Magnesium in PDB 3bl5: Crystal Structure of Quec From Bacillus Subtilis: An Enzyme Involved in PREQ1 Biosynthesis

The structure of Crystal Structure of Quec From Bacillus Subtilis: An Enzyme Involved in PREQ1 Biosynthesis, PDB code: 3bl5 was solved by N.Cicmil, R.H.Huang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.95
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	172.057, 75.542, 131.023, 90.00, 94.73, 90.00
R / Rfree (%)	22.2 / 27.2

The structure of Crystal Structure of Quec From Bacillus Subtilis: An Enzyme Involved in PREQ1 Biosynthesis also contains other interesting chemical elements:

Zinc

(Zn)

6 atoms

The binding sites of Magnesium atom in the Crystal Structure of Quec From Bacillus Subtilis: An Enzyme Involved in PREQ1 Biosynthesis (pdb code 3bl5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of Quec From Bacillus Subtilis: An Enzyme Involved in PREQ1 Biosynthesis, PDB code: 3bl5:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Crystal Structure of Quec From Bacillus Subtilis: An Enzyme Involved in PREQ1 Biosynthesis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Quec From Bacillus Subtilis: An Enzyme Involved in PREQ1 Biosynthesis within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg400 b:65.8 occ:1.00 O2 A:PO4500 3.0 84.5 1.0 OG A:SER16 3.0 61.8 1.0 N A:SER16 3.0 60.8 1.0 OG A:SER11 3.0 58.7 1.0 CA A:GLY13 3.5 57.9 1.0 CB A:SER16 3.6 61.0 1.0 N A:GLY13 3.7 58.7 1.0 C A:GLY13 3.7 58.9 1.0 CB A:ASP15 3.8 68.4 1.0 N A:ASP15 3.8 61.9 1.0 CA A:SER16 3.9 59.6 1.0 O A:GLY13 3.9 57.9 1.0 P A:PO4500 3.9 85.5 1.0 C A:ASP15 4.0 62.9 1.0 O4 A:PO4500 4.0 86.8 1.0 CA A:ASP15 4.0 63.9 1.0 O1 A:PO4500 4.3 86.1 1.0 N A:GLN14 4.4 59.6 1.0 CB A:SER11 4.4 58.9 1.0 OD2 A:ASP15 4.8 74.8 1.0 C A:GLN14 4.8 61.3 1.0 CG A:ASP15 4.8 73.6 1.0 N A:THR17 5.0 58.5 1.0

Magnesium binding site 2 out of 6 in the Crystal Structure of Quec From Bacillus Subtilis: An Enzyme Involved in PREQ1 Biosynthesis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Quec From Bacillus Subtilis: An Enzyme Involved in PREQ1 Biosynthesis within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg400 b:63.2 occ:1.00 O2 B:PO4500 3.0 88.6 1.0 OG B:SER16 3.0 61.7 1.0 OG B:SER11 3.0 61.7 1.0 N B:SER16 3.1 62.0 1.0 CA B:GLY13 3.3 59.0 1.0 CB B:SER16 3.6 62.5 1.0 N B:GLY13 3.6 59.4 1.0 C B:GLY13 3.6 59.2 1.0 CB B:ASP15 3.8 67.3 1.0 N B:ASP15 3.8 64.4 1.0 P B:PO4500 3.9 88.5 1.0 O B:GLY13 3.9 59.2 1.0 O4 B:PO4500 3.9 90.2 1.0 CA B:SER16 4.0 60.4 1.0 C B:ASP15 4.0 64.6 1.0 CA B:ASP15 4.0 65.3 1.0 O1 B:PO4500 4.2 89.3 1.0 N B:GLN14 4.3 59.7 1.0 CB B:SER11 4.4 60.5 1.0 C B:GLN14 4.7 62.9 1.0 OD2 B:ASP15 4.8 73.7 1.0 CG B:ASP15 4.8 71.2 1.0 C B:GLY12 4.9 59.8 1.0

Magnesium binding site 3 out of 6 in the Crystal Structure of Quec From Bacillus Subtilis: An Enzyme Involved in PREQ1 Biosynthesis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Quec From Bacillus Subtilis: An Enzyme Involved in PREQ1 Biosynthesis within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg400 b:59.6 occ:1.00 O3 C:PO4500 2.7 92.8 1.0 OG C:SER11 2.9 61.8 1.0 OG C:SER16 3.1 59.5 1.0 N C:SER16 3.4 57.9 1.0 CA C:GLY13 3.7 65.3 1.0 CB C:SER16 3.8 58.0 1.0 CB C:ASP15 3.8 65.4 1.0 P C:PO4500 3.8 93.7 1.0 N C:GLY13 4.0 66.0 1.0 C C:GLY13 4.1 63.8 1.0 O1 C:PO4500 4.1 94.2 1.0 O4 C:PO4500 4.1 94.2 1.0 CA C:SER16 4.2 57.0 1.0 N C:ASP15 4.2 62.7 1.0 CB C:SER11 4.3 60.5 1.0 CA C:ASP15 4.3 62.2 1.0 C C:ASP15 4.3 60.6 1.0 O C:GLY13 4.5 62.4 1.0 N C:GLN14 4.6 63.6 1.0 CG C:ASP15 4.9 68.2 1.0

Magnesium binding site 4 out of 6 in the Crystal Structure of Quec From Bacillus Subtilis: An Enzyme Involved in PREQ1 Biosynthesis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Quec From Bacillus Subtilis: An Enzyme Involved in PREQ1 Biosynthesis within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg400 b:62.8 occ:1.00 O3 D:PO4500 2.8 98.8 1.0 OG D:SER11 3.0 62.8 1.0 OG D:SER16 3.1 68.4 1.0 N D:SER16 3.3 61.5 1.0 CB D:SER16 3.7 63.3 1.0 CB D:ASP15 3.7 68.1 1.0 CA D:GLY13 3.7 65.8 1.0 P D:PO4500 3.9 0.5 1.0 N D:GLY13 4.0 66.8 1.0 C D:GLY13 4.0 65.7 1.0 CA D:SER16 4.1 60.9 1.0 N D:ASP15 4.2 64.8 1.0 O4 D:PO4500 4.2 99.8 1.0 CA D:ASP15 4.2 64.7 1.0 C D:ASP15 4.2 63.6 1.0 O1 D:PO4500 4.2 100.0 1.0 CB D:SER11 4.3 60.8 1.0 O D:GLY13 4.4 64.9 1.0 N D:GLN14 4.6 64.9 1.0 CG D:ASP15 4.8 70.6 1.0

Magnesium binding site 5 out of 6 in the Crystal Structure of Quec From Bacillus Subtilis: An Enzyme Involved in PREQ1 Biosynthesis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Quec From Bacillus Subtilis: An Enzyme Involved in PREQ1 Biosynthesis within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg400 b:69.3 occ:1.00 O2 E:PO4500 2.5 90.0 1.0 N E:SER16 3.1 68.6 1.0 OG E:SER16 3.1 67.2 1.0 CB E:ASP15 3.5 72.8 1.0 N E:ASP15 3.5 68.5 1.0 CA E:GLY13 3.6 65.8 1.0 CB E:SER16 3.7 67.4 1.0 C E:GLY13 3.7 65.5 1.0 CA E:ASP15 3.8 69.2 1.0 C E:ASP15 3.8 68.8 1.0 OG E:SER11 3.9 74.6 1.0 P E:PO4500 3.9 91.1 1.0 CA E:SER16 4.0 68.4 1.0 N E:GLY13 4.0 66.8 1.0 N E:GLN14 4.1 64.5 1.0 O E:GLY13 4.1 63.9 1.0 O1 E:PO4500 4.2 92.6 1.0 C E:GLN14 4.5 66.9 1.0 OD1 E:ASP15 4.5 75.9 1.0 CG E:ASP15 4.5 74.8 1.0 O3 E:PO4500 4.6 89.9 1.0 CA E:GLN14 4.9 65.5 1.0 O4 E:PO4500 4.9 90.7 1.0

Magnesium binding site 6 out of 6 in the Crystal Structure of Quec From Bacillus Subtilis: An Enzyme Involved in PREQ1 Biosynthesis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Quec From Bacillus Subtilis: An Enzyme Involved in PREQ1 Biosynthesis within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg400 b:73.5 occ:1.00 N F:SER16 2.3 88.9 1.0 OG F:SER16 2.8 86.9 1.0 O4 F:PO4500 3.0 0.1 1.0 N F:ASP15 3.1 88.3 1.0 CB F:SER16 3.2 88.0 1.0 C F:ASP15 3.2 88.7 1.0 C F:GLY13 3.2 85.9 1.0 CA F:SER16 3.3 88.8 1.0 CA F:ASP15 3.3 89.0 1.0 O F:GLY13 3.3 85.0 1.0 CA F:GLY13 3.4 85.7 1.0 CB F:ASP15 3.4 91.6 1.0 OG F:SER11 3.6 87.0 1.0 N F:GLY13 3.8 86.5 1.0 N F:GLN14 3.8 85.7 1.0 C F:GLN14 4.0 86.8 1.0 N F:THR17 4.2 90.3 1.0 C F:SER16 4.3 89.6 1.0 CG F:ASP15 4.4 93.9 1.0 O F:ASP15 4.4 87.8 1.0 P F:PO4500 4.4 0.7 1.0 CA F:GLN14 4.5 85.9 1.0 OD2 F:ASP15 4.6 94.4 1.0 O F:GLN14 4.7 86.0 1.0 O2 F:PO4500 4.8 0.7 1.0 C F:GLY12 4.8 86.7 1.0 CB F:SER11 4.9 87.5 1.0

N.Cicmil, R.H.Huang. Crystal Structure of Quec From Bacillus Subtilis: An Enzyme Involved in Preq(1) Biosynthesis. Proteins V. 72 1084 2008.
ISSN: ISSN 0887-3585
PubMed: 18491386
DOI: 10.1002/PROT.22098