Magnesium in PDB 5m1r: X-Ray Structure of Human G166D Pgk-1 Mutant

All present enzymatic activity of X-Ray Structure of Human G166D Pgk-1 Mutant:
2.7.2.3;

The structure of X-Ray Structure of Human G166D Pgk-1 Mutant, PDB code: 5m1r was solved by A.Ilari, A.Cipollone, A.Fiorillo, M.Petrosino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	52.78 / 1.64
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	35.721, 105.570, 50.002, 90.00, 97.76, 90.00
R / Rfree (%)	16.4 / 20.1

The binding sites of Magnesium atom in the X-Ray Structure of Human G166D Pgk-1 Mutant (pdb code 5m1r). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the X-Ray Structure of Human G166D Pgk-1 Mutant, PDB code: 5m1r:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the X-Ray Structure of Human G166D Pgk-1 Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of X-Ray Structure of Human G166D Pgk-1 Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:43.3 occ:1.00 O A:HOH608 1.9 47.4 1.0 O1B A:ADP501 2.0 21.0 0.5 O A:GLY372 2.5 25.3 1.0 OG1 A:THR375 2.7 24.9 1.0 PB A:ADP501 3.0 20.6 0.5 N A:THR375 3.3 16.8 1.0 CB A:THR375 3.5 21.2 1.0 O3B A:ADP501 3.5 21.1 0.5 O2B A:ADP501 3.6 18.9 0.5 ND2 A:ASN336 3.6 26.9 1.0 N A:ASP374 3.6 18.8 1.0 C A:GLY372 3.7 23.8 1.0 O A:GLY371 3.8 22.4 1.0 CA A:THR375 4.0 18.1 1.0 N A:GLY337 4.0 15.7 1.0 CG A:ASN336 4.0 25.1 1.0 C A:GLY373 4.0 20.9 1.0 C A:GLY371 4.0 20.9 1.0 OD1 A:ASN336 4.1 24.6 1.0 O3A A:ADP501 4.3 21.1 0.5 C A:ASP374 4.3 17.3 1.0 CA A:GLY373 4.4 21.9 1.0 CA A:ASP374 4.4 18.8 1.0 CA A:ASN336 4.4 15.7 1.0 N A:GLY372 4.4 22.6 1.0 N A:GLY373 4.5 24.2 1.0 C A:ASN336 4.6 15.8 1.0 CA A:GLY371 4.6 20.0 1.0 CA A:GLY337 4.6 15.9 1.0 CA A:GLY372 4.7 23.4 1.0 O A:GLY373 4.7 19.9 1.0 N A:ALA376 4.7 16.2 1.0 CG2 A:THR375 4.8 22.1 1.0 CB A:ASN336 4.8 19.6 1.0 CB A:ASP374 4.9 20.8 1.0 C A:THR375 4.9 16.8 1.0

Magnesium binding site 2 out of 2 in the X-Ray Structure of Human G166D Pgk-1 Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of X-Ray Structure of Human G166D Pgk-1 Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:46.5 occ:1.00 O A:HOH605 2.1 30.6 1.0 O A:HOH810 2.5 22.0 1.0 O A:HOH722 3.1 29.0 1.0 CA A:ALA151 3.4 13.6 1.0 N A:ALA151 3.4 13.7 1.0 C A:ARG150 3.6 12.7 1.0 O A:ARG150 3.7 13.6 1.0 OE2 A:GLU147 3.8 21.7 0.5 OG A:SER154 3.8 14.5 1.0 CB A:ASN179 3.8 21.5 1.0 CB A:ALA151 3.8 13.9 1.0 CB A:ARG150 3.9 11.7 1.0 O A:GLY177 4.0 17.6 1.0 OE1 A:GLU147 4.3 23.6 0.5 CD A:GLU147 4.4 20.9 0.5 ND2 A:ASN179 4.4 28.8 1.0 CA A:ARG150 4.4 12.0 1.0 O A:HOH734 4.4 35.1 1.0 O A:GLU147 4.4 15.5 1.0 CB A:SER154 4.5 13.9 1.0 CG A:ASN179 4.6 25.7 1.0 N A:ASN179 4.7 17.6 1.0 O A:HOH696 4.7 20.8 1.0 C A:ALA151 4.7 14.2 1.0 CA A:ASN179 4.9 19.8 1.0

A.Fiorillo, M.Petrosino, A.Ilari, A.Pasquo, A.Cipollone, M.Maggi, R.Chiaraluce, V.Consalvi. The Phosphoglycerate Kinase 1 Variants Found in Carcinoma Cells Display Different Catalytic Activity and Conformational Stability Compared to the Native Enzyme. Plos One V. 13 99191 2018.
ISSN: ESSN 1932-6203
PubMed: 29995887
DOI: 10.1371/JOURNAL.PONE.0199191