Magnesium in PDB 1t5a: Human Pyruvate Kinase M2

All present enzymatic activity of Human Pyruvate Kinase M2:
2.7.1.40;

The structure of Human Pyruvate Kinase M2, PDB code: 1t5a was solved by J.D.Dombrauckas, B.D.Santarsiero, A.D.Mesecar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	108.209, 145.006, 159.260, 90.00, 90.00, 90.00
R / Rfree (%)	23.1 / 27.8

The structure of Human Pyruvate Kinase M2 also contains other interesting chemical elements:

Potassium

(K)

4 atoms

The binding sites of Magnesium atom in the Human Pyruvate Kinase M2 (pdb code 1t5a). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Human Pyruvate Kinase M2, PDB code: 1t5a:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Human Pyruvate Kinase M2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human Pyruvate Kinase M2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:66.4 occ:1.00 OD2 A:ASP296 2.4 87.5 1.0 O4 A:OXL533 2.4 66.4 1.0 OE2 A:GLU272 2.4 49.7 1.0 O1 A:OXL533 2.6 66.4 1.0 O A:HOH729 2.6 66.4 1.0 C2 A:OXL533 3.2 66.4 1.0 C1 A:OXL533 3.3 66.4 1.0 CG A:ASP296 3.6 87.5 1.0 CD A:GLU272 3.6 49.7 1.0 O A:HOH734 3.7 66.4 1.0 NZ A:LYS270 4.0 62.0 1.0 OD1 A:ASP296 4.4 87.5 1.0 OE1 A:GLU272 4.4 49.7 1.0 O2 A:OXL533 4.4 66.4 1.0 K A:K701 4.4 66.4 1.0 CB A:ASP296 4.5 87.5 1.0 O3 A:OXL533 4.5 66.4 1.0 CG A:GLU272 4.6 49.7 1.0 CE1 A:PHE244 4.8 65.6 1.0 CZ A:PHE244 4.8 65.6 1.0 N A:ASP296 5.0 98.6 1.0

Magnesium binding site 2 out of 4 in the Human Pyruvate Kinase M2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human Pyruvate Kinase M2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg602 b:66.4 occ:1.00 OD2 B:ASP296 2.4 65.8 1.0 OE2 B:GLU272 2.4 63.5 1.0 O4 B:OXL533 2.5 66.4 1.0 O1 B:OXL533 2.6 66.4 1.0 C2 B:OXL533 3.2 66.4 1.0 C1 B:OXL533 3.3 66.4 1.0 O B:HOH723 3.6 66.4 1.0 CG B:ASP296 3.6 65.8 1.0 CD B:GLU272 3.7 63.5 1.0 NZ B:LYS270 4.0 77.3 1.0 OE1 B:GLU272 4.3 63.5 1.0 O2 B:OXL533 4.4 66.4 1.0 OD1 B:ASP296 4.4 65.8 1.0 O3 B:OXL533 4.5 66.4 1.0 CB B:ASP296 4.6 65.8 1.0 CE1 B:PHE244 4.6 72.6 1.0 K B:K702 4.6 66.4 1.0 CZ B:PHE244 4.7 72.6 1.0 CG B:GLU272 4.7 63.5 1.0

Magnesium binding site 3 out of 4 in the Human Pyruvate Kinase M2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Human Pyruvate Kinase M2 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg603 b:66.4 occ:1.00 OE2 C:GLU272 2.1 66.5 1.0 OD2 C:ASP296 2.4 69.3 1.0 O2 C:OXL533 2.5 66.4 1.0 O3 C:OXL533 2.7 66.4 1.0 CD C:GLU272 3.3 66.5 1.0 C2 C:OXL533 3.3 66.4 1.0 C1 C:OXL533 3.4 66.4 1.0 O C:HOH725 3.6 66.4 1.0 NZ C:LYS270 3.7 48.4 1.0 CG C:ASP296 3.7 69.3 1.0 OE1 C:GLU272 3.8 66.5 1.0 CE1 C:PHE244 4.1 67.3 1.0 CZ C:PHE244 4.3 67.3 1.0 CG C:GLU272 4.5 66.5 1.0 OD1 C:ASP296 4.5 69.3 1.0 O4 C:OXL533 4.5 66.4 1.0 CB C:ASP296 4.6 69.3 1.0 O1 C:OXL533 4.6 66.4 1.0 CE C:LYS270 4.7 48.4 1.0 OG C:SER243 4.7 35.3 1.0 K C:K703 4.7 66.4 1.0 CD1 C:PHE244 5.0 67.3 1.0

Magnesium binding site 4 out of 4 in the Human Pyruvate Kinase M2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Human Pyruvate Kinase M2 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg604 b:66.4 occ:1.00 O1 D:OXL533 2.5 66.4 1.0 OD2 D:ASP296 2.6 81.9 1.0 O4 D:OXL533 2.6 66.4 1.0 OE2 D:GLU272 2.9 59.8 1.0 C1 D:OXL533 3.2 66.4 1.0 O D:HOH719 3.2 66.4 1.0 C2 D:OXL533 3.3 66.4 1.0 CG D:ASP296 3.8 81.9 1.0 K D:K704 4.1 66.4 1.0 CD D:GLU272 4.1 59.8 1.0 NZ D:LYS270 4.2 46.1 1.0 O3 D:OXL533 4.3 66.4 1.0 O2 D:OXL533 4.4 66.4 1.0 OD1 D:ASP296 4.5 81.9 1.0 OE1 D:GLU272 4.8 59.8 1.0 CB D:ASP296 4.8 81.9 1.0 CE1 D:PHE244 4.9 89.2 1.0 CZ D:PHE244 5.0 89.2 1.0

J.D.Dombrauckas, B.D.Santarsiero, A.D.Mesecar. Structural Basis For Tumor Pyruvate Kinase M2 Allosteric Regulation and Catalysis. Biochemistry V. 44 9417 2005.
ISSN: ISSN 0006-2960
PubMed: 15996096
DOI: 10.1021/BI0474923