Manganese in PDB 5ie9: Crystal Structure of the Bacillus-Conserved Mazg Protein, A Nucleotide Pyrophosphohydrolase

The structure of Crystal Structure of the Bacillus-Conserved Mazg Protein, A Nucleotide Pyrophosphohydrolase, PDB code: 5ie9 was solved by M.Kim, M.Hong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.80
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	90.578, 90.578, 97.056, 90.00, 90.00, 120.00
R / Rfree (%)	22.2 / 25.4

The binding sites of Manganese atom in the Crystal Structure of the Bacillus-Conserved Mazg Protein, A Nucleotide Pyrophosphohydrolase (pdb code 5ie9). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Crystal Structure of the Bacillus-Conserved Mazg Protein, A Nucleotide Pyrophosphohydrolase, PDB code: 5ie9:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Crystal Structure of the Bacillus-Conserved Mazg Protein, A Nucleotide Pyrophosphohydrolase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of the Bacillus-Conserved Mazg Protein, A Nucleotide Pyrophosphohydrolase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn201 b:88.6 occ:0.50 OE1 A:GLU66 2.2 87.5 1.0 OE1 A:GLU37 2.7 74.9 1.0 O A:GLU66 3.0 75.8 1.0 O A:GLU37 3.1 62.7 1.0 CD A:GLU66 3.2 89.2 1.0 CB A:GLU66 3.3 81.0 1.0 CB A:GLU40 3.4 66.3 1.0 CA A:GLU66 3.4 79.3 1.0 CB A:ASP69 3.5 77.1 1.0 OE1 A:GLU40 3.6 80.1 1.0 C A:GLU66 3.6 75.8 1.0 CG A:GLU66 3.7 86.5 1.0 N A:LEU41 3.8 56.7 1.0 CD A:GLU37 3.8 72.0 1.0 C A:GLU37 3.9 61.0 1.0 OD2 A:ASP69 4.0 88.2 1.0 CA A:GLU37 4.1 61.8 1.0 CB A:GLU37 4.1 62.7 1.0 C A:GLU40 4.1 60.7 1.0 OE2 A:GLU66 4.3 93.6 1.0 CA A:GLU40 4.3 63.0 1.0 CG A:ASP69 4.3 84.1 1.0 CG A:GLU37 4.4 67.0 1.0 CD A:GLU40 4.5 77.9 1.0 CA A:LEU41 4.5 56.2 1.0 CG A:GLU40 4.5 71.3 1.0 N A:VAL70 4.6 68.2 1.0 CB A:LEU41 4.6 54.9 1.0 CA A:ASP69 4.7 73.2 1.0 OE2 A:GLU37 4.8 75.3 1.0 N A:GLU66 4.8 81.5 1.0 C A:ASP69 4.9 70.2 1.0 N A:GLU40 4.9 61.7 1.0 O A:GLU40 4.9 63.0 1.0 N A:LEU67 4.9 73.9 1.0

Manganese binding site 2 out of 4 in the Crystal Structure of the Bacillus-Conserved Mazg Protein, A Nucleotide Pyrophosphohydrolase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of the Bacillus-Conserved Mazg Protein, A Nucleotide Pyrophosphohydrolase within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn201 b:97.7 occ:0.50 OE1 B:GLU66 2.1 89.1 1.0 OE1 B:GLU37 2.6 70.5 1.0 CD B:GLU66 3.1 91.6 1.0 CB B:GLU66 3.3 83.6 1.0 CB B:GLU40 3.3 66.0 1.0 O B:GLU37 3.4 61.8 1.0 O B:GLU66 3.4 76.2 1.0 CB B:ASP69 3.5 76.0 1.0 CA B:GLU66 3.5 81.4 1.0 OE1 B:GLU40 3.6 81.1 1.0 CG B:GLU66 3.7 89.4 1.0 CD B:GLU37 3.8 68.5 1.0 C B:GLU66 3.9 77.1 1.0 OD2 B:ASP69 4.0 86.3 1.0 N B:LEU41 4.1 58.1 1.0 OE2 B:GLU66 4.1 95.7 1.0 C B:GLU37 4.2 60.1 1.0 CA B:GLU37 4.2 60.5 1.0 CB B:GLU37 4.2 61.4 1.0 CG B:ASP69 4.2 81.9 1.0 C B:GLU40 4.2 61.6 1.0 CA B:GLU40 4.3 63.1 1.0 CD B:GLU40 4.3 77.0 1.0 CG B:GLU40 4.4 70.6 1.0 CG B:GLU37 4.5 64.8 1.0 CG2 B:VAL70 4.5 64.5 1.0 CA B:ASP69 4.7 72.2 1.0 OE2 B:GLU37 4.8 71.2 1.0 N B:VAL70 4.8 66.4 1.0 N B:GLU66 4.8 83.4 1.0 O B:GLU40 4.9 64.8 1.0 CA B:LEU41 4.9 57.8 1.0 C B:ASP69 4.9 68.9 1.0

Manganese binding site 3 out of 4 in the Crystal Structure of the Bacillus-Conserved Mazg Protein, A Nucleotide Pyrophosphohydrolase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of the Bacillus-Conserved Mazg Protein, A Nucleotide Pyrophosphohydrolase within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn201 b:93.3 occ:0.50 OE1 C:GLU66 2.1 86.4 1.0 OE1 C:GLU37 2.8 70.3 1.0 O C:GLU37 2.9 63.4 1.0 O C:GLU66 3.0 76.8 1.0 CD C:GLU66 3.2 87.5 1.0 CB C:GLU66 3.3 81.1 1.0 CB C:GLU40 3.4 66.9 1.0 CB C:ASP69 3.5 73.9 1.0 CA C:GLU66 3.5 80.3 1.0 N C:LEU41 3.7 58.3 1.0 C C:GLU66 3.7 77.0 1.0 CG C:GLU66 3.7 85.1 1.0 C C:GLU37 3.8 61.3 1.0 CD C:GLU37 3.9 68.6 1.0 OD2 C:ASP69 3.9 80.3 1.0 OE1 C:GLU40 4.0 76.2 1.0 C C:GLU40 4.0 61.5 1.0 CA C:GLU37 4.0 62.0 1.0 CG2 C:VAL70 4.1 64.0 1.0 CB C:GLU37 4.2 61.6 1.0 CA C:GLU40 4.2 63.4 1.0 CG C:ASP69 4.3 77.8 1.0 OE2 C:GLU66 4.3 90.4 1.0 CA C:LEU41 4.4 57.9 1.0 CB C:LEU41 4.5 55.3 1.0 CG C:GLU37 4.5 64.7 1.0 N C:VAL70 4.5 66.9 1.0 CG C:GLU40 4.6 71.3 1.0 CD C:GLU40 4.7 76.3 1.0 CA C:ASP69 4.7 71.5 1.0 N C:GLU40 4.7 61.2 1.0 O C:GLU40 4.8 63.6 1.0 C C:ASP69 4.9 68.5 1.0 N C:GLU66 4.9 82.5 1.0 OE2 C:GLU37 4.9 71.4 1.0 N C:LEU67 5.0 74.9 1.0

Manganese binding site 4 out of 4 in the Crystal Structure of the Bacillus-Conserved Mazg Protein, A Nucleotide Pyrophosphohydrolase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of the Bacillus-Conserved Mazg Protein, A Nucleotide Pyrophosphohydrolase within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn201 b:83.1 occ:0.50 OE1 D:GLU66 2.1 84.4 1.0 OE1 D:GLU37 2.8 68.8 1.0 O D:GLU66 2.9 73.5 1.0 O D:GLU37 3.0 60.7 1.0 CD D:GLU66 3.2 86.5 1.0 CB D:GLU66 3.3 79.3 1.0 CB D:ASP69 3.4 74.0 1.0 CA D:GLU66 3.4 77.7 1.0 CB D:GLU40 3.5 65.4 1.0 C D:GLU66 3.6 73.8 1.0 CG D:GLU66 3.7 84.2 1.0 OE1 D:GLU40 3.8 80.7 1.0 N D:LEU41 3.8 57.4 1.0 C D:GLU37 3.8 59.7 1.0 CD D:GLU37 3.9 67.2 1.0 CA D:GLU37 4.0 60.0 1.0 OD2 D:ASP69 4.0 82.8 1.0 CB D:GLU37 4.0 60.4 1.0 C D:GLU40 4.2 60.3 1.0 CG D:ASP69 4.3 79.6 1.0 OE2 D:GLU66 4.3 90.7 1.0 CA D:GLU40 4.4 62.0 1.0 N D:VAL70 4.4 67.9 1.0 CG D:GLU37 4.5 63.4 1.0 CA D:LEU41 4.5 57.5 1.0 CB D:LEU41 4.6 56.4 1.0 CA D:ASP69 4.6 71.4 1.0 CD D:GLU40 4.6 78.3 1.0 CG D:GLU40 4.6 70.8 1.0 C D:ASP69 4.7 68.8 1.0 N D:GLU66 4.8 80.2 1.0 O D:GLU40 4.9 62.3 1.0 N D:LEU67 4.9 72.5 1.0 N D:GLU40 4.9 60.9 1.0 OE2 D:GLU37 4.9 70.2 1.0

M.I.Kim, M.Hong. Crystal Structure of the Bacillus-Conserved Mazg Protein, A Nucleotide Pyrophosphohydrolase. Biochem.Biophys.Res.Commun. V. 472 237 2016.
ISSN: ESSN 1090-2104
PubMed: 26920050
DOI: 10.1016/J.BBRC.2016.02.097