Manganese in PDB 1i74: Streptococcus Mutans Inorganic Pyrophosphatase

All present enzymatic activity of Streptococcus Mutans Inorganic Pyrophosphatase:
3.6.1.1;

The structure of Streptococcus Mutans Inorganic Pyrophosphatase, PDB code: 1i74 was solved by M.C.Merckel, I.P.Fabrichniy, A.Goldman, R.Lahti, A.Salminen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.76 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	75.600, 95.300, 95.500, 90.00, 90.00, 90.00
R / Rfree (%)	20.9 / 25.7

The structure of Streptococcus Mutans Inorganic Pyrophosphatase also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Manganese atom in the Streptococcus Mutans Inorganic Pyrophosphatase (pdb code 1i74). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Streptococcus Mutans Inorganic Pyrophosphatase, PDB code: 1i74:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Streptococcus Mutans Inorganic Pyrophosphatase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Streptococcus Mutans Inorganic Pyrophosphatase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn401 b:29.7 occ:1.00 O A:HOH406 1.9 19.3 1.0 O1 A:SO4405 2.0 24.5 1.0 OD2 A:ASP75 2.1 22.4 1.0 OD2 A:ASP12 2.2 17.7 1.0 NE2 A:HIS8 2.3 22.9 1.0 OD1 A:ASP12 2.5 16.4 1.0 CG A:ASP12 2.6 19.3 1.0 CG A:ASP75 3.1 19.7 1.0 S A:SO4405 3.1 25.5 1.0 CD2 A:HIS8 3.2 23.2 1.0 OD1 A:ASP75 3.3 19.1 1.0 MN A:MN402 3.3 24.2 1.0 CE1 A:HIS8 3.3 21.5 1.0 O3 A:SO4405 3.5 23.0 1.0 O4 A:SO4405 3.6 23.6 1.0 O A:HOH504 4.0 35.4 1.0 O A:HOH502 4.0 26.0 1.0 N A:ALA15 4.1 19.5 1.0 CB A:ASP12 4.1 18.2 1.0 CB A:ALA15 4.2 19.4 1.0 O2 A:SO4405 4.3 20.4 1.0 OD1 A:ASP149 4.4 22.9 1.0 CB A:ASP14 4.4 18.9 1.0 CG A:HIS8 4.4 22.0 1.0 ND1 A:HIS8 4.4 24.1 1.0 CB A:ASP75 4.4 19.8 1.0 O A:HOH664 4.5 19.2 1.0 O A:ASP75 4.5 19.6 1.0 OD2 A:ASP14 4.6 20.2 1.0 CA A:ALA15 4.6 20.1 1.0 OD2 A:ASP149 4.7 24.4 1.0 N A:ASP12 4.8 19.1 1.0 MG A:MG403 4.9 26.5 1.0 C A:ASP14 4.9 19.6 1.0 O A:HOH668 5.0 27.4 1.0 CE1 A:HIS98 5.0 21.8 1.0 CG A:ASP149 5.0 23.3 1.0

Manganese binding site 2 out of 4 in the Streptococcus Mutans Inorganic Pyrophosphatase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Streptococcus Mutans Inorganic Pyrophosphatase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn402 b:24.2 occ:1.00 O A:HOH406 2.1 19.3 1.0 OD2 A:ASP149 2.1 24.4 1.0 OD1 A:ASP75 2.1 19.1 1.0 O3 A:SO4405 2.2 23.0 1.0 OD2 A:ASP14 2.3 20.2 1.0 NE2 A:HIS97 2.4 19.6 1.0 CG A:ASP75 3.1 19.7 1.0 CG A:ASP149 3.1 23.3 1.0 CE1 A:HIS97 3.2 19.4 1.0 CG A:ASP14 3.3 21.8 1.0 S A:SO4405 3.3 25.5 1.0 MN A:MN401 3.3 29.7 1.0 OD2 A:ASP75 3.4 22.4 1.0 O1 A:SO4405 3.4 24.5 1.0 OD1 A:ASP149 3.4 22.9 1.0 CB A:ASP14 3.6 18.9 1.0 CD2 A:HIS97 3.6 20.0 1.0 O4 A:SO4405 3.8 23.6 1.0 CE1 A:HIS98 4.0 21.8 1.0 CB A:ASP75 4.4 19.8 1.0 N A:ALA119 4.4 18.7 1.0 OD1 A:ASP14 4.4 22.6 1.0 NE2 A:HIS98 4.4 21.8 1.0 ND1 A:HIS97 4.4 19.8 1.0 CB A:ASP149 4.5 22.5 1.0 O2 A:SO4405 4.5 20.4 1.0 CG A:HIS97 4.6 19.1 1.0 CA A:SER118 4.7 19.0 1.0 O A:HOH562 4.8 40.7 1.0 OD2 A:ASP12 4.8 17.7 1.0 CB A:ALA119 4.9 19.4 1.0 CA A:ASP14 4.9 20.0 1.0 OD1 A:ASP12 5.0 16.4 1.0 O A:ASP75 5.0 19.6 1.0 CA A:ASP75 5.0 19.5 1.0

Manganese binding site 3 out of 4 in the Streptococcus Mutans Inorganic Pyrophosphatase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Streptococcus Mutans Inorganic Pyrophosphatase within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn401 b:38.8 occ:1.00 O B:HOH1406 2.0 35.0 1.0 OD2 B:ASP75 2.1 26.6 1.0 NE2 B:HIS8 2.2 27.7 1.0 OD2 B:ASP12 2.3 29.2 1.0 OD1 B:ASP12 2.4 29.1 1.0 O1 B:SO41405 2.4 51.1 1.0 CG B:ASP12 2.6 30.5 1.0 CG B:ASP75 3.0 25.1 1.0 CE1 B:HIS8 3.1 31.0 1.0 CD2 B:HIS8 3.2 30.0 1.0 OD1 B:ASP75 3.3 23.9 1.0 S B:SO41405 3.5 54.4 1.0 MN B:MN402 3.5 34.9 1.0 O3 B:SO41405 3.7 52.0 1.0 O4 B:SO41405 3.8 53.7 1.0 O B:HOH695 4.0 41.7 1.0 CB B:ASP12 4.1 28.9 1.0 ND1 B:HIS8 4.3 30.3 1.0 N B:ALA15 4.3 27.1 1.0 CB B:ALA15 4.3 26.1 1.0 CG B:HIS8 4.3 30.2 1.0 CB B:ASP75 4.4 24.3 1.0 OD1 B:ASP149 4.4 31.9 1.0 O B:ASP75 4.4 23.0 1.0 CB B:ASP14 4.5 26.4 1.0 OD2 B:ASP149 4.6 32.1 1.0 NE2 B:HIS98 4.7 32.8 1.0 N B:ASP12 4.7 29.6 1.0 CA B:ALA15 4.7 26.5 1.0 OD2 B:ASP14 4.7 28.9 1.0 O2 B:SO41405 4.8 54.0 1.0 CG B:ASP149 4.9 32.9 1.0

Manganese binding site 4 out of 4 in the Streptococcus Mutans Inorganic Pyrophosphatase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Streptococcus Mutans Inorganic Pyrophosphatase within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn402 b:34.9 occ:1.00 OD2 B:ASP149 2.0 32.1 1.0 OD1 B:ASP75 2.1 23.9 1.0 O B:HOH1406 2.2 35.0 1.0 NE2 B:HIS97 2.2 21.1 1.0 OD2 B:ASP14 2.3 28.9 1.0 O3 B:SO41405 2.5 52.0 1.0 CE1 B:HIS97 3.0 21.0 1.0 CG B:ASP149 3.1 32.9 1.0 CG B:ASP75 3.1 25.1 1.0 CG B:ASP14 3.1 27.1 1.0 CD2 B:HIS97 3.3 21.4 1.0 CB B:ASP14 3.4 26.4 1.0 MN B:MN401 3.5 38.8 1.0 OD2 B:ASP75 3.5 26.6 1.0 OD1 B:ASP149 3.5 31.9 1.0 S B:SO41405 3.7 54.4 1.0 NE2 B:HIS98 3.9 32.8 1.0 O1 B:SO41405 3.9 51.1 1.0 O4 B:SO41405 4.1 53.7 1.0 ND1 B:HIS97 4.2 21.8 1.0 N B:ALA119 4.2 19.6 1.0 OD1 B:ASP14 4.2 26.6 1.0 CB B:ASP75 4.3 24.3 1.0 CB B:ASP149 4.4 30.7 1.0 CG B:HIS97 4.4 22.0 1.0 CA B:SER118 4.5 21.9 1.0 CE1 B:HIS98 4.7 31.6 1.0 CB B:ALA119 4.7 20.9 1.0 CD2 B:HIS98 4.8 29.4 1.0 OD1 B:ASP12 4.8 29.1 1.0 CA B:ASP14 4.8 27.0 1.0 CA B:ASP75 4.9 23.4 1.0 O B:ASP75 4.9 23.0 1.0 C B:SER118 4.9 21.1 1.0 CB B:SER118 4.9 22.3 1.0 O2 B:SO41405 4.9 54.0 1.0

M.C.Merckel, I.P.Fabrichniy, A.Salminen, N.Kalkkinen, A.A.Baykov, R.Lahti, A.Goldman. Crystal Structure of Streptococcus Mutans Pyrophosphatase: A New Fold For An Old Mechanism. Structure V. 9 289 2001.
ISSN: ISSN 0969-2126
PubMed: 11525166
DOI: 10.1016/S0969-2126(01)00587-1