Magnesium in PDB 1l7m: High Resolution Liganded Structure of Phosphoserine Phosphatase (Pi Complex)

All present enzymatic activity of High Resolution Liganded Structure of Phosphoserine Phosphatase (Pi Complex):
3.1.3.3;

The structure of High Resolution Liganded Structure of Phosphoserine Phosphatase (Pi Complex), PDB code: 1l7m was solved by W.Wang, H.S.Cho, R.Kim, J.Jancarik, H.Yokota, H.H.Nguyen, I.V.Grigoriev, D.E.Wemmer, S.H.Kim, Berkeley Structural Genomics Center (Bsgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.00 / 1.48
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	69.073, 70.270, 90.924, 90.00, 90.00, 90.00
R / Rfree (%)	20.2 / 23.2

The binding sites of Magnesium atom in the High Resolution Liganded Structure of Phosphoserine Phosphatase (Pi Complex) (pdb code 1l7m). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the High Resolution Liganded Structure of Phosphoserine Phosphatase (Pi Complex), PDB code: 1l7m:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the High Resolution Liganded Structure of Phosphoserine Phosphatase (Pi Complex)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of High Resolution Liganded Structure of Phosphoserine Phosphatase (Pi Complex) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg721 b:12.5 occ:0.95 OD2 A:ASP167 2.3 17.9 1.0 OD1 A:ASP11 2.3 7.6 0.5 O A:ASP13 2.4 11.4 1.0 O2 A:PO4720 2.4 11.6 1.0 O A:HOH956 2.6 15.3 1.0 OD2 A:ASP11 2.9 13.8 0.5 CG A:ASP167 3.1 16.4 1.0 CG A:ASP11 3.1 7.5 0.5 OD1 A:ASP167 3.3 18.3 1.0 OD2 A:ASP11 3.3 8.3 0.5 OG A:SER14 3.4 11.5 0.5 C A:ASP13 3.5 10.2 1.0 P A:PO4720 3.9 10.8 1.0 O A:HOH873 4.0 21.2 1.0 CG A:ASP11 4.0 12.4 0.5 CB A:ASP13 4.1 10.9 1.0 CA A:ASP13 4.1 10.2 1.0 N A:ASP13 4.3 9.9 1.0 OE2 A:GLU20 4.3 17.7 1.0 O A:HOH831 4.3 12.6 1.0 CB A:SER14 4.3 12.3 0.5 OG1 A:THR15 4.4 13.8 1.0 SE A:MSE43 4.5 16.6 1.0 O3 A:PO4720 4.5 12.1 0.9 CB A:ASP11 4.5 7.5 0.5 CB A:ASP11 4.5 11.7 0.5 O4 A:PO4720 4.5 12.2 1.0 OD2 A:ASP171 4.5 11.9 1.0 N A:SER14 4.5 10.2 0.5 N A:SER14 4.5 11.4 0.5 CB A:ASP167 4.6 14.0 1.0 N A:GLY168 4.6 10.8 1.0 CB A:SER14 4.7 10.8 0.5 O1 A:PO4720 4.7 10.4 1.0 C A:ASP167 4.8 11.8 1.0 CA A:SER14 4.9 11.9 0.5 CA A:SER14 4.9 10.3 0.5 N A:THR15 4.9 11.2 1.0 OG A:SER14 4.9 13.0 0.5 N A:ASP167 4.9 11.0 1.0 C A:PHE12 5.0 9.9 1.0 CA A:ASP167 5.0 12.1 1.0

Magnesium binding site 2 out of 2 in the High Resolution Liganded Structure of Phosphoserine Phosphatase (Pi Complex)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of High Resolution Liganded Structure of Phosphoserine Phosphatase (Pi Complex) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg221 b:13.5 occ:0.97 OD2 B:ASP511 2.1 13.2 0.5 OD2 B:ASP667 2.3 17.2 1.0 O1 B:PO4220 2.4 10.9 1.0 O B:ASP513 2.4 11.4 1.0 OD2 B:ASP511 2.5 8.6 0.5 O B:HOH960 2.6 13.3 1.0 CG B:ASP511 3.1 12.9 0.5 CG B:ASP667 3.2 15.9 1.0 OD1 B:ASP511 3.4 13.0 0.5 OD1 B:ASP667 3.5 18.8 1.0 C B:ASP513 3.5 11.0 1.0 CG B:ASP511 3.7 9.4 0.5 O B:HOH984 3.8 21.0 1.0 P B:PO4220 3.9 10.5 1.0 CB B:ASP513 4.1 9.9 1.0 OE2 B:GLU520 4.2 20.1 1.0 CA B:ASP513 4.2 10.2 1.0 O B:HOH857 4.2 15.7 1.0 CB B:SER514 4.3 14.5 1.0 N B:ASP513 4.3 9.7 1.0 SE B:MSE543 4.4 14.5 1.0 CB B:ASP511 4.4 11.8 0.5 OD2 B:ASP671 4.4 10.2 1.0 CB B:ASP511 4.5 8.7 0.5 O2 B:PO4220 4.5 11.9 1.0 N B:GLY668 4.5 11.2 1.0 O4 B:PO4220 4.5 12.7 1.0 OG1 B:THR515 4.5 13.1 1.0 N B:SER514 4.6 12.1 1.0 OD1 B:ASP511 4.6 10.5 0.5 CB B:ASP667 4.6 14.2 1.0 O3 B:PO4220 4.8 11.2 1.0 OG B:SER514 4.8 17.5 1.0 C B:ASP667 4.8 12.0 1.0 CA B:SER514 4.8 13.2 1.0 N B:ASP667 4.9 10.9 1.0 N B:THR515 5.0 12.2 1.0 CA B:ASP667 5.0 12.2 1.0 CA B:GLY668 5.0 11.1 1.0

W.Wang, H.S.Cho, R.Kim, J.Jancarik, H.Yokota, H.H.Nguyen, I.V.Grigoriev, D.E.Wemmer, S.H.Kim. Structural Characterization of the Reaction Pathway in Phosphoserine Phosphatase: Crystallographic "Snapshots" of Intermediate States. J.Mol.Biol. V. 319 421 2002.
ISSN: ISSN 0022-2836
PubMed: 12051918
DOI: 10.1016/S0022-2836(02)00324-8