Magnesium in PDB 4yj5: Crystal Structure of PKM2 Mutant

All present enzymatic activity of Crystal Structure of PKM2 Mutant:
2.7.1.40;

The structure of Crystal Structure of PKM2 Mutant, PDB code: 4yj5 was solved by J.-S.Liu, C.-W.Wu, W.-C.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.41
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	73.217, 140.887, 108.720, 90.00, 93.97, 90.00
R / Rfree (%)	14.4 / 21.7

The binding sites of Magnesium atom in the Crystal Structure of PKM2 Mutant (pdb code 4yj5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of PKM2 Mutant, PDB code: 4yj5:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of PKM2 Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of PKM2 Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:15.1 occ:1.00 OD1 A:ASP113 2.5 30.3 1.0 O A:THR114 2.6 26.4 1.0 OD1 A:ASN75 2.6 28.3 1.0 O A:HOH729 2.7 26.3 1.0 O A:HOH766 2.8 33.4 1.0 OG A:SER77 2.8 28.9 1.0 CG A:ASN75 3.6 26.7 1.0 CG A:ASP113 3.6 31.5 1.0 C A:THR114 3.7 27.1 1.0 OG A:SER243 3.8 27.5 1.0 CB A:SER77 3.8 31.6 1.0 NZ A:LYS270 3.9 21.7 1.0 O A:ASP113 4.0 28.8 1.0 ND2 A:ASN75 4.0 26.8 1.0 CA A:LYS115 4.2 26.3 1.0 OE1 A:GLU118 4.2 35.8 1.0 N A:SER77 4.2 28.9 1.0 C A:ASP113 4.3 26.1 1.0 N A:LYS115 4.3 26.1 1.0 NH2 A:ARG73 4.3 24.4 1.0 OD2 A:ASP113 4.4 34.2 1.0 CB A:ASP113 4.5 27.3 1.0 N A:THR114 4.5 25.1 1.0 O A:LYS115 4.5 23.4 1.0 CA A:SER77 4.5 32.8 1.0 CA A:THR114 4.7 25.4 1.0 C A:LYS115 4.7 27.0 1.0 N A:PHE76 4.8 26.5 1.0 CB A:ASN75 4.8 24.7 1.0 CB A:SER243 4.9 26.7 1.0 CA A:ASN75 5.0 28.0 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of PKM2 Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of PKM2 Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg602 b:18.3 occ:1.00 OD1 B:ASP113 2.6 32.1 1.0 O B:THR114 2.6 32.9 1.0 OG B:SER77 2.7 28.9 1.0 OD1 B:ASN75 2.7 26.5 1.0 O B:HOH718 3.0 37.9 1.0 C B:THR114 3.7 30.5 1.0 CG B:ASP113 3.7 32.7 1.0 CG B:ASN75 3.8 25.9 1.0 CB B:SER77 3.8 29.2 1.0 OG B:SER243 3.8 25.4 1.0 NZ B:LYS270 3.8 33.8 1.0 O B:ASP113 4.0 23.7 1.0 O B:HOH793 4.1 55.5 1.0 CA B:LYS115 4.2 29.9 1.0 N B:LYS115 4.2 27.5 1.0 N B:SER77 4.2 31.5 1.0 NH2 B:ARG73 4.2 24.1 1.0 ND2 B:ASN75 4.3 27.0 1.0 C B:ASP113 4.3 24.7 1.0 OD2 B:ASP113 4.5 36.8 1.0 CA B:SER77 4.5 33.3 1.0 O B:LYS115 4.5 31.4 1.0 OE1 B:GLU118 4.5 43.8 1.0 CB B:ASP113 4.6 28.0 1.0 N B:THR114 4.7 25.0 1.0 C B:LYS115 4.7 29.8 1.0 CA B:THR114 4.8 28.0 1.0 N B:PHE76 4.9 28.5 1.0 CB B:SER243 4.9 22.7 1.0 CB B:ASN75 5.0 22.8 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of PKM2 Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of PKM2 Mutant within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg602 b:20.5 occ:1.00 OD1 C:ASP113 2.5 35.1 1.0 OD1 C:ASN75 2.6 30.3 1.0 O C:THR114 2.7 35.9 1.0 OG C:SER77 2.8 32.7 1.0 O C:HOH737 3.0 41.5 1.0 CG C:ASN75 3.5 31.8 1.0 C C:THR114 3.6 36.7 1.0 CG C:ASP113 3.7 35.4 1.0 O C:HOH745 3.8 39.5 1.0 NZ C:LYS270 3.8 27.7 1.0 OG C:SER243 3.9 39.2 1.0 ND2 C:ASN75 3.9 26.8 1.0 CB C:SER77 4.0 31.6 1.0 O C:ASP113 4.0 35.4 1.0 CA C:LYS115 4.2 36.6 1.0 N C:LYS115 4.2 37.6 1.0 N C:SER77 4.2 32.9 1.0 OE1 C:GLU118 4.2 47.0 1.0 C C:ASP113 4.3 30.9 1.0 O C:HOH723 4.3 32.1 1.0 NH2 C:ARG73 4.4 23.4 1.0 O C:LYS115 4.5 34.5 1.0 N C:THR114 4.5 30.8 1.0 OD2 C:ASP113 4.5 37.1 1.0 CB C:ASP113 4.5 27.1 1.0 CA C:THR114 4.7 33.1 1.0 CA C:SER77 4.7 29.9 1.0 C C:LYS115 4.7 35.6 1.0 CB C:ASN75 4.7 28.8 1.0 N C:PHE76 4.8 30.4 1.0 CB C:SER243 5.0 36.0 1.0 CA C:ASP113 5.0 28.6 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of PKM2 Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of PKM2 Mutant within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg602 b:39.8 occ:1.00 OD1 D:ASP113 2.4 40.1 1.0 OD1 D:ASN75 2.4 38.8 1.0 O D:THR114 2.5 39.2 1.0 OG D:SER77 3.0 55.8 1.0 OE1 D:GLU118 3.3 89.2 1.0 CG D:ASN75 3.5 36.9 1.0 CG D:ASP113 3.5 39.5 1.0 OG D:SER243 3.5 37.5 1.0 C D:THR114 3.6 39.9 1.0 O D:ASP113 3.7 29.4 1.0 CB D:SER77 3.9 53.0 1.0 ND2 D:ASN75 3.9 39.0 1.0 C D:ASP113 4.0 30.0 1.0 NZ D:LYS270 4.1 32.7 1.0 N D:SER77 4.2 46.4 1.0 OD2 D:ASP113 4.3 39.6 1.0 CB D:ASP113 4.3 31.2 1.0 N D:THR114 4.4 31.9 1.0 NH2 D:ARG73 4.4 27.6 1.0 CA D:LYS115 4.4 40.6 1.0 N D:LYS115 4.5 39.6 1.0 CD D:GLU118 4.5 99.1 1.0 CA D:THR114 4.6 37.2 1.0 CA D:SER77 4.6 54.2 1.0 NH2 D:ARG120 4.6 44.4 1.0 N D:PHE76 4.7 39.8 1.0 CB D:ASN75 4.8 33.9 1.0 CA D:ASP113 4.8 31.4 1.0 CB D:SER243 4.9 36.1 1.0 C D:PHE76 4.9 43.9 1.0 CA D:ASN75 5.0 32.3 1.0

T.J.Chen, H.J.Wang, J.S.Liu, H.H.Cheng, S.C.Hsu, M.C.Wu, C.H.Lu, Y.F.Wu, J.W.Wu, Y.Y.Liu, H.J.Kung, W.C.Wang. Mutations in the PKM2 Exon-10 Region Are Associated with Reduced Allostery and Increased Nuclear Translocation Commun Biol V. 2 2019.
ISSN: ESSN 2399-3642
DOI: 10.1038/S42003-019-0343-4