Magnesium in PDB 7cd4: Crystal Structure of the S103F Mutant of Bacillus Subtilis (Natto) Yabj Protein.

The structure of Crystal Structure of the S103F Mutant of Bacillus Subtilis (Natto) Yabj Protein., PDB code: 7cd4 was solved by Z.Fujimoto, N.Kishine, K.Kimura, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	66.68 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	64.101, 85.506, 106.537, 90, 90, 90
R / Rfree (%)	18.5 / 22.5

The structure of Crystal Structure of the S103F Mutant of Bacillus Subtilis (Natto) Yabj Protein. also contains other interesting chemical elements:

Chlorine	(Cl)	10 atoms
Zinc	(Zn)	3 atoms

The binding sites of Magnesium atom in the Crystal Structure of the S103F Mutant of Bacillus Subtilis (Natto) Yabj Protein. (pdb code 7cd4). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of the S103F Mutant of Bacillus Subtilis (Natto) Yabj Protein., PDB code: 7cd4:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of the S103F Mutant of Bacillus Subtilis (Natto) Yabj Protein.


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 the S103F Mutant of Bacillus Subtilis (Natto) Yabj Protein. within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg203 b:39.0 occ:1.00 O B:HOH307 2.0 33.8 1.0 O B:HOH310 2.1 30.9 1.0 O B:HOH324 2.1 30.8 1.0 O B:HOH308 2.1 36.6 1.0 OD1 B:ASP96 2.2 25.9 1.0 CG B:ASP96 3.1 26.1 1.0 OD2 B:ASP96 3.3 30.4 1.0 O B:TYR94 4.0 27.1 1.0 OE2 B:GLU69 4.1 31.6 1.0 OG1 B:THR97 4.1 28.7 1.0 O B:GLN93 4.3 24.8 1.0 O B:HOH339 4.5 36.7 1.0 CB B:ASP96 4.5 25.7 1.0 N B:ASP96 4.7 24.9 1.0 N B:THR97 4.7 27.9 1.0 C B:TYR94 4.8 25.7 1.0 CB B:THR97 5.0 28.0 1.0 CA B:ASP96 5.0 26.5 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of the S103F Mutant of Bacillus Subtilis (Natto) Yabj Protein.


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 the S103F Mutant of Bacillus Subtilis (Natto) Yabj Protein. within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg203 b:43.7 occ:1.00 O C:HOH326 1.9 53.5 1.0 O C:HOH311 2.0 52.1 1.0 O A:HOH307 2.0 36.5 1.0 O A:HOH308 2.1 37.9 1.0 O C:HOH337 2.2 45.3 1.0 OE2 C:GLU119 2.3 30.5 1.0 CD C:GLU119 3.3 30.6 1.0 OE1 C:GLU119 3.6 34.5 1.0 O A:HOH350 3.8 43.4 1.0 OE2 A:GLU106 3.9 41.1 1.0 O C:HOH313 4.0 29.4 1.0 OE1 A:GLU106 4.0 35.1 1.0 O A:HOH321 4.3 41.2 1.0 CE1 A:PHE77 4.3 26.1 1.0 CD A:GLU106 4.4 34.9 1.0 CZ C:PHE77 4.4 28.1 1.0 O C:HOH306 4.5 37.3 1.0 CG C:GLU119 4.6 29.6 1.0 CZ A:PHE77 4.7 27.1 1.0 NH1 B:ARG102 4.8 27.4 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of the S103F Mutant of Bacillus Subtilis (Natto) Yabj Protein.


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 the S103F Mutant of Bacillus Subtilis (Natto) Yabj Protein. within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg204 b:53.9 occ:1.00 O D:HOH324 1.8 48.8 1.0 O D:HOH319 2.0 45.2 1.0 O B:HOH320 2.0 43.5 1.0 O B:HOH331 2.3 42.1 1.0 OE2 D:GLU119 2.3 34.4 1.0 O D:HOH327 2.3 44.5 1.0 CD D:GLU119 3.3 34.5 1.0 OE1 D:GLU119 3.8 35.4 1.0 O D:HOH311 3.9 35.6 1.0 O D:HOH312 4.1 36.3 1.0 OE1 B:GLU106 4.1 36.5 1.0 O B:HOH312 4.3 41.4 1.0 CZ D:PHE77 4.4 33.8 1.0 OE2 B:GLU106 4.6 41.0 1.0 CG D:GLU119 4.6 33.6 1.0 NH1 A:ARG102 4.8 28.9 1.0 CD B:GLU106 4.8 36.1 1.0 O D:HOH301 4.9 50.0 1.0 OG1 D:THR75 4.9 29.4 1.0 CE1 B:PHE77 5.0 28.5 1.0

Z.Fujimoto, L.T.T.Hong, N.Kishine, N.Suzuki, K.Kimura. Tetramer Formation of Bacillus Subtilis Yabj Protein That Belongs to Yjgf/YER057C/UK114 Family. Biosci.Biotechnol.Biochem. V. 85 297 2021.
ISSN: ISSN 0916-8451
PubMed: 33590041
DOI: 10.1093/BBB/ZBAA037