Manganese in PDB 1k20: Inorganic Pyrophosphatase (Family II) From Streptococcus Gordonii at 1.5 A Resolution

All present enzymatic activity of Inorganic Pyrophosphatase (Family II) From Streptococcus Gordonii at 1.5 A Resolution:
3.6.1.1;

The structure of Inorganic Pyrophosphatase (Family II) From Streptococcus Gordonii at 1.5 A Resolution, PDB code: 1k20 was solved by S.Ahn, A.J.Milner, K.Futterer, M.Konopka, M.Ilias, T.W.Young, S.A.White, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.32 / 1.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.197, 87.552, 130.027, 90.00, 90.00, 90.00
R / Rfree (%)	17.5 / 18.8

The binding sites of Manganese atom in the Inorganic Pyrophosphatase (Family II) From Streptococcus Gordonii at 1.5 A Resolution (pdb code 1k20). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Inorganic Pyrophosphatase (Family II) From Streptococcus Gordonii at 1.5 A Resolution, PDB code: 1k20:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Inorganic Pyrophosphatase (Family II) From Streptococcus Gordonii at 1.5 A Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Inorganic Pyrophosphatase (Family II) From Streptococcus Gordonii at 1.5 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn701 b:43.8 occ:0.50 OD1 A:ASP77 2.0 15.7 1.0 O A:HOH712 2.0 26.7 1.0 O A:HOH711 2.2 22.7 1.0 NE2 A:HIS9 2.4 11.2 1.0 OD2 A:ASP13 2.4 10.1 1.0 OD1 A:ASP13 2.5 12.5 1.0 CG A:ASP13 2.7 11.3 1.0 CG A:ASP77 3.0 14.0 1.0 CE1 A:HIS9 3.3 9.6 1.0 CD2 A:HIS9 3.4 9.9 1.0 O A:HOH1004 3.5 31.1 1.0 OD2 A:ASP77 3.6 13.3 1.0 MN A:MN702 3.8 37.7 0.5 CB A:ALA16 4.0 8.2 1.0 N A:ALA16 4.0 7.4 1.0 CB A:ASP77 4.1 9.3 1.0 O A:HOH1047 4.2 33.2 1.0 CB A:ASP13 4.2 9.5 1.0 NZ A:LYS207 4.2 13.6 1.0 ND1 A:HIS9 4.4 10.1 1.0 CA A:ALA16 4.4 7.7 1.0 CB A:ASP15 4.5 9.2 1.0 CG A:HIS9 4.5 9.5 1.0 O A:ASP77 4.5 9.0 1.0 N A:ASP13 4.6 8.4 1.0 CE A:LYS207 4.6 12.5 1.0 OD2 A:ASP151 4.7 16.9 1.0 CE1 A:HIS100 4.7 8.5 1.0 OD1 A:ASP151 4.7 14.5 1.0 O A:HOH722 4.8 10.6 1.0 C A:ASP15 4.8 8.1 1.0 OD2 A:ASP15 4.9 11.5 1.0 CA A:ASP13 4.9 8.5 1.0 O1 A:SO4705 5.0 11.1 1.0

Manganese binding site 2 out of 4 in the Inorganic Pyrophosphatase (Family II) From Streptococcus Gordonii at 1.5 A Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Inorganic Pyrophosphatase (Family II) From Streptococcus Gordonii at 1.5 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn702 b:37.7 occ:0.50 OD2 A:ASP151 2.0 16.9 1.0 NE2 A:HIS99 2.0 9.3 1.0 O A:HOH711 2.1 22.7 1.0 OD2 A:ASP15 2.1 11.5 1.0 OD2 A:ASP77 2.3 13.3 1.0 CE1 A:HIS99 2.7 10.8 1.0 CG A:ASP77 3.1 14.0 1.0 CG A:ASP15 3.1 11.8 1.0 OD1 A:ASP77 3.2 15.7 1.0 CD2 A:HIS99 3.2 9.1 1.0 CG A:ASP151 3.2 13.4 1.0 CB A:ASP15 3.4 9.2 1.0 MN A:MN701 3.8 43.8 0.5 OD1 A:ASP151 3.9 14.5 1.0 CE1 A:HIS100 3.9 8.5 1.0 O A:HOH712 3.9 26.7 1.0 N A:ALA121 3.9 8.1 1.0 ND1 A:HIS99 3.9 11.3 1.0 CG A:HIS99 4.2 8.6 1.0 CA A:SER120 4.2 8.0 1.0 OD1 A:ASP15 4.2 10.6 1.0 NE2 A:HIS100 4.4 8.4 1.0 CB A:ASP151 4.4 11.1 1.0 O A:HOH808 4.4 16.0 1.0 CB A:ASP77 4.5 9.3 1.0 C A:SER120 4.6 8.4 1.0 CB A:ALA121 4.6 8.9 1.0 O1 A:SO4705 4.6 11.1 1.0 CB A:SER120 4.6 9.1 1.0 O A:HOH1047 4.7 33.2 1.0 CA A:ASP15 4.8 8.4 1.0 CA A:ALA121 4.9 8.2 1.0 O A:GLY119 4.9 8.8 1.0 ND1 A:HIS100 4.9 8.6 1.0 OD1 A:ASP13 5.0 12.5 1.0

Manganese binding site 3 out of 4 in the Inorganic Pyrophosphatase (Family II) From Streptococcus Gordonii at 1.5 A Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Inorganic Pyrophosphatase (Family II) From Streptococcus Gordonii at 1.5 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn703 b:41.6 occ:0.50 O B:HOH713 2.0 26.7 1.0 O B:HOH712 2.0 22.1 1.0 OD1 B:ASP77 2.1 18.8 1.0 OD2 B:ASP13 2.3 12.0 1.0 OD1 B:ASP13 2.4 15.5 1.0 NE2 B:HIS9 2.6 11.6 1.0 CG B:ASP13 2.6 11.5 1.0 CG B:ASP77 3.1 15.4 1.0 O B:HOH950 3.4 29.8 1.0 CE1 B:HIS9 3.5 10.0 1.0 MN B:MN704 3.6 45.7 0.5 OD2 B:ASP77 3.7 13.8 1.0 CD2 B:HIS9 3.7 10.6 1.0 N B:ALA16 3.9 9.2 1.0 CB B:ALA16 4.0 8.2 1.0 CB B:ASP13 4.1 10.6 1.0 CB B:ASP77 4.2 10.7 1.0 CB B:ASP15 4.3 9.5 1.0 NZ B:LYS207 4.3 11.8 1.0 CA B:ALA16 4.4 8.8 1.0 N B:ASP13 4.6 9.9 1.0 OD1 B:ASP151 4.6 18.4 1.0 OD2 B:ASP151 4.6 14.7 1.0 ND1 B:HIS9 4.6 9.9 1.0 O B:HOH729 4.7 10.4 1.0 O B:ASP77 4.7 9.7 1.0 CE1 B:HIS100 4.7 8.1 1.0 C B:ASP15 4.7 8.9 1.0 CG B:HIS9 4.8 9.7 1.0 O2 B:SO4706 4.8 13.0 1.0 OD1 B:ASP15 4.8 11.8 1.0 CE B:LYS207 4.8 12.1 1.0 CA B:ASP13 4.8 10.0 1.0 O B:HOH960 4.9 36.4 1.0 CA B:ASP15 4.9 9.8 1.0 NE2 B:HIS100 5.0 10.3 1.0

Manganese binding site 4 out of 4 in the Inorganic Pyrophosphatase (Family II) From Streptococcus Gordonii at 1.5 A Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Inorganic Pyrophosphatase (Family II) From Streptococcus Gordonii at 1.5 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn704 b:45.7 occ:0.50 O B:HOH712 2.0 22.1 1.0 NE2 B:HIS99 2.0 9.8 1.0 OD1 B:ASP151 2.1 18.4 1.0 OD2 B:ASP77 2.2 13.8 1.0 OD1 B:ASP15 2.3 11.8 1.0 CE1 B:HIS99 2.7 11.3 1.0 CG B:ASP77 3.0 15.4 1.0 OD1 B:ASP77 3.1 18.8 1.0 CG B:ASP15 3.2 11.0 1.0 CD2 B:HIS99 3.2 8.7 1.0 CG B:ASP151 3.3 16.0 1.0 CB B:ASP15 3.5 9.5 1.0 MN B:MN703 3.6 41.6 0.5 O B:HOH713 3.8 26.7 1.0 CE1 B:HIS100 3.8 8.1 1.0 OD2 B:ASP151 3.9 14.7 1.0 ND1 B:HIS99 3.9 11.3 1.0 N B:ALA121 4.1 9.3 1.0 CG B:HIS99 4.2 9.2 1.0 O B:HOH924 4.2 18.2 1.0 NE2 B:HIS100 4.3 10.3 1.0 CA B:SER120 4.4 9.5 1.0 OD2 B:ASP15 4.4 11.3 1.0 CB B:ASP77 4.4 10.7 1.0 CB B:ASP151 4.5 11.4 1.0 O2 B:SO4706 4.5 13.0 1.0 CB B:ALA121 4.7 9.4 1.0 C B:SER120 4.8 9.0 1.0 OD1 B:ASP13 4.8 15.5 1.0 CB B:SER120 4.8 10.0 1.0 ND1 B:HIS100 4.8 7.6 1.0 CA B:ASP15 4.9 9.8 1.0 CA B:ASP77 5.0 9.4 1.0 O B:GLY119 5.0 10.2 1.0

S.Ahn, A.J.Milner, K.Futterer, M.Konopka, M.Ilias, T.W.Young, S.A.White. The "Open" and "Closed" Structures of the Type-C Inorganic Pyrophosphatases From Bacillus Subtilis and Streptococcus Gordonii. J.Mol.Biol. V. 313 797 2001.
ISSN: ISSN 0022-2836
PubMed: 11697905
DOI: 10.1006/JMBI.2001.5070