.70, A:D.71, A:D.139, H2O.1, D5M.2 CO.4: 5 residues within 4Å: Chain B: H.35, H.70, D.71, D.139 Ligands: D5M.5 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:H.35, B:H.70, B:D.71, B:D.139, D5M.5 CO.6: 5 residues within 4Å: Chain C: H.35, H.70, D.71, D.139 Ligands: D5M.7 6 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: C:H.35, C:H.70, C:D.71, C:D.139, H2O.3, D5M.7 CO.9: 5 residues within 4Å: Chain D: H.35, H.70, D.71, D.139 Ligands: D5M.10 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Ligand interactions Metal complexes: D:H.35, D:H.70, D:D.71, D:D.139, D5M.10 CO.11: 5 residues within 4Å: Chain E: H.35, H.70, D.71, D.139 Ligands: D5M.12 6 PLIP interactions: 4 interactions with chain E, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: E:H.35, E:H.70, E:D.71, E:D.139, H2O.5, D5M.12 CO.14: 5 residues within 4Å: Chain F: H.35, H.70, D.71, D.139 Ligands: D5M.15 5 PLIP interactions: 4 interactions with chain F, 1 Ligand-Ligand interactions Metal complexes: F:H.35, F:H.70, F:D.71, F:D.139, D5M.15

6 x D5M: 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE(Non-covalent)

D5M.2: 13 residues within 4Å: Chain A: R.20, W.21, P.22, M.24, H.35, D.71, D.79, P.81, T.82, D.139, A.161, R.164 Ligands: CO.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:W.21 Hydrogen bonds: A:W.21, A:D.79, A:T.82, A:T.82 Salt bridges: A:R.20, A:H.35 pi-Stacking: A:W.21 D5M.5: 13 residues within 4Å: Chain B: R.20, W.21, P.22, H.35, D.71, D.79, L.80, P.81, T.82, P.83, D.139, A.161 Ligands: CO.4 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:W.21, B:D.79, B:T.82, B:T.82 Salt bridges: B:R.20, B:H.35 pi-Stacking: B:W.21 D5M.7: 13 residues within 4Å: Chain C: R.20, W.21, P.22, M.24, H.35, D.71, D.79, P.81, T.82, D.139, A.161, R.164 Ligands: CO.6 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:W.21 Hydrogen bonds: C:W.21, C:D.79, C:T.82, C:T.82 Salt bridges: C:R.20, C:H.35 pi-Stacking: C:W.21 D5M.10: 13 residues within 4Å: Chain D: R.20, W.21, P.22, H.35, D.71, D.79, L.80, P.81, T.82, P.83, D.139, A.161 Ligands: CO.9 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:W.21, D:D.79, D:T.82, D:T.82 Salt bridges: D:R.20, D:H.35 pi-Stacking: D:W.21 D5M.12: 13 residues within 4Å: Chain E: R.20, W.21, P.22, M.24, H.35, D.71, D.79, P.81, T.82, D.139, A.161, R.164 Ligands: CO.11 8 PLIP interactions: 8 interactions with chain E Hydrophobic interactions: E:W.21 Hydrogen bonds: E:W.21, E:D.79, E:T.82, E:T.82 Salt bridges: E:R.20, E:H.35 pi-Stacking: E:W.21 D5M.15: 13 residues within 4Å: Chain F: R.20, W.21, P.22, H.35, D.71, D.79, L.80, P.81, T.82, P.83, D.139, A.161 Ligands: CO.14 7 PLIP interactions: 7 interactions with chain F Hydrogen bonds: F:W.21, F:D.79, F:T.82, F:T.82 Salt bridges: F:R.20, F:H.35 pi-Stacking: F:W.21

3 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.3: 5 residues within 4Å: Chain A: H.70, E.124, Y.127, K.136, D.139 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.136, A:D.139 PEG.8: 5 residues within 4Å: Chain C: H.70, E.124, Y.127, K.136, D.139 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.136, C:D.139 PEG.13: 5 residues within 4Å: Chain E: H.70, E.124, Y.127, K.136, D.139 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:K.136, E:D.139

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zimmerman, M.D. et al., Structural insight into the mechanism of substrate specificity and catalytic activity of an HD-domain phosphohydrolase: the 5'-deoxyribonucleotidase YfbR from Escherichia coli. J.Mol.Biol. (2008)

Release Date

2008-03-04

Peptides

5'-deoxynucleotidase YfbR: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

5'-deoxynucleotidase YfbR

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