Magnesium in PDB 5m3u: The X-Ray Structure of Human V216F Phosphoglycerate Kinase 1 Mutant

All present enzymatic activity of The X-Ray Structure of Human V216F Phosphoglycerate Kinase 1 Mutant:
2.7.2.3;

The structure of The X-Ray Structure of Human V216F Phosphoglycerate Kinase 1 Mutant, PDB code: 5m3u was solved by A.Ilari, A.Fiorillo, A.Cipollone, M.Petrosino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.81
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	35.650, 106.031, 50.097, 90.00, 98.71, 90.00
R / Rfree (%)	19.2 / 24.2

The binding sites of Magnesium atom in the The X-Ray Structure of Human V216F Phosphoglycerate Kinase 1 Mutant (pdb code 5m3u). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the The X-Ray Structure of Human V216F Phosphoglycerate Kinase 1 Mutant, PDB code: 5m3u:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the The X-Ray Structure of Human V216F Phosphoglycerate Kinase 1 Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The X-Ray Structure of Human V216F Phosphoglycerate Kinase 1 Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:36.7 occ:1.00 O1A A:ADP501 2.0 33.9 1.0 O A:HOH601 2.0 38.9 1.0 O A:HOH728 2.3 45.2 1.0 OD2 A:ASP374 2.3 41.2 1.0 O2B A:ADP501 2.4 41.9 1.0 PA A:ADP501 3.4 31.3 1.0 CG A:ASP374 3.4 38.8 1.0 PB A:ADP501 3.7 41.4 1.0 O3A A:ADP501 3.8 33.2 1.0 O A:HOH703 3.8 45.2 1.0 O5' A:ADP501 4.2 28.4 1.0 CB A:ASP374 4.2 38.6 1.0 OD1 A:ASP374 4.3 38.9 1.0 O A:HOH721 4.3 32.5 1.0 C5' A:ADP501 4.3 24.9 1.0 O2A A:ADP501 4.5 36.3 1.0 N A:ASP374 4.5 40.9 1.0 O3B A:ADP501 4.6 39.5 1.0 O1B A:ADP501 4.8 42.0 1.0

Magnesium binding site 2 out of 3 in the The X-Ray Structure of Human V216F Phosphoglycerate Kinase 1 Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The X-Ray Structure of Human V216F Phosphoglycerate Kinase 1 Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg504 b:42.3 occ:1.00 O A:HOH664 2.0 34.0 1.0 O A:LEU413 2.6 24.3 1.0 NZ A:LYS5 2.8 44.1 1.0 O A:ASP411 2.9 24.3 1.0 OD1 A:ASN415 3.3 35.0 1.0 CG A:ASN415 3.7 41.0 1.0 C A:LEU413 3.9 26.9 1.0 ND2 A:ASN415 3.9 44.9 1.0 C A:ASP411 4.0 23.3 1.0 N A:ASN415 4.2 30.1 1.0 CE A:LYS5 4.3 40.7 1.0 C A:SER414 4.4 30.4 1.0 CB A:ASN415 4.5 37.5 1.0 CA A:SER414 4.6 28.0 1.0 O A:HOH686 4.6 37.1 1.0 C A:ALA412 4.7 23.3 1.0 N A:SER414 4.7 25.8 1.0 N A:LEU413 4.7 23.4 1.0 CA A:ASN415 4.8 36.4 1.0 O A:ALA412 4.9 22.4 1.0 CD A:LYS5 4.9 36.2 1.0 CA A:ASP411 4.9 22.9 1.0 CA A:LEU413 4.9 23.6 1.0 N A:ALA412 4.9 20.1 1.0 O A:SER414 5.0 28.1 1.0

Magnesium binding site 3 out of 3 in the The X-Ray Structure of Human V216F Phosphoglycerate Kinase 1 Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The X-Ray Structure of Human V216F Phosphoglycerate Kinase 1 Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg505 b:46.7 occ:1.00 O2 A:3PG502 2.2 69.6 1.0 C1 A:3PG502 3.4 62.7 1.0 N A:GLY395 3.5 28.2 1.0 O A:HOH656 3.6 32.2 1.0 CA A:GLY395 3.7 30.0 1.0 N A:GLY396 3.9 24.3 1.0 O1 A:3PG502 4.2 62.5 1.0 C A:GLY395 4.3 28.0 1.0 C2 A:3PG502 4.5 59.0 1.0 C A:GLY394 4.7 25.5 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