Magnesium in PDB 3quq: Crystal Structure of Pyrophosphatase From Bacteroides Thetaiotaomicron, An Open Cap Conformation

All present enzymatic activity of Crystal Structure of Pyrophosphatase From Bacteroides Thetaiotaomicron, An Open Cap Conformation:
3.6.1.1;

The structure of Crystal Structure of Pyrophosphatase From Bacteroides Thetaiotaomicron, An Open Cap Conformation, PDB code: 3quq was solved by Y.Patskovsky, H.Huang, R.Toro, J.A.Gerlt, S.K.Burley, D.Dunaway-Mariano, S.C.Almo, New York Sgx Research Center For Structural Genomics(Nysgxrc), Enzyme Function Initiative (Efi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.45 / 1.65
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	45.203, 65.336, 75.617, 90.00, 90.00, 90.00
R / Rfree (%)	16.3 / 17.8

The structure of Crystal Structure of Pyrophosphatase From Bacteroides Thetaiotaomicron, An Open Cap Conformation also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Magnesium atom in the Crystal Structure of Pyrophosphatase From Bacteroides Thetaiotaomicron, An Open Cap Conformation (pdb code 3quq). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Pyrophosphatase From Bacteroides Thetaiotaomicron, An Open Cap Conformation, PDB code: 3quq:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Pyrophosphatase From Bacteroides Thetaiotaomicron, An Open Cap Conformation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Pyrophosphatase From Bacteroides Thetaiotaomicron, An Open Cap Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg225 b:10.3 occ:1.00 OE2 A:GLU47 1.9 13.3 1.0 OD2 A:ASP11 2.0 10.7 1.0 O A:ASP13 2.1 9.6 1.0 OD1 A:ASN172 2.1 10.0 1.0 O A:HOH326 2.1 14.2 1.0 O A:HOH325 2.2 12.8 1.0 CG A:ASP11 3.0 12.8 1.0 CD A:GLU47 3.1 11.9 1.0 CG A:ASN172 3.1 11.2 1.0 C A:ASP13 3.3 8.4 1.0 OD1 A:ASP11 3.4 11.5 1.0 ND2 A:ASN172 3.5 10.0 1.0 OE1 A:GLU47 3.8 11.5 1.0 CA A:ASP13 4.0 9.1 1.0 OE1 A:GLU171 4.1 11.5 1.0 CG A:GLU47 4.1 11.3 1.0 CB A:ASP13 4.1 9.0 1.0 N A:ASP13 4.1 10.8 1.0 N A:GLY14 4.3 8.4 1.0 O1 A:FMT227 4.3 24.8 1.0 CB A:ASP11 4.3 9.6 1.0 CB A:ALA173 4.4 13.0 1.0 O A:HOH232 4.4 12.7 1.0 CB A:ASN172 4.5 9.0 1.0 CA A:GLY14 4.5 8.7 1.0 N1 A:UNL230 4.6 47.8 1.0 O A:HOH234 4.6 12.6 1.0 N A:ASN172 4.6 9.1 1.0 N A:ALA173 4.7 8.7 1.0 CG2 A:VAL15 4.8 11.0 1.0 C A:MET12 4.8 10.8 1.0 C A:GLY14 4.9 8.5 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Pyrophosphatase From Bacteroides Thetaiotaomicron, An Open Cap Conformation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Pyrophosphatase From Bacteroides Thetaiotaomicron, An Open Cap Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg226 b:16.1 occ:1.00 O A:PRO210 2.3 14.7 1.0 O A:ASN191 2.3 12.4 1.0 O A:HOH238 2.3 15.8 1.0 O A:HOH301 2.4 21.1 1.0 C A:PRO210 3.3 13.5 1.0 C A:ASN191 3.5 11.3 1.0 CA A:PRO210 3.6 13.6 1.0 CB A:PRO210 3.8 15.1 1.0 CB A:ASN191 4.2 11.6 1.0 O A:HOH381 4.2 33.9 1.0 CA A:ASN191 4.4 9.6 1.0 CA A:THR192 4.4 9.9 1.0 N A:THR192 4.4 11.4 1.0 N A:SER211 4.5 11.6 1.0 O A:GLY193 4.5 13.5 1.0 CG A:ASN191 4.6 13.3 1.0 C A:THR192 4.7 11.0 1.0 ND2 A:ASN191 4.9 14.7 1.0 O A:HOH239 4.9 19.9 1.0 N A:GLY193 4.9 11.7 1.0 O A:HOH302 5.0 17.5 1.0 N A:ASN191 5.0 10.8 1.0 CA A:SER211 5.0 10.9 1.0

H.Huang, Y.Patskovsky, R.Toro, J.D.Farelli, C.Pandya, S.C.Almo, K.N.Allen, D.Dunaway-Mariano. Divergence of Structure and Function in the Haloacid Dehalogenase Enzyme Superfamily: Bacteroides Thetaiotaomicron BT2127 Is An Inorganic Pyrophosphatase. Biochemistry V. 50 8937 2011.
ISSN: ISSN 0006-2960
PubMed: 21894910
DOI: 10.1021/BI201181Q