Magnesium in PDB 6puq: 1.56 A Crystal Structure of Flavodoxin-Like Domain of Schizosaccharomyces Japonicus Putative Trnaphe 4-Demethylwyosine Synthase TYW1 in Complex with Fmn

The structure of 1.56 A Crystal Structure of Flavodoxin-Like Domain of Schizosaccharomyces Japonicus Putative Trnaphe 4-Demethylwyosine Synthase TYW1 in Complex with Fmn, PDB code: 6puq was solved by L.Sjekloca, A.R.Ferre D'amare, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.50 / 1.56
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	28.298, 73.087, 42.518, 90.00, 91.86, 90.00
R / Rfree (%)	19.6 / 22.7

The binding sites of Magnesium atom in the 1.56 A Crystal Structure of Flavodoxin-Like Domain of Schizosaccharomyces Japonicus Putative Trnaphe 4-Demethylwyosine Synthase TYW1 in Complex with Fmn (pdb code 6puq). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the 1.56 A Crystal Structure of Flavodoxin-Like Domain of Schizosaccharomyces Japonicus Putative Trnaphe 4-Demethylwyosine Synthase TYW1 in Complex with Fmn, PDB code: 6puq:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the 1.56 A Crystal Structure of Flavodoxin-Like Domain of Schizosaccharomyces Japonicus Putative Trnaphe 4-Demethylwyosine Synthase TYW1 in Complex with Fmn


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of 1.56 A Crystal Structure of Flavodoxin-Like Domain of Schizosaccharomyces Japonicus Putative Trnaphe 4-Demethylwyosine Synthase TYW1 in Complex with Fmn within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:28.9 occ:1.00 O4' A:FMN301 2.6 22.2 1.0 OG1 A:THR99 2.9 19.8 1.0 OG A:SER98 2.9 21.8 1.0 O5' A:FMN301 3.3 20.0 1.0 CB A:PHE187 3.3 18.5 1.0 CE2 A:PHE102 3.4 19.3 1.0 CG A:PHE187 3.5 19.4 1.0 C4' A:FMN301 3.6 20.9 1.0 CD2 A:PHE102 3.6 22.1 1.0 N A:THR99 3.7 22.0 1.0 CA A:THR99 3.9 21.6 1.0 CB A:THR99 3.9 18.6 1.0 CD1 A:PHE187 4.0 21.9 1.0 C5' A:FMN301 4.0 21.3 1.0 CB A:SER98 4.0 22.4 1.0 CD2 A:PHE187 4.1 17.1 1.0 O2P A:FMN301 4.1 20.2 1.0 CG1 A:VAL225 4.1 21.6 1.0 P A:FMN301 4.2 21.7 1.0 C A:SER98 4.2 18.3 1.0 O A:HOH440 4.3 33.0 1.0 CB A:PRO147 4.4 20.0 1.0 O1P A:FMN301 4.5 23.9 1.0 CZ A:PHE102 4.6 25.4 1.0 CG2 A:THR99 4.6 20.3 1.0 CA A:SER98 4.7 20.1 1.0 CA A:PHE187 4.8 17.8 1.0 O A:SER98 4.8 19.6 1.0 CE1 A:PHE187 4.8 24.2 1.0 CE2 A:PHE187 4.9 17.0 1.0 C3' A:FMN301 4.9 22.4 1.0 CG A:PHE102 4.9 20.2 1.0

Magnesium binding site 2 out of 5 in the 1.56 A Crystal Structure of Flavodoxin-Like Domain of Schizosaccharomyces Japonicus Putative Trnaphe 4-Demethylwyosine Synthase TYW1 in Complex with Fmn


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of 1.56 A Crystal Structure of Flavodoxin-Like Domain of Schizosaccharomyces Japonicus Putative Trnaphe 4-Demethylwyosine Synthase TYW1 in Complex with Fmn within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg303 b:27.7 occ:1.00 OG A:SER148 2.8 21.7 1.0 O A:LEU146 2.8 17.4 1.0 O A:PHE187 2.9 18.5 1.0 CA A:CYS199 3.3 22.1 0.5 N A:PHE187 3.3 16.3 1.0 N A:SER148 3.3 18.1 1.0 CA A:CYS199 3.3 22.0 0.5 CB A:ALA202 3.4 17.7 1.0 CB A:CYS199 3.4 22.3 0.5 C A:PRO147 3.4 22.6 1.0 SG A:CYS199 3.6 18.6 0.5 CB A:SER148 3.6 22.6 1.0 CB A:CYS199 3.7 22.2 0.5 CA A:GLY186 3.7 15.8 1.0 C A:PHE187 3.7 19.9 1.0 CA A:PRO147 3.7 19.9 1.0 C A:LEU146 3.8 20.2 1.0 SG A:CYS199 3.8 17.7 0.5 C A:CYS199 3.8 22.8 0.5 N A:ALA202 3.8 18.5 1.0 O A:PRO147 3.9 21.3 1.0 C A:GLY186 3.9 18.1 1.0 C A:CYS199 3.9 22.8 0.5 O A:CYS199 3.9 21.7 0.5 CA A:SER148 4.0 19.8 1.0 O A:CYS199 4.0 21.9 0.5 CA A:PHE187 4.1 17.8 1.0 N A:PRO147 4.2 17.6 1.0 CA A:ALA202 4.2 17.9 1.0 N A:CYS199 4.5 25.1 0.5 N A:CYS199 4.5 25.1 0.5 N A:GLY188 4.7 19.9 1.0 N A:TYR200 4.8 18.8 1.0 N A:GLN201 4.8 20.3 1.0 CB A:LEU146 4.9 20.9 0.5 CA A:LEU146 4.9 18.1 0.5 C A:GLN201 4.9 18.6 1.0 CA A:LEU146 4.9 18.0 0.5 CB A:LEU146 4.9 20.9 0.5 O A:GLY186 4.9 20.5 1.0 CA A:GLY188 5.0 21.8 1.0

Magnesium binding site 3 out of 5 in the 1.56 A Crystal Structure of Flavodoxin-Like Domain of Schizosaccharomyces Japonicus Putative Trnaphe 4-Demethylwyosine Synthase TYW1 in Complex with Fmn


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of 1.56 A Crystal Structure of Flavodoxin-Like Domain of Schizosaccharomyces Japonicus Putative Trnaphe 4-Demethylwyosine Synthase TYW1 in Complex with Fmn within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg304 b:25.3 occ:1.00 O A:ALA218 2.8 21.0 1.0 OD1 A:ASP206 2.9 19.4 1.0 N A:VAL184 2.9 16.7 1.0 N A:LEU220 3.3 19.6 1.0 O A:HOH414 3.3 29.0 1.0 CA A:LEU220 3.5 17.4 1.0 CA A:ALA183 3.5 14.8 1.0 C A:PRO219 3.6 18.1 1.0 C A:ALA183 3.7 18.4 1.0 O A:VAL184 3.8 16.1 1.0 CA A:VAL184 3.9 16.5 1.0 CB A:VAL184 3.9 14.1 1.0 O A:PRO219 3.9 21.0 1.0 CG A:ASP206 3.9 25.2 1.0 C A:ALA218 4.0 24.3 1.0 CG A:ARG216 4.0 20.4 1.0 CB A:ALA183 4.0 20.8 1.0 CE2 A:PHE182 4.1 17.6 1.0 CD A:ARG216 4.1 22.2 1.0 CB A:LEU220 4.1 18.4 1.0 CG2 A:VAL184 4.2 14.8 1.0 CA A:PRO219 4.3 22.6 1.0 C A:VAL184 4.3 18.2 1.0 NE A:ARG216 4.3 20.2 1.0 CD2 A:PHE182 4.5 18.2 1.0 N A:PRO219 4.6 22.9 1.0 N A:ALA183 4.7 17.3 1.0 CB A:ASP206 4.7 18.8 1.0 OD2 A:ASP206 4.7 26.7 1.0 C A:LEU220 4.7 19.7 1.0 O A:PHE182 4.7 18.1 1.0 CZ A:PHE182 4.9 15.1 1.0 O A:ALA183 4.9 16.5 1.0 CD1 A:LEU220 4.9 16.2 1.0

Magnesium binding site 4 out of 5 in the 1.56 A Crystal Structure of Flavodoxin-Like Domain of Schizosaccharomyces Japonicus Putative Trnaphe 4-Demethylwyosine Synthase TYW1 in Complex with Fmn


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of 1.56 A Crystal Structure of Flavodoxin-Like Domain of Schizosaccharomyces Japonicus Putative Trnaphe 4-Demethylwyosine Synthase TYW1 in Complex with Fmn within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg305 b:38.9 occ:1.00 OG A:SER153 2.5 30.9 1.0 O A:ILE151 2.7 38.2 1.0 NE2 A:GLN201 3.0 25.8 1.0 O A:TYR149 3.1 31.1 1.0 OD2 A:ASP156 3.3 42.1 1.0 OD1 A:ASP156 3.4 40.2 1.0 CB A:SER153 3.4 29.7 1.0 CG A:ASP156 3.5 38.6 1.0 N A:SER153 3.5 33.8 1.0 OE1 A:GLN201 3.5 27.7 1.0 CD A:GLN201 3.6 22.6 1.0 CB A:TYR149 3.7 24.6 1.0 C A:ILE151 3.9 41.1 1.0 CA A:SER153 3.9 27.2 1.0 C A:TYR149 4.0 35.0 1.0 C A:GLU152 4.0 38.8 1.0 N A:ASP156 4.2 24.9 1.0 CA A:GLU152 4.2 41.2 1.0 CA A:TYR149 4.3 22.9 1.0 OH A:TYR200 4.3 28.2 1.0 CB A:ILE155 4.4 24.6 1.0 O A:SER153 4.4 26.9 1.0 C A:SER153 4.4 34.0 1.0 N A:TYR149 4.4 24.3 1.0 N A:GLU152 4.6 38.8 1.0 CB A:ASP156 4.6 30.2 1.0 O A:GLU152 4.7 45.9 1.0 CD1 A:ILE155 4.8 36.0 1.0 CA A:ASP156 4.8 24.5 1.0 N A:ILE151 4.9 34.0 1.0 N A:ILE155 4.9 27.6 1.0 C A:ILE155 4.9 25.1 1.0 CA A:ILE155 5.0 25.4 1.0 CG A:TYR149 5.0 27.5 1.0

Magnesium binding site 5 out of 5 in the 1.56 A Crystal Structure of Flavodoxin-Like Domain of Schizosaccharomyces Japonicus Putative Trnaphe 4-Demethylwyosine Synthase TYW1 in Complex with Fmn


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of 1.56 A Crystal Structure of Flavodoxin-Like Domain of Schizosaccharomyces Japonicus Putative Trnaphe 4-Demethylwyosine Synthase TYW1 in Complex with Fmn within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg306 b:42.4 occ:1.00 OD2 A:ASP125 2.3 45.6 1.0 O A:HOH459 2.7 37.5 1.0 N A:THR94 2.9 20.4 1.0 OG A:SER93 2.9 42.8 1.0 OD1 A:ASN123 2.9 21.0 1.0 CG A:ASP125 3.0 37.8 1.0 O A:THR94 3.2 27.0 1.0 CA A:SER93 3.3 20.1 1.0 C A:SER93 3.6 21.8 1.0 OD1 A:ASP125 3.6 48.1 1.0 CB A:ASP125 3.7 23.3 1.0 CB A:SER93 3.7 24.5 1.0 CG A:ASN123 3.7 20.8 1.0 ND2 A:ASN123 3.7 24.7 1.0 CA A:THR94 4.0 20.8 1.0 C A:THR94 4.0 27.7 1.0 OG A:SER154 4.3 38.0 1.0 CG2 A:THR94 4.3 22.2 1.0 N A:ASP125 4.3 20.7 1.0 O A:TYR92 4.6 17.7 1.0 N A:SER93 4.6 20.5 1.0 CB A:THR94 4.6 23.5 1.0 CA A:ASP125 4.7 23.1 1.0 O A:SER93 4.8 17.6 1.0

L.Sjekloca, A.R.Ferre D'amare. Crystal Structure of Flavodoxin-Like Domain of Schizosaccharomyces Japonicus Putative Trnaphe 4-Demethylwyosine Synthase TYW1 in Complex with Fmn To Be Published.