Magnesium in PDB 1j97: Phospho-Aspartyl Intermediate Analogue of Phosphoserine Phosphatase

All present enzymatic activity of Phospho-Aspartyl Intermediate Analogue of Phosphoserine Phosphatase:
3.1.3.3;

The structure of Phospho-Aspartyl Intermediate Analogue of Phosphoserine Phosphatase, PDB code: 1j97 was solved by H.Cho, W.Wang, R.Kim, H.Yokota, S.Damo, S.-H.Kim, D.Wemmer, S.Kustu, D.Yan, 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 / 1.50
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	68.836, 69.829, 91.625, 90.00, 90.00, 90.00
R / Rfree (%)	18.9 / 20.9

The structure of Phospho-Aspartyl Intermediate Analogue of Phosphoserine Phosphatase also contains other interesting chemical elements:

Fluorine

(F)

6 atoms

The binding sites of Magnesium atom in the Phospho-Aspartyl Intermediate Analogue of Phosphoserine Phosphatase (pdb code 1j97). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Phospho-Aspartyl Intermediate Analogue of Phosphoserine Phosphatase, PDB code: 1j97:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Phospho-Aspartyl Intermediate Analogue of Phosphoserine Phosphatase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Phospho-Aspartyl Intermediate Analogue of Phosphoserine Phosphatase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg220 b:9.1 occ:1.00 F2 A:BFD11 2.0 10.5 1.0 OD2 A:BFD11 2.1 8.7 1.0 O A:HOH828 2.1 8.6 1.0 O A:ASP13 2.1 10.3 1.0 OD1 A:ASP167 2.1 9.0 1.0 O A:HOH808 2.1 8.1 1.0 CG A:BFD11 3.0 9.5 1.0 CG A:ASP167 3.1 11.1 1.0 BE A:BFD11 3.1 9.9 1.0 C A:ASP13 3.3 10.4 1.0 OD1 A:BFD11 3.3 9.7 1.0 OD2 A:ASP167 3.4 11.2 1.0 CA A:ASP13 4.0 9.5 1.0 F1 A:BFD11 4.1 10.4 1.0 CB A:ASP13 4.1 10.1 1.0 OD2 A:ASP171 4.1 10.1 1.0 N A:ASP13 4.2 9.3 1.0 F3 A:BFD11 4.2 9.7 1.0 OG1 A:THR15 4.2 10.8 1.0 OE2 A:GLU20 4.3 12.4 1.0 CB A:SER14 4.3 11.7 1.0 CB A:BFD11 4.3 8.8 1.0 N A:SER14 4.3 9.5 1.0 O A:HOH817 4.3 10.7 1.0 CB A:ASP167 4.4 11.2 1.0 SD A:MET43 4.5 13.5 1.0 N A:GLY168 4.5 10.1 1.0 CA A:SER14 4.7 10.6 1.0 N A:THR15 4.7 8.8 1.0 N A:ASP167 4.7 10.6 1.0 OD1 A:ASN170 4.7 10.1 1.0 C A:PHE12 4.8 8.9 1.0 C A:SER14 4.8 10.4 1.0 CB A:THR15 5.0 10.4 1.0 CA A:ASP167 5.0 10.5 1.0

Magnesium binding site 2 out of 2 in the Phospho-Aspartyl Intermediate Analogue of Phosphoserine Phosphatase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Phospho-Aspartyl Intermediate Analogue of Phosphoserine Phosphatase within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg720 b:8.9 occ:1.00 F3 B:BFD511 2.0 8.8 1.0 OD2 B:BFD511 2.1 8.4 1.0 O B:HOH821 2.1 9.7 1.0 OD1 B:ASP667 2.1 8.6 1.0 O B:ASP513 2.1 9.2 1.0 O B:HOH809 2.1 8.0 1.0 CG B:BFD511 3.0 8.0 1.0 CG B:ASP667 3.1 9.2 1.0 BE B:BFD511 3.2 8.2 1.0 C B:ASP513 3.3 8.8 1.0 OD1 B:BFD511 3.3 7.7 1.0 OD2 B:ASP667 3.4 10.6 1.0 CA B:ASP513 4.0 8.6 1.0 N B:ASP513 4.1 8.1 1.0 CB B:ASP513 4.1 10.6 1.0 F1 B:BFD511 4.2 8.9 1.0 F2 B:BFD511 4.2 9.3 1.0 OG1 B:THR515 4.2 9.1 1.0 OD2 B:ASP671 4.2 8.7 1.0 OE2 B:GLU520 4.3 10.2 1.0 CB B:SER514 4.3 9.4 1.0 CB B:BFD511 4.3 7.4 1.0 N B:SER514 4.3 9.5 1.0 O B:HOH833 4.4 10.3 1.0 CB B:ASP667 4.5 9.4 1.0 SD B:MET543 4.5 12.2 1.0 N B:GLY668 4.5 8.7 1.0 N B:THR515 4.6 8.5 1.0 CA B:SER514 4.7 8.7 1.0 N B:ASP667 4.7 9.4 1.0 OD1 B:ASN670 4.7 8.5 1.0 C B:PHE512 4.8 8.2 1.0 C B:SER514 4.8 9.3 1.0 CB B:THR515 4.9 8.7 1.0

H.Cho, W.Wang, R.Kim, H.Yokota, S.Damo, S.-H.Kim, D.Wemmer, S.Kustu, D.Yan. Bef(3)(-) Acts As A Phosphate Analog in Proteins Phosphorylated on Aspartate: Structure of A Bef(3)(-) Complex with Phosphoserine Phosphatase. Proc.Natl.Acad.Sci.Usa V. 98 8525 2001.
ISSN: ISSN 0027-8424
PubMed: 11438683
DOI: 10.1073/PNAS.131213698