Magnesium in PDB 3kc2: Crystal Structure of Mitochondrial Had-Like Phosphatase From Saccharomyces Cerevisiae

The structure of Crystal Structure of Mitochondrial Had-Like Phosphatase From Saccharomyces Cerevisiae, PDB code: 3kc2 was solved by B.Nocek, E.Evdokimova, K.Kuznetsova, A.Iakunine, A.Savchenko, A.Joachimiak, Midwest Center For Structural Genomics (Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 1.55
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	143.734, 67.095, 76.899, 90.00, 110.45, 90.00
R / Rfree (%)	14.4 / 16.9

The binding sites of Magnesium atom in the Crystal Structure of Mitochondrial Had-Like Phosphatase From Saccharomyces Cerevisiae (pdb code 3kc2). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Mitochondrial Had-Like Phosphatase From Saccharomyces Cerevisiae, PDB code: 3kc2:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of Mitochondrial Had-Like Phosphatase From Saccharomyces Cerevisiae


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 Mitochondrial Had-Like Phosphatase From Saccharomyces Cerevisiae within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg355 b:13.4 occ:1.00 O2 A:PO4353 2.0 18.7 1.0 OD1 A:ASP298 2.0 7.8 1.0 O A:HOH894 2.0 5.9 1.0 OD2 A:ASP19 2.1 10.4 1.0 O A:ASP21 2.1 7.8 1.0 O A:HOH893 2.1 6.4 1.0 CG A:ASP298 3.0 7.9 1.0 CG A:ASP19 3.1 11.1 1.0 C A:ASP21 3.3 7.3 1.0 OD2 A:ASP298 3.3 7.5 1.0 P A:PO4353 3.4 20.7 1.0 OD1 A:ASP19 3.5 12.4 1.0 O3 A:PO4353 4.0 17.5 1.0 CA A:ASP21 4.0 7.8 1.0 O A:HOH423 4.0 5.5 1.0 OD2 A:ASP303 4.1 9.5 1.0 CB A:ASP21 4.1 7.5 1.0 O1 A:PO4353 4.1 17.2 1.0 N A:ASP21 4.2 7.4 1.0 O A:HOH895 4.3 8.1 1.0 N A:GLY22 4.3 7.2 1.0 CB A:ASP19 4.4 9.2 1.0 CB A:ASP298 4.4 7.9 1.0 O4 A:PO4353 4.4 20.3 1.0 N A:ASP298 4.6 8.1 1.0 CA A:GLY22 4.6 6.7 1.0 CG2 A:VAL23 4.9 9.3 1.0 C A:ILE20 4.9 7.4 1.0 OD1 A:ASP303 4.9 12.5 1.0 CB A:ASN299 4.9 7.4 1.0 CA A:ASP298 4.9 7.8 1.0 CG A:ASP303 4.9 10.1 1.0 N A:ASN299 5.0 7.5 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of Mitochondrial Had-Like Phosphatase From Saccharomyces Cerevisiae


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 Mitochondrial Had-Like Phosphatase From Saccharomyces Cerevisiae within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg353 b:12.0 occ:1.00 O1 B:PO4354 1.9 17.4 1.0 OD2 B:ASP19 2.0 9.7 1.0 O B:HOH892 2.1 5.7 1.0 OD1 B:ASP298 2.1 7.1 1.0 O B:ASP21 2.1 6.0 1.0 O B:HOH891 2.1 4.5 1.0 CG B:ASP19 3.1 8.0 1.0 CG B:ASP298 3.1 6.5 1.0 C B:ASP21 3.3 6.0 1.0 P B:PO4354 3.4 20.2 1.0 OD2 B:ASP298 3.4 7.0 1.0 OD1 B:ASP19 3.5 13.6 1.0 CA B:ASP21 4.0 6.2 1.0 O B:HOH418 4.0 5.6 1.0 O3 B:PO4354 4.0 16.8 1.0 CB B:ASP21 4.1 6.3 1.0 OD2 B:ASP303 4.1 6.9 1.0 N B:ASP21 4.1 6.5 1.0 O2 B:PO4354 4.1 16.4 1.0 O B:HOH454 4.3 9.7 1.0 N B:GLY22 4.3 6.0 1.0 CB B:ASP19 4.4 6.6 1.0 O4 B:PO4354 4.4 22.0 1.0 CB B:ASP298 4.4 6.2 1.0 N B:ASP298 4.6 6.0 1.0 CA B:GLY22 4.6 5.4 1.0 C B:ILE20 4.9 6.1 1.0 CG2 B:VAL23 4.9 5.1 1.0 CG B:ASP303 5.0 7.8 1.0 CA B:ASP298 5.0 5.4 1.0 CB B:ASN299 5.0 6.2 1.0 N B:ASN299 5.0 6.4 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of Mitochondrial Had-Like Phosphatase From Saccharomyces Cerevisiae


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Mitochondrial Had-Like Phosphatase From Saccharomyces Cerevisiae within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg356 b:16.1 occ:1.00 O B:HOH429 2.4 6.5 1.0 O B:HOH362 2.4 5.9 1.0 O A:GLY134 2.4 7.0 1.0 OE1 B:GLN139 2.4 8.1 1.0 OE1 A:GLN139 2.4 9.7 1.0 O B:GLY134 2.4 5.0 1.0 C A:GLY134 3.2 6.9 1.0 C B:GLY134 3.2 5.4 1.0 CD B:GLN139 3.3 7.0 1.0 CD A:GLN139 3.3 8.5 1.0 NE2 B:GLN139 3.5 8.8 1.0 NE2 A:GLN139 3.5 11.3 1.0 CA B:LEU135 3.9 7.7 1.0 N B:LEU135 3.9 7.1 1.0 CA A:LEU135 3.9 7.7 1.0 N A:LEU135 3.9 6.7 1.0 CA A:GLY134 4.1 6.2 1.0 O B:HOH422 4.1 7.9 1.0 N B:SER136 4.1 7.2 1.0 N A:SER136 4.1 10.2 1.0 CA B:GLY134 4.2 4.8 1.0 C A:LEU135 4.4 8.0 1.0 C B:LEU135 4.4 6.9 1.0 O A:HOH475 4.6 8.7 1.0 O B:HOH394 4.7 6.8 1.0 CG A:GLN139 4.7 8.3 1.0 CG B:GLN139 4.7 7.6 1.0

B.Nocek, E.Evdokimova, K.Kuznetsova, A.Iakunine, A.Savchenko, A.Edwards, A.Joachimiak. Crystal Structure of Mitochondrial Had-Like Phosphatase From Saccharomyces Cerevisiae To Be Published.