Chlorine in PDB 5bv3: Yeast Scavenger Decapping Enzyme in Complex with M7GDP

All present enzymatic activity of Yeast Scavenger Decapping Enzyme in Complex with M7GDP:
3.6.1.59;

The structure of Yeast Scavenger Decapping Enzyme in Complex with M7GDP, PDB code: 5bv3 was solved by A.Neu, U.Neu, R.Sprangers, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.89 / 2.25
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	87.990, 104.520, 189.960, 90.00, 90.00, 90.00
R / Rfree (%)	22.2 / 24.8

The binding sites of Chlorine atom in the Yeast Scavenger Decapping Enzyme in Complex with M7GDP (pdb code 5bv3). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Yeast Scavenger Decapping Enzyme in Complex with M7GDP, PDB code: 5bv3:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Yeast Scavenger Decapping Enzyme in Complex with M7GDP


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Yeast Scavenger Decapping Enzyme in Complex with M7GDP within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl404 b:76.4 occ:1.00 O B:HOH523 3.4 51.3 1.0 N A:GLU87 3.9 62.9 1.0 CB A:GLU87 4.1 66.1 1.0 CA A:GLU87 4.6 62.8 1.0 CA A:LYS86 4.7 66.3 1.0 C A:LYS86 4.8 65.1 1.0 O A:GLU87 4.9 58.6 1.0

Chlorine binding site 2 out of 4 in the Yeast Scavenger Decapping Enzyme in Complex with M7GDP


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Yeast Scavenger Decapping Enzyme in Complex with M7GDP within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl403 b:73.7 occ:1.00 NH1 C:ARG336 2.9 99.5 1.0 CZ C:ARG336 4.0 99.7 1.0 NH1 C:ARG136 4.1 72.8 1.0 CG C:GLN333 4.2 76.9 1.0 CG2 C:THR138 4.3 72.0 1.0 NE2 C:GLN333 4.4 78.6 1.0 CD C:GLN333 4.7 75.2 1.0 NH2 C:ARG336 4.7 0.8 1.0 NE C:ARG136 4.8 72.5 1.0 NE C:ARG336 4.9 96.2 1.0 CZ C:ARG136 4.9 72.0 1.0

Chlorine binding site 3 out of 4 in the Yeast Scavenger Decapping Enzyme in Complex with M7GDP


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Yeast Scavenger Decapping Enzyme in Complex with M7GDP within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl403 b:78.3 occ:1.00 NH1 D:ARG336 3.0 96.6 1.0 NH2 D:ARG136 4.0 69.2 1.0 CG D:GLN333 4.0 71.5 1.0 NE2 D:GLN333 4.1 72.9 1.0 CZ D:ARG336 4.2 97.3 1.0 CG2 D:THR138 4.2 72.7 1.0 CD D:GLN333 4.4 71.4 1.0 NE D:ARG136 4.5 69.1 1.0 CZ D:ARG136 4.7 66.8 1.0 NH2 D:ARG336 4.7 0.7 1.0 CB D:GLN333 5.0 65.7 1.0

Chlorine binding site 4 out of 4 in the Yeast Scavenger Decapping Enzyme in Complex with M7GDP


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Yeast Scavenger Decapping Enzyme in Complex with M7GDP within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl404 b:63.2 occ:1.00 O D:PRO277 3.5 62.8 1.0 ND2 C:ASN24 3.7 35.2 1.0 N C:GLY280 3.7 41.3 1.0 CG2 C:THR27 3.8 34.2 1.0 CA C:GLY280 4.0 36.7 1.0 O C:HOH507 4.0 33.5 1.0 C D:PRO277 4.2 47.5 1.0 NE2 D:GLN26 4.3 47.7 1.0 CA D:PRO277 4.4 44.8 1.0 O C:GLY280 4.7 34.4 1.0 CG C:ASN24 4.8 38.2 1.0 C C:LEU279 4.8 40.8 1.0 C C:GLY280 4.9 35.7 1.0

A.Neu, U.Neu, A.L.Fuchs, B.Schlager, R.Sprangers. An Excess of Catalytically Required Motions Inhibits the Scavenger Decapping Enzyme. Nat.Chem.Biol. V. 11 697 2015.
ISSN: ESSN 1552-4469
PubMed: 26258763
DOI: 10.1038/NCHEMBIO.1866