Manganese in PDB 6omp: Crystal Structure of Apo PTMU3

The structure of Crystal Structure of Apo PTMU3, PDB code: 6omp was solved by Y.C.Liu, L.B.Dong, B.Shen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.57 / 1.70
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	114.237, 121.957, 138.159, 90.00, 90.00, 90.00
R / Rfree (%)	20.1 / 24.7

The binding sites of Manganese atom in the Crystal Structure of Apo PTMU3 (pdb code 6omp). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 7 binding sites of Manganese where determined in the Crystal Structure of Apo PTMU3, PDB code: 6omp:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7;

Manganese binding site 1 out of 7 in the Crystal Structure of Apo PTMU3


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 Apo PTMU3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn406 b:4.8 occ:1.00 OD1 A:ASP308 2.0 4.7 1.0 OE1 A:GLU241 2.2 6.9 1.0 OD1 A:ASP10 2.2 4.5 1.0 NE2 A:HIS12 2.3 5.2 1.0 NE2 A:HIS189 2.3 5.6 1.0 OD2 A:ASP10 2.4 5.4 1.0 CG A:ASP10 2.6 4.9 1.0 CG A:ASP308 3.1 4.8 1.0 CD2 A:HIS12 3.2 5.9 1.0 CE1 A:HIS12 3.2 5.5 1.0 CD A:GLU241 3.3 6.3 1.0 CD2 A:HIS189 3.3 5.5 1.0 CE1 A:HIS189 3.3 5.6 1.0 OD2 A:ASP308 3.7 4.5 1.0 MN A:MN407 3.8 7.1 1.0 CG A:GLU241 3.8 6.5 1.0 CB A:GLU241 3.9 6.3 1.0 CB A:ASP308 4.1 4.9 1.0 CB A:ASP10 4.1 4.9 1.0 OE2 A:GLU241 4.3 6.4 1.0 ND1 A:HIS12 4.4 5.7 1.0 CG A:HIS12 4.4 5.5 1.0 ND1 A:HIS311 4.4 6.8 1.0 ND1 A:HIS189 4.4 5.5 1.0 CG A:HIS189 4.5 5.9 1.0 O A:HOH772 4.5 10.9 1.0 CA A:ASP308 4.5 4.8 1.0 CE1 A:HIS311 4.6 6.8 1.0 N A:SER11 4.7 5.4 1.0 C A:ASP10 4.9 4.7 1.0 CD2 A:PHE88 4.9 6.2 1.0 CA A:ASP10 4.9 5.1 1.0

Manganese binding site 2 out of 7 in the Crystal Structure of Apo PTMU3


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 Apo PTMU3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn407 b:7.1 occ:1.00 OE2 A:GLU313 2.1 6.3 1.0 OD2 A:ASP308 2.2 4.5 1.0 OE2 A:GLU241 2.2 6.4 1.0 ND1 A:HIS311 2.3 6.8 1.0 O A:HOH772 2.3 10.9 1.0 OE1 A:GLU241 2.3 6.9 1.0 CD A:GLU241 2.6 6.3 1.0 CG A:ASP308 3.0 4.8 1.0 CD A:GLU313 3.2 6.0 1.0 CE1 A:HIS311 3.2 6.8 1.0 OD1 A:ASP308 3.2 4.7 1.0 CG A:HIS311 3.3 6.9 1.0 CB A:HIS311 3.5 6.9 1.0 CG A:GLU313 3.6 6.3 1.0 MN A:MN406 3.8 4.8 1.0 CG A:GLU241 4.0 6.5 1.0 OE1 A:GLU313 4.2 7.2 1.0 O A:HOH925 4.3 39.0 1.0 NE2 A:HIS12 4.3 5.2 1.0 NE2 A:HIS311 4.3 7.3 1.0 O A:HOH809 4.4 32.7 1.0 CD2 A:HIS311 4.4 6.9 1.0 CB A:ASP308 4.4 4.9 1.0 O A:HOH696 4.5 34.7 1.0 O A:HOH899 4.5 42.7 1.0 CD2 A:HIS12 4.7 5.9 1.0 O A:HOH604 4.7 26.7 1.0 CE1 A:HIS189 4.7 5.6 1.0 NE2 A:HIS189 4.8 5.6 1.0

Manganese binding site 3 out of 7 in the Crystal Structure of Apo PTMU3


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 Apo PTMU3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn408 b:28.6 occ:1.00 O A:LEU312 2.3 8.1 1.0 OE1 B:GLN260 2.4 9.1 1.0 O A:GLY314 2.5 6.3 1.0 O A:HOH744 2.5 7.7 1.0 O B:HOH830 2.5 9.9 1.0 O A:HOH587 2.6 7.6 1.0 CD B:GLN260 3.3 10.7 1.0 O B:HOH554 3.4 22.1 1.0 C A:LEU312 3.4 8.0 1.0 C A:GLY314 3.6 7.0 1.0 O A:PHE316 4.0 9.7 1.0 CG B:GLN260 4.1 9.7 1.0 N A:GLY314 4.1 6.8 1.0 CA A:LEU312 4.1 9.2 1.0 O A:HIS311 4.2 6.6 1.0 O A:HOH697 4.3 25.4 1.0 NE2 B:GLN260 4.3 10.0 1.0 O A:HOH657 4.3 12.8 1.0 CB B:GLN260 4.3 10.3 1.0 N A:GLU313 4.4 7.3 1.0 C A:GLU313 4.4 7.0 1.0 CA A:GLY314 4.4 6.4 1.0 O B:HOH653 4.5 12.3 1.0 N A:THR315 4.5 6.7 1.0 O A:HOH929 4.5 48.9 1.0 CA A:GLU313 4.6 7.0 1.0 O A:HOH826 4.6 26.1 1.0 C A:THR315 4.7 7.0 1.0 CA A:THR315 4.7 6.8 1.0 CE1 A:HIS287 4.7 6.3 1.0 N A:PHE316 4.9 7.5 1.0 NE2 A:HIS287 4.9 6.2 1.0 O A:THR315 5.0 7.5 1.0 O A:GLU313 5.0 7.4 1.0

Manganese binding site 4 out of 7 in the Crystal Structure of Apo PTMU3


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 Apo PTMU3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn409 b:19.1 occ:1.00 O A:HOH801 2.4 22.5 1.0 O A:HOH533 2.4 9.9 1.0 OD1 A:ASP38 2.4 23.7 1.0 CG A:ASP38 3.3 19.3 1.0 OD2 A:ASP38 3.6 16.3 1.0 O A:HOH581 3.6 31.3 1.0 O A:HOH914 4.2 31.7 1.0 O A:HOH749 4.4 26.3 1.0 CB A:ASP38 4.6 16.9 1.0 O A:HOH734 4.8 29.7 1.0

Manganese binding site 5 out of 7 in the Crystal Structure of Apo PTMU3


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Crystal Structure of Apo PTMU3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn406 b:7.5 occ:1.00 OD1 B:ASP10 1.9 8.7 1.0 OD1 B:ASP308 2.0 8.4 1.0 OE1 B:GLU241 2.1 8.6 1.0 NE2 B:HIS12 2.3 6.5 1.0 NE2 B:HIS189 2.4 5.9 1.0 OD2 B:ASP10 2.5 7.3 1.0 CG B:ASP10 2.6 8.4 1.0 CG B:ASP308 3.0 8.0 1.0 CD2 B:HIS12 3.2 8.6 1.0 CE1 B:HIS12 3.2 8.2 1.0 CD B:GLU241 3.3 7.2 1.0 CD2 B:HIS189 3.3 5.8 1.0 CE1 B:HIS189 3.4 6.1 1.0 OD2 B:ASP308 3.6 8.8 1.0 MN B:MN407 3.7 12.1 1.0 CG B:GLU241 3.9 7.3 1.0 CB B:GLU241 3.9 7.4 1.0 CB B:ASP308 4.1 9.3 1.0 CB B:ASP10 4.1 8.2 1.0 OE2 B:GLU241 4.3 8.3 1.0 CG B:HIS12 4.4 8.1 1.0 ND1 B:HIS12 4.4 8.0 1.0 CA B:ASP308 4.4 9.3 1.0 ND1 B:HIS189 4.5 6.0 1.0 O B:HOH734 4.5 13.3 1.0 CG B:HIS189 4.5 6.1 1.0 ND1 B:HIS311 4.5 14.3 1.0 CE1 B:HIS311 4.6 16.5 1.0 N B:SER11 4.8 8.1 1.0 C B:ASP10 4.9 8.1 1.0 CA B:ASP10 4.9 8.1 1.0

Manganese binding site 6 out of 7 in the Crystal Structure of Apo PTMU3


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Crystal Structure of Apo PTMU3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn407 b:12.1 occ:1.00 OE1 B:GLU313 1.6 8.8 1.0 OD2 B:ASP308 2.1 8.8 1.0 OE2 B:GLU241 2.2 8.3 1.0 O B:HOH734 2.3 13.3 1.0 ND1 B:HIS311 2.3 14.3 1.0 OE1 B:GLU241 2.4 8.6 1.0 CD B:GLU241 2.5 7.2 1.0 CD B:GLU313 2.9 10.9 1.0 CG B:ASP308 3.0 8.0 1.0 OD1 B:ASP308 3.2 8.4 1.0 CE1 B:HIS311 3.2 16.5 1.0 CG B:HIS311 3.3 16.6 1.0 CG B:GLU313 3.5 11.1 1.0 CB B:HIS311 3.5 16.3 1.0 MN B:MN406 3.7 7.5 1.0 CG B:GLU241 4.0 7.3 1.0 OE2 B:GLU313 4.0 14.0 1.0 O B:HOH788 4.0 38.0 1.0 O B:HOH855 4.2 40.3 1.0 CB B:ASP308 4.4 9.3 1.0 NE2 B:HIS12 4.4 6.5 1.0 NE2 B:HIS311 4.4 15.7 1.0 CD2 B:HIS311 4.4 17.0 1.0 O B:HOH568 4.6 32.2 1.0 CE1 B:HIS189 4.7 6.1 1.0 NE2 B:HIS189 4.8 5.9 1.0 CD2 B:HIS12 4.8 8.6 1.0

Manganese binding site 7 out of 7 in the Crystal Structure of Apo PTMU3


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Crystal Structure of Apo PTMU3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn408 b:41.2 occ:1.00 O B:LEU312 2.3 13.6 1.0 O B:GLY314 2.3 11.2 1.0 O B:HOH654 2.4 15.5 1.0 OE1 A:GLN260 2.5 15.8 1.0 O B:HOH793 2.6 19.2 1.0 O A:HOH827 2.7 21.0 1.0 O A:HOH517 3.2 41.1 1.0 CD A:GLN260 3.4 16.9 1.0 C B:GLY314 3.4 9.8 1.0 C B:LEU312 3.4 16.6 1.0 N B:GLY314 3.9 11.6 1.0 O B:HOH633 4.1 18.6 1.0 CG A:GLN260 4.1 16.4 1.0 O B:PHE316 4.1 20.2 1.0 CA B:LEU312 4.2 17.6 1.0 CA B:GLY314 4.3 11.6 1.0 C B:GLU313 4.3 12.6 1.0 NE2 A:GLN260 4.3 17.4 1.0 N B:THR315 4.3 11.2 1.0 O B:HIS311 4.3 16.6 1.0 N B:GLU313 4.3 15.0 1.0 CB A:GLN260 4.4 17.2 1.0 O B:HOH932 4.5 33.9 1.0 CA B:THR315 4.6 11.9 1.0 CE1 B:HIS287 4.6 14.6 1.0 CA B:GLU313 4.6 13.0 1.0 C B:THR315 4.6 14.5 1.0 O A:HOH537 4.7 21.8 1.0 O B:HOH894 4.7 38.0 1.0 O B:THR315 4.8 14.0 1.0 NE2 B:HIS287 4.8 13.2 1.0 O B:GLU313 4.9 12.2 1.0 N B:PHE316 5.0 17.2 1.0

L.B.Dong, Y.C.Liu, A.J.Cepeda, E.Kalkreuter, M.R.Deng, J.D.Rudolf, C.Chang, A.Joachimiak, G.N.Phillips Jr., B.Shen. Characterization and Crystal Structure of A Nonheme Diiron Monooxygenase Involved in Platensimycin and Platencin Biosynthesis. J.Am.Chem.Soc. V. 141 12406 2019.
ISSN: ESSN 1520-5126
PubMed: 31291107
DOI: 10.1021/JACS.9B06183