SMTL ID : 4wwl.1

E. coli 5'-nucleotidase mutant I521C labeled with MTSL (intermediate form)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.23 Å

Oligo State

monomer

Ligands

1 x MTN: S-[(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)methyl] methanesulfonothioate(Covalent)

MTN.1: 9 residues within 4Å: Chain A: D.68, L.69, D.95, N.96, Y.395, L.399, C.496, A.498, E.499 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.69, A:D.95 Water bridges: A:D.68, A:N.96, A:N.96 Salt bridges: A:D.68

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 6 residues within 4Å: Chain A: D.59, N.91, H.192, H.227 Ligands: ZN.3, CO3.13 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.59, A:H.192, A:H.227 ZN.3: 7 residues within 4Å: Chain A: D.16, H.18, D.59, H.227, Q.229 Ligands: ZN.2, CO3.13 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.16, A:H.18, A:D.59

9 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 3 residues within 4Å: Chain A: S.51, R.135, Q.136 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.136 Water bridges: A:V.52, A:R.135 SO4.5: 3 residues within 4Å: Chain A: D.85, F.133, R.135 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.85 Water bridges: A:R.135 Salt bridges: A:R.135 SO4.6: 4 residues within 4Å: Chain A: R.77, N.80, W.107, K.109 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.80, A:W.107 Water bridges: A:R.77 Salt bridges: A:R.77, A:K.109 SO4.7: 2 residues within 4Å: Chain A: R.77, K.106 5 PLIP interactions: 5 interactions with chain A Water bridges: A:R.77, A:R.77, A:K.106 Salt bridges: A:R.77, A:K.106 SO4.8: 2 residues within 4Å: Chain A: W.22, R.23 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.23 SO4.9: 2 residues within 4Å: Chain A: K.396, N.397 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.397 SO4.10: 3 residues within 4Å: Chain A: L.450, N.451, D.452 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.451, A:D.452, A:D.452 Water bridges: A:D.452, A:L.453, A:L.453, A:L.453 SO4.11: 4 residues within 4Å: Chain A: K.8, E.44, E.48, R.272 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.272, A:R.272, A:R.272 Salt bridges: A:K.8 SO4.12: 3 residues within 4Å: Chain A: R.350, R.354, R.385 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:R.350, A:R.354, A:R.385

2 x CO3: CARBONATE ION(Non-functional Binders)

CO3.13: 7 residues within 4Å: Chain A: D.59, N.91, H.92, H.227, Q.229 Ligands: ZN.2, ZN.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.229 CO3.14: 4 residues within 4Å: Chain A: R.354, D.431, S.432, G.433 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.433 Water bridges: A:D.431

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.15: 5 residues within 4Å: Chain A: N.80, G.83, Y.84, K.109, F.110 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.84

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Krug, U. et al., E. coli 5'-nucleotidase mutant I521C labeled with MTSL (intermediate form). To Be Published

Release Date

2014-11-26

Peptides

Protein UshA: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Protein UshA