Manganese in PDB 2au8: Catalytic Intermediate Structure of Inorganic Pyrophosphatase

All present enzymatic activity of Catalytic Intermediate Structure of Inorganic Pyrophosphatase:
3.6.1.1;

The structure of Catalytic Intermediate Structure of Inorganic Pyrophosphatase, PDB code: 2au8 was solved by V.R.Samygina, A.N.Popov, S.M.Avaeva, H.D.Bartunik, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 1.65
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	110.661, 110.661, 73.970, 90.00, 90.00, 120.00
R / Rfree (%)	16.5 / 20.8

The structure of Catalytic Intermediate Structure of Inorganic Pyrophosphatase also contains other interesting chemical elements:

Chlorine	(Cl)	3 atoms
Sodium	(Na)	1 atom

The binding sites of Manganese atom in the Catalytic Intermediate Structure of Inorganic Pyrophosphatase (pdb code 2au8). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Catalytic Intermediate Structure of Inorganic Pyrophosphatase, PDB code: 2au8:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Catalytic Intermediate Structure of Inorganic Pyrophosphatase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Catalytic Intermediate Structure of Inorganic Pyrophosphatase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn201 b:28.3 occ:1.00 O A:HOH322 2.1 29.4 1.0 OD1 A:ASP65 2.2 30.3 1.0 OD2 A:ASP70 2.2 27.1 1.0 OD1 A:ASP102 2.2 36.4 1.0 O4 A:PO4180 2.3 24.2 0.8 O3 A:PO4180 2.3 23.9 0.8 P A:PO4180 2.8 26.5 0.8 CG A:ASP70 3.1 24.8 1.0 CG A:ASP102 3.1 35.5 1.0 CG A:ASP65 3.1 36.6 1.0 OD2 A:ASP102 3.4 38.5 1.0 OD1 A:ASP70 3.4 28.7 1.0 OD2 A:ASP65 3.6 33.9 1.0 O2 A:PO4180 3.7 23.4 0.8 O A:HOH364 3.8 29.8 1.0 MN A:MN203 3.8 26.2 0.8 MN A:MN202 3.8 27.9 1.0 O A:HOH314 3.9 27.8 1.0 NZ A:LYS104 3.9 31.7 1.0 O1 A:PO4180 4.0 24.8 0.8 CB A:ASP65 4.3 38.3 1.0 CB A:ASP70 4.4 24.1 1.0 CB A:ASP102 4.4 33.3 1.0 O A:HOH356 4.5 27.2 0.6 O A:PRO68 4.5 30.2 1.0 O A:HOH315 4.6 26.5 1.0 OH A:TYR55 4.6 26.6 1.0 CA A:ASP102 5.0 33.5 1.0

Manganese binding site 2 out of 4 in the Catalytic Intermediate Structure of Inorganic Pyrophosphatase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Catalytic Intermediate Structure of Inorganic Pyrophosphatase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn202 b:27.9 occ:1.00 OD1 A:ASP70 2.1 28.7 1.0 O A:HOH315 2.2 26.5 1.0 O A:HOH308 2.2 26.0 1.0 O2 A:PO4180 2.2 23.4 0.8 O A:HOH352 2.2 31.5 1.0 O4 A:PO4180 2.3 24.2 0.8 P A:PO4180 2.7 26.5 0.8 CG A:ASP70 3.1 24.8 1.0 OD2 A:ASP70 3.6 27.1 1.0 O1 A:PO4180 3.8 24.8 0.8 MN A:MN201 3.8 28.3 1.0 OH A:TYR55 3.9 26.6 1.0 O3 A:PO4180 3.9 23.9 0.8 OE1 A:GLU20 4.1 30.1 1.0 O A:HOH316 4.1 38.3 0.5 O A:HOH322 4.1 29.4 1.0 O A:PRO68 4.1 30.2 1.0 O A:HOH356 4.1 27.2 0.6 CB A:ASP70 4.3 24.1 1.0 CE2 A:TYR55 4.3 24.2 1.0 NZ A:LYS29 4.4 38.6 1.0 CZ A:TYR55 4.4 23.7 1.0 OE2 A:GLU31 4.5 38.7 1.0 O A:GLY56 4.7 20.9 1.0 O A:HOH307 4.7 31.2 1.0 CA A:ASP70 4.8 25.5 1.0 CB A:ASP67 4.9 44.1 1.0 CB A:TYR57 4.9 23.3 1.0

Manganese binding site 3 out of 4 in the Catalytic Intermediate Structure of Inorganic Pyrophosphatase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Catalytic Intermediate Structure of Inorganic Pyrophosphatase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn203 b:26.2 occ:0.80 OD2 A:ASP97 2.1 36.7 1.0 OD2 A:ASP102 2.2 38.5 1.0 O3 A:PO4180 2.2 23.9 0.8 O A:HOH416 2.2 29.9 0.8 O A:HOH364 2.4 29.8 1.0 CL A:CL208 2.5 44.0 0.8 CG A:ASP97 3.0 41.0 1.0 CG A:ASP102 3.3 35.5 1.0 P A:PO4180 3.5 26.5 0.8 OD1 A:ASP97 3.6 40.6 1.0 O1 A:PO4180 3.7 24.8 0.8 NZ A:LYS104 3.7 31.7 1.0 MN A:MN201 3.8 28.3 1.0 OD1 A:ASP102 3.9 36.4 1.0 OD1 A:ASP65 4.1 30.3 1.0 CB A:ASP97 4.1 36.9 1.0 O A:HOH378 4.2 27.9 0.6 NZ A:LYS142 4.3 39.2 1.0 O A:HOH425 4.3 33.0 0.5 O4 A:PO4180 4.4 24.2 0.8 CB A:ASP102 4.4 33.3 1.0 OH A:TYR141 4.5 44.9 1.0 O2 A:PO4180 4.5 23.4 0.8 O A:HOH344 4.7 33.5 1.0 CE A:LYS142 4.8 32.0 1.0 CE A:LYS104 4.9 28.9 1.0 OD2 A:ASP70 4.9 27.1 1.0

Manganese binding site 4 out of 4 in the Catalytic Intermediate Structure of Inorganic Pyrophosphatase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Catalytic Intermediate Structure of Inorganic Pyrophosphatase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn204 b:26.9 occ:0.60 O A:HOH358 1.7 34.1 0.6 O A:HOH356 1.8 27.2 0.6 O1 A:PO4180 2.1 24.8 0.8 OE2 A:GLU31 2.2 38.7 1.0 O A:HOH377 2.2 35.2 0.6 O A:HOH378 2.3 27.9 0.6 CD A:GLU31 3.2 35.5 1.0 OE1 A:GLU31 3.4 35.0 1.0 P A:PO4180 3.4 26.5 0.8 O4 A:PO4180 3.6 24.2 0.8 O A:HOH416 3.8 29.9 0.8 NZ A:LYS29 4.0 38.6 1.0 O A:HOH404 4.1 41.0 0.5 OD2 A:ASP42 4.2 56.5 1.0 O3 A:PO4180 4.3 23.9 0.8 O A:HOH352 4.3 31.5 1.0 OD2 A:ASP67 4.3 50.0 1.0 O2 A:PO4180 4.4 23.4 0.8 O A:HOH364 4.5 29.8 1.0 CG A:GLU31 4.5 31.9 1.0 CE A:LYS29 4.9 36.1 1.0 O A:HOH425 4.9 33.0 0.5 CG A:ASP42 4.9 39.8 1.0

V.R.Samygina, V.M.Moiseev, E.V.Rodina, N.N.Vorobyeva, A.N.Popov, S.A.Kurilova, T.I.Nazarova, S.M.Avaeva, H.D.Bartunik. Reversible Inhibition of Escherichia Coli Inorganic Pyrophosphatase By Fluoride: Trapped Catalytic Intermediates in Cryo-Crystallographic Studies J.Mol.Biol. V. 366 1305 2007.
ISSN: ISSN 0022-2836
PubMed: 17196979
DOI: 10.1016/J.JMB.2006.11.082