Manganese in PDB 6b9v: Crystal Structure of A New Diphosphatase From the Phnp Family

The structure of Crystal Structure of A New Diphosphatase From the Phnp Family, PDB code: 6b9v was solved by Q.Li, S.D.Bruner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.28 / 1.88
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	125.780, 41.364, 96.034, 90.00, 95.20, 90.00
R / Rfree (%)	15.9 / 19.6

The structure of Crystal Structure of A New Diphosphatase From the Phnp Family also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Manganese atom in the Crystal Structure of A New Diphosphatase From the Phnp Family (pdb code 6b9v). 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 A New Diphosphatase From the Phnp Family, PDB code: 6b9v:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Crystal Structure of A New Diphosphatase From the Phnp Family


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 A New Diphosphatase From the Phnp Family within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn301 b:14.9 occ:1.00 O1 A:PO4303 2.2 21.9 1.0 NE2 A:HIS231 2.2 13.9 1.0 NE2 A:HIS83 2.2 20.6 1.0 OD1 A:ASP178 2.2 15.7 1.0 OD2 A:ASP82 2.2 15.9 1.0 O2 A:PO4303 2.9 48.7 1.0 CG A:ASP178 3.0 15.0 1.0 OD2 A:ASP178 3.0 16.1 1.0 P A:PO4303 3.1 44.9 1.0 CD2 A:HIS231 3.1 13.9 1.0 CD2 A:HIS83 3.1 17.5 1.0 CG A:ASP82 3.2 16.2 1.0 CE1 A:HIS231 3.2 13.4 1.0 CE1 A:HIS83 3.2 15.4 1.0 OD1 A:ASP82 3.4 16.1 1.0 MN A:MN302 3.5 16.4 1.0 O3 A:PO4303 4.0 33.7 1.0 O4 A:PO4303 4.2 47.4 1.0 NE2 A:HIS78 4.2 16.4 1.0 CE1 A:HIS209 4.3 19.4 1.0 CG A:HIS231 4.3 17.4 1.0 CG A:HIS83 4.3 13.7 1.0 ND1 A:HIS231 4.3 11.6 1.0 ND1 A:HIS83 4.3 14.9 1.0 CE1 A:HIS78 4.3 14.5 1.0 CG A:PRO40 4.4 17.3 1.0 CB A:ASP178 4.4 15.6 1.0 CB A:ASP82 4.5 10.6 1.0 NE2 A:HIS209 4.7 14.8 1.0 CB A:SER15 4.9 15.2 1.0

Manganese binding site 2 out of 4 in the Crystal Structure of A New Diphosphatase From the Phnp Family


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 A New Diphosphatase From the Phnp Family within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn302 b:16.4 occ:1.00 ND1 A:HIS80 2.0 19.0 1.0 O1 A:PO4303 2.2 21.9 1.0 NE2 A:HIS160 2.2 16.3 1.0 NE2 A:HIS78 2.2 16.4 1.0 OD1 A:ASP178 2.4 15.7 1.0 O3 A:PO4303 2.6 33.7 1.0 P A:PO4303 2.9 44.9 1.0 CE1 A:HIS80 2.9 23.9 1.0 CD2 A:HIS78 3.1 13.3 1.0 CD2 A:HIS160 3.1 18.2 1.0 CG A:HIS80 3.1 18.9 1.0 CE1 A:HIS160 3.3 15.7 1.0 CE1 A:HIS78 3.3 14.5 1.0 CG A:ASP178 3.4 15.0 1.0 MN A:MN301 3.5 14.9 1.0 CB A:HIS80 3.5 15.4 1.0 CB A:ASP178 3.8 15.6 1.0 O4 A:PO4303 3.9 47.4 1.0 O2 A:PO4303 4.0 48.7 1.0 NE2 A:HIS80 4.1 24.9 1.0 NE2 A:HIS83 4.1 20.6 1.0 CD2 A:HIS80 4.2 25.8 1.0 CG A:HIS160 4.3 21.1 1.0 CG A:HIS78 4.3 15.6 1.0 CD2 A:HIS83 4.3 17.5 1.0 ND1 A:HIS160 4.3 16.8 1.0 ND1 A:HIS78 4.4 16.6 1.0 OD2 A:ASP178 4.4 16.1 1.0 O A:HOH404 4.4 30.6 1.0 OD1 A:ASP82 4.6 16.1 1.0 NE2 A:HIS209 4.9 14.8 1.0 CE1 A:HIS209 4.9 19.4 1.0 CA A:HIS80 5.0 16.7 1.0

Manganese binding site 3 out of 4 in the Crystal Structure of A New Diphosphatase From the Phnp Family


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 A New Diphosphatase From the Phnp Family within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn301 b:21.6 occ:1.00 ND1 B:HIS80 2.1 25.1 1.0 O4 B:PO4303 2.1 30.7 1.0 NE2 B:HIS78 2.2 25.2 1.0 NE2 B:HIS160 2.2 21.8 1.0 OD1 B:ASP178 2.4 24.5 1.0 O1 B:PO4303 2.6 26.6 1.0 P B:PO4303 2.9 34.9 1.0 CE1 B:HIS80 3.0 27.8 1.0 CD2 B:HIS160 3.1 21.6 1.0 CD2 B:HIS78 3.1 21.0 1.0 CG B:HIS80 3.1 23.8 1.0 CE1 B:HIS78 3.3 21.6 1.0 CE1 B:HIS160 3.3 20.2 1.0 CG B:ASP178 3.4 21.6 1.0 CB B:HIS80 3.5 19.4 1.0 MN B:MN302 3.6 19.4 1.0 CB B:ASP178 3.9 20.6 1.0 O2 B:PO4303 3.9 39.6 1.0 O3 B:PO4303 4.0 34.3 1.0 NE2 B:HIS80 4.1 31.2 1.0 NE2 B:HIS83 4.2 22.2 1.0 CD2 B:HIS80 4.2 27.6 1.0 CG B:HIS160 4.3 24.7 1.0 CG B:HIS78 4.3 24.5 1.0 CD2 B:HIS83 4.3 17.1 1.0 ND1 B:HIS78 4.3 19.2 1.0 ND1 B:HIS160 4.3 22.9 1.0 OD2 B:ASP178 4.5 22.6 1.0 O B:HOH439 4.5 31.4 1.0 OD2 B:ASP82 4.7 20.1 1.0 NE2 B:HIS209 4.8 22.4 1.0 CA B:HIS80 5.0 20.4 1.0 CE1 B:HIS209 5.0 19.7 1.0

Manganese binding site 4 out of 4 in the Crystal Structure of A New Diphosphatase From the Phnp Family


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 A New Diphosphatase From the Phnp Family within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn302 b:19.4 occ:1.00 NE2 B:HIS231 2.2 22.0 1.0 NE2 B:HIS83 2.2 22.2 1.0 OD1 B:ASP178 2.2 24.5 1.0 OD1 B:ASP82 2.3 17.9 1.0 O4 B:PO4303 2.5 30.7 1.0 O2 B:PO4303 2.5 39.6 1.0 CG B:ASP178 2.9 21.6 1.0 OD2 B:ASP178 3.0 22.6 1.0 CD2 B:HIS231 3.1 21.2 1.0 P B:PO4303 3.1 34.9 1.0 CD2 B:HIS83 3.1 17.1 1.0 CG B:ASP82 3.2 22.2 1.0 CE1 B:HIS231 3.2 21.2 1.0 CE1 B:HIS83 3.3 19.2 1.0 OD2 B:ASP82 3.5 20.1 1.0 MN B:MN301 3.6 21.6 1.0 O1 B:PO4303 4.0 26.6 1.0 CE1 B:HIS209 4.1 19.7 1.0 O3 B:PO4303 4.2 34.3 1.0 CG B:HIS231 4.2 21.0 1.0 CG B:HIS83 4.3 21.9 1.0 ND1 B:HIS231 4.3 19.1 1.0 ND1 B:HIS83 4.3 21.1 1.0 CE1 B:HIS78 4.4 21.6 1.0 NE2 B:HIS78 4.4 25.2 1.0 CB B:ASP178 4.4 20.6 1.0 CG B:PRO40 4.4 16.2 1.0 NE2 B:HIS209 4.5 22.4 1.0 CB B:ASP82 4.6 14.0 1.0 CB B:SER15 4.7 25.4 1.0 O B:HOH437 5.0 39.6 1.0

G.A.W.Beaudoin, Q.Li, S.D.Bruner, A.D.Hanson. An Unusual Diphosphatase From the Phnp Family Cleaves Reactive Fad Photoproducts. Biochem.J. V. 475 261 2018.
ISSN: ESSN 1470-8728
PubMed: 29229761
DOI: 10.1042/BCJ20170817