Magnesium in PDB 1rkq: Crystal Structure of Had-Like Phosphatase Yida From E. Coli

The structure of Crystal Structure of Had-Like Phosphatase Yida From E. Coli, PDB code: 1rkq was solved by U.A.Ramagopal, S.C.Almo, S.K.Burley, New York Sgx Research Center Forstructural Genomics (Nysgxrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.50 / 1.40
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	45.120, 54.871, 67.725, 112.58, 96.37, 106.79
R / Rfree (%)	17.7 / 21.3

The structure of Crystal Structure of Had-Like Phosphatase Yida From E. Coli also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Magnesium atom in the Crystal Structure of Had-Like Phosphatase Yida From E. Coli (pdb code 1rkq). 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 Had-Like Phosphatase Yida From E. Coli, PDB code: 1rkq:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Had-Like Phosphatase Yida From E. Coli


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 Had-Like Phosphatase Yida From E. Coli within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1273 b:14.2 occ:1.00 O A:HOH1276 2.2 15.5 1.0 OD2 A:ASP10 2.2 16.7 1.0 O A:ASP12 2.2 15.3 1.0 O A:HOH1275 2.2 16.4 1.0 O A:HOH1274 2.2 15.5 1.0 OD1 A:ASP221 2.2 15.8 1.0 CG A:ASP10 3.1 12.9 1.0 CG A:ASP221 3.2 17.1 1.0 C A:ASP12 3.4 14.8 1.0 OD1 A:ASP10 3.5 14.3 1.0 OD2 A:ASP221 3.5 18.8 1.0 OD2 A:ASP225 4.0 14.1 1.0 CA A:ASP12 4.2 15.5 1.0 O A:SER184 4.2 16.2 1.0 N A:ASP12 4.2 14.1 1.0 OG1 A:THR14 4.2 16.8 1.0 CB A:ASP12 4.3 14.1 1.0 O A:HOH1379 4.3 25.2 1.0 N A:GLY13 4.3 15.2 1.0 CB A:ASP10 4.4 12.4 1.0 CB A:ASP221 4.4 15.8 1.0 CA A:GLY13 4.5 16.4 1.0 CL A:CL1272 4.5 15.0 1.0 O A:HOH1280 4.6 14.3 1.0 O A:HOH1288 4.6 18.1 1.0 CB A:GLN222 4.6 15.1 1.0 N A:GLN222 4.8 15.1 1.0 N A:ASP221 4.9 15.1 1.0 C A:MET11 4.9 13.6 1.0 N A:THR14 4.9 15.1 1.0 C A:GLY13 4.9 16.4 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Had-Like Phosphatase Yida From E. Coli


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 Had-Like Phosphatase Yida From E. Coli within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2273 b:12.6 occ:1.00 OD1 B:ASP221 2.1 15.0 1.0 O B:HOH2276 2.1 15.1 1.0 OD2 B:ASP10 2.2 16.5 1.0 O B:HOH2275 2.2 13.4 1.0 O B:HOH2274 2.2 14.8 1.0 O B:ASP12 2.2 14.7 1.0 CG B:ASP10 3.1 14.5 1.0 CG B:ASP221 3.1 12.7 1.0 C B:ASP12 3.4 13.2 1.0 OD1 B:ASP10 3.5 14.6 1.0 OD2 B:ASP221 3.5 16.2 1.0 OD2 B:ASP225 4.0 12.4 1.0 CA B:ASP12 4.2 12.4 1.0 N B:ASP12 4.2 13.7 1.0 OG1 B:THR14 4.2 14.5 1.0 O B:SER184 4.3 14.9 1.0 N B:GLY13 4.3 13.9 1.0 O B:HOH2339 4.3 26.0 1.0 CB B:ASP10 4.4 12.9 1.0 CB B:ASP12 4.4 13.3 1.0 CA B:GLY13 4.5 13.6 1.0 CB B:ASP221 4.5 13.5 1.0 CL B:CL2272 4.5 14.7 1.0 O B:HOH2278 4.6 14.6 1.0 CB B:GLN222 4.6 13.2 1.0 O B:HOH2330 4.6 19.8 1.0 N B:GLN222 4.8 12.0 1.0 N B:ASP221 4.8 13.0 1.0 C B:MET11 4.9 12.0 1.0 C B:GLY13 4.9 15.3 1.0 N B:THR14 4.9 12.9 1.0 CG B:ASP225 5.0 13.4 1.0

U.A.Ramagopal, S.C.Almo. Crystal Structure of Nysgrc Target T1436: A Hypothetical Protein Yida. To Be Published.