Manganese in PDB 7zcc: Yxbc From Bacillus Subtilis in Complex with Mn and N-Oxalylglycine (Nog)

The structure of Yxbc From Bacillus Subtilis in Complex with Mn and N-Oxalylglycine (Nog), PDB code: 7zcc was solved by R.Chowdhury, C.J.Schofield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.65 / 1.85
Space group	P 31 1 2
Cell size a, b, c (Å), α, β, γ (°)	109.733, 109.733, 192.191, 90, 90, 120
R / Rfree (%)	16.5 / 20

The binding sites of Manganese atom in the Yxbc From Bacillus Subtilis in Complex with Mn and N-Oxalylglycine (Nog) (pdb code 7zcc). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Yxbc From Bacillus Subtilis in Complex with Mn and N-Oxalylglycine (Nog), PDB code: 7zcc:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Yxbc From Bacillus Subtilis in Complex with Mn and N-Oxalylglycine (Nog)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Yxbc From Bacillus Subtilis in Complex with Mn and N-Oxalylglycine (Nog) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn401 b:24.4 occ:1.00 O A:HOH573 2.0 26.2 0.3 OD2 A:ASP147 2.0 28.0 1.0 O2' A:OGA402 2.0 27.0 1.0 O3 A:GOL403 2.1 25.2 0.7 O1 A:OGA402 2.1 25.3 1.0 NE2 A:HIS145 2.1 27.2 1.0 NE2 A:HIS224 2.1 21.3 1.0 C2 A:OGA402 2.8 37.9 1.0 C1 A:OGA402 2.8 30.8 1.0 H31 A:GOL403 2.8 40.5 0.7 C3 A:GOL403 2.9 33.8 0.7 CE1 A:HIS224 3.0 20.5 1.0 CE1 A:HIS145 3.0 26.7 1.0 CG A:ASP147 3.0 27.6 1.0 HE1 A:HIS224 3.1 24.6 1.0 HE1 A:HIS145 3.2 32.0 1.0 CD2 A:HIS145 3.2 25.8 1.0 CD2 A:HIS224 3.2 25.0 1.0 H32 A:GOL403 3.2 40.5 0.7 HO2 A:GOL406 3.2 90.5 1.0 HD2 A:HIS145 3.4 30.9 1.0 OD1 A:ASP147 3.4 29.4 1.0 HD2 A:HIS224 3.4 30.0 1.0 O2 A:GOL406 4.0 88.8 1.0 O2 A:OGA402 4.1 30.2 1.0 H32 A:GOL406 4.1 91.8 1.0 ND1 A:HIS145 4.2 27.4 1.0 ND1 A:HIS224 4.2 22.5 1.0 N1 A:OGA402 4.2 29.4 1.0 HD21 A:LEU218 4.2 38.0 1.0 C2 A:GOL403 4.3 50.4 0.7 HO2 A:GOL403 4.3 64.5 0.7 CG A:HIS145 4.3 25.7 1.0 CG A:HIS224 4.3 20.4 1.0 CB A:ASP147 4.4 23.9 1.0 HB2 A:ASP147 4.4 28.7 1.0 HE1 A:HIS176 4.5 48.5 1.0 O2 A:GOL403 4.5 53.8 0.7 HD23 A:LEU218 4.5 38.0 1.0 O1 A:GOL406 4.7 87.8 1.0 H4C2 A:OGA402 4.8 35.3 1.0 H1 A:OGA402 4.8 35.3 1.0 CD2 A:LEU218 4.8 31.7 1.0 H2 A:GOL403 4.8 60.4 0.7 H11 A:GOL403 4.9 61.8 0.7 HB3 A:ASP147 4.9 28.7 1.0 C3 A:GOL406 4.9 89.8 1.0 HD1 A:HIS145 4.9 32.9 1.0 C4 A:OGA402 4.9 29.4 1.0 HD1 A:HIS224 4.9 27.0 1.0 C2 A:GOL406 4.9 89.5 1.0 H4C1 A:OGA402 4.9 35.3 1.0

Manganese binding site 2 out of 4 in the Yxbc From Bacillus Subtilis in Complex with Mn and N-Oxalylglycine (Nog)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Yxbc From Bacillus Subtilis in Complex with Mn and N-Oxalylglycine (Nog) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn401 b:22.8 occ:1.00 OD2 B:ASP147 1.9 22.8 1.0 O2 B:OGA402 2.0 25.6 1.0 O2' B:OGA402 2.0 25.1 1.0 NE2 B:HIS145 2.0 21.9 1.0 NE2 B:HIS224 2.1 21.8 1.0 O1 B:GOL403 2.2 62.1 1.0 C1 B:OGA402 2.7 26.7 1.0 C2 B:OGA402 2.7 25.1 1.0 CE1 B:HIS145 3.0 24.9 1.0 CE1 B:HIS224 3.0 24.6 1.0 CG B:ASP147 3.0 23.5 1.0 CD2 B:HIS145 3.1 26.8 1.0 HE1 B:HIS224 3.1 29.5 1.0 HE1 B:HIS145 3.1 29.9 1.0 CD2 B:HIS224 3.1 26.0 1.0 HO2 B:GOL404 3.3 92.2 1.0 HD2 B:HIS145 3.3 32.1 1.0 HD2 B:HIS224 3.3 31.2 1.0 C1 B:GOL403 3.4 67.4 1.0 OD1 B:ASP147 3.4 24.0 1.0 H12 B:GOL403 3.5 80.9 1.0 H11 B:GOL403 3.8 80.9 1.0 O1 B:OGA402 3.9 28.0 1.0 O2 B:GOL404 4.0 81.9 1.0 ND1 B:HIS145 4.1 24.2 1.0 ND1 B:HIS224 4.1 23.4 1.0 N1 B:OGA402 4.1 24.8 1.0 CG B:HIS145 4.2 24.2 1.0 H31 B:GOL404 4.2 96.7 1.0 CG B:HIS224 4.2 22.7 1.0 HD21 B:LEU218 4.3 33.2 1.0 CB B:ASP147 4.3 24.3 1.0 HB2 B:ASP147 4.4 29.2 1.0 C2 B:GOL403 4.5 72.7 1.0 H2 B:GOL403 4.5 87.2 1.0 H1 B:OGA402 4.7 29.7 1.0 H4C2 B:OGA402 4.7 29.9 1.0 HD23 B:LEU218 4.8 33.2 1.0 HD1 B:HIS145 4.8 29.1 1.0 HB3 B:ASP147 4.8 29.2 1.0 HO1 B:GOL404 4.9 91.2 1.0 HE1 B:HIS176 4.9 51.5 1.0 HD1 B:HIS224 4.9 28.1 1.0 C4 B:OGA402 4.9 24.9 1.0 CD2 B:LEU218 4.9 27.6 1.0 O2 B:GOL403 4.9 76.2 1.0 H4C1 B:OGA402 4.9 29.9 1.0 C3 B:GOL404 4.9 85.6 1.0 HH2 B:TRP162 5.0 30.8 1.0 C2 B:GOL404 5.0 84.1 1.0

Manganese binding site 3 out of 4 in the Yxbc From Bacillus Subtilis in Complex with Mn and N-Oxalylglycine (Nog)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Yxbc From Bacillus Subtilis in Complex with Mn and N-Oxalylglycine (Nog) within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn401 b:21.6 occ:1.00 OD2 C:ASP147 2.0 29.0 1.0 O2' C:OGA402 2.0 25.8 1.0 O1 C:GOL403 2.0 28.3 0.7 O2 C:OGA402 2.1 28.2 1.0 O C:HOH579 2.1 25.3 0.4 NE2 C:HIS224 2.1 24.1 1.0 NE2 C:HIS145 2.1 25.7 1.0 C2 C:OGA402 2.7 31.9 1.0 C1 C:OGA402 2.7 29.7 1.0 C1 C:GOL403 3.0 33.7 0.7 CE1 C:HIS224 3.0 22.4 1.0 CG C:ASP147 3.0 27.5 1.0 CE1 C:HIS145 3.0 25.0 1.0 H12 C:GOL403 3.1 40.4 0.7 HE1 C:HIS224 3.1 26.9 1.0 CD2 C:HIS145 3.1 24.2 1.0 CD2 C:HIS224 3.1 25.7 1.0 HE1 C:HIS145 3.2 30.0 1.0 H11 C:GOL403 3.2 40.4 0.7 HD2 C:HIS145 3.3 29.1 1.0 HD2 C:HIS224 3.4 30.9 1.0 OD1 C:ASP147 3.4 31.6 1.0 O1 C:OGA402 4.0 32.1 1.0 ND1 C:HIS224 4.1 22.9 1.0 N1 C:OGA402 4.1 26.4 1.0 ND1 C:HIS145 4.2 24.2 1.0 HD21 C:LEU218 4.2 35.6 1.0 O C:HOH654 4.2 37.6 1.0 CG C:HIS145 4.2 24.9 1.0 CG C:HIS224 4.2 21.7 1.0 C2 C:GOL403 4.3 49.6 0.7 CB C:ASP147 4.4 26.2 1.0 HB2 C:ASP147 4.4 31.4 1.0 H2 C:GOL403 4.5 59.6 0.7 HD23 C:LEU218 4.6 35.6 1.0 O2 C:GOL403 4.7 52.2 0.7 H1 C:OGA402 4.7 31.7 1.0 HE1 C:HIS176 4.7 50.4 1.0 H4C1 C:OGA402 4.7 34.8 1.0 HO2 C:GOL403 4.8 62.6 0.7 CD2 C:LEU218 4.8 29.6 1.0 HD1 C:HIS224 4.9 27.5 1.0 HD1 C:HIS145 4.9 29.1 1.0 HB3 C:ASP147 4.9 31.4 1.0 C4 C:OGA402 4.9 29.0 1.0

Manganese binding site 4 out of 4 in the Yxbc From Bacillus Subtilis in Complex with Mn and N-Oxalylglycine (Nog)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Yxbc From Bacillus Subtilis in Complex with Mn and N-Oxalylglycine (Nog) within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn401 b:22.2 occ:1.00 O2 D:OGA402 1.8 23.6 1.0 OD2 D:ASP147 1.9 23.2 1.0 O2' D:OGA402 2.0 26.0 1.0 O D:HOH530 2.0 29.8 0.4 NE2 D:HIS145 2.1 24.3 1.0 NE2 D:HIS224 2.1 22.9 1.0 O3 D:GOL403 2.3 32.5 0.8 C1 D:OGA402 2.7 27.2 1.0 C2 D:OGA402 2.7 22.1 1.0 H31 D:GOL403 2.9 47.2 0.8 CE1 D:HIS145 3.0 23.3 1.0 CE1 D:HIS224 3.0 21.8 1.0 C3 D:GOL403 3.0 39.3 0.8 CG D:ASP147 3.0 26.5 1.0 CD2 D:HIS145 3.1 24.5 1.0 HE1 D:HIS224 3.1 26.1 1.0 HE1 D:HIS145 3.1 28.0 1.0 CD2 D:HIS224 3.1 24.9 1.0 H32 D:GOL403 3.1 47.2 0.8 HO2 D:GOL406 3.3 93.8 1.0 HD2 D:HIS145 3.3 29.4 1.0 HD2 D:HIS224 3.4 29.8 1.0 OD1 D:ASP147 3.4 25.9 1.0 O1 D:OGA402 3.9 29.9 1.0 O D:HOH578 4.0 40.4 1.0 O2 D:GOL406 4.0 81.5 1.0 ND1 D:HIS145 4.1 22.5 1.0 ND1 D:HIS224 4.1 25.8 1.0 N1 D:OGA402 4.1 24.1 1.0 CG D:HIS145 4.2 26.0 1.0 CG D:HIS224 4.2 24.6 1.0 CB D:ASP147 4.4 22.9 1.0 HD21 D:LEU218 4.4 36.0 1.0 HB2 D:ASP147 4.4 27.4 1.0 H31 D:GOL406 4.4 97.6 1.0 C2 D:GOL403 4.5 55.3 0.8 H4C2 D:OGA402 4.7 29.3 1.0 H1 D:OGA402 4.7 28.9 1.0 HO2 D:GOL403 4.8 93.1 0.8 H4C1 D:OGA402 4.8 29.3 1.0 C4 D:OGA402 4.8 24.4 1.0 HO1 D:GOL406 4.8 90.8 1.0 H12 D:GOL403 4.8 74.6 0.8 HD1 D:HIS145 4.8 27.0 1.0 HD1 D:HIS224 4.9 30.9 1.0 HD23 D:LEU218 4.9 36.0 1.0 HB3 D:ASP147 4.9 27.4 1.0 HE1 D:HIS176 4.9 53.3 1.0 H32 D:GOL406 4.9 97.6 1.0 HH2 D:TRP162 5.0 30.1 1.0 H2 D:GOL403 5.0 66.4 0.8

R.Chowdhury, C.J.Schofield. Yxbc From Bacillus Subtilis in Complex with Mn and N-Oxalylglycine (Nog) To Be Published.