Manganese in PDB 2vgb: Human Erythrocyte Pyruvate Kinase

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

The structure of Human Erythrocyte Pyruvate Kinase, PDB code: 2vgb was solved by G.Valentini, L.Chiarelli, R.Fortin, M.Dolzan, A.Galizzi, D.J.Abraham, C.Wang, P.Bianchi, A.Zanella, A.Mattevi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.73
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	74.413, 172.058, 85.512, 90.00, 92.46, 90.00
R / Rfree (%)	22.7 / 27.1

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

Potassium

(K)

4 atoms

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

Manganese binding site 1 out of 4 in the Human Erythrocyte Pyruvate Kinase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Human Erythrocyte Pyruvate Kinase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn583 b:70.9 occ:1.00 OE2 A:GLU315 1.6 41.6 1.0 OD2 A:ASP339 1.9 40.5 1.0 O1P A:PGA581 2.1 0.1 1.0 O1 A:PGA581 2.3 0.4 1.0 O4P A:PGA581 2.4 0.5 1.0 P A:PGA581 2.7 0.9 1.0 CD A:GLU315 2.9 42.5 1.0 C1 A:PGA581 3.0 0.8 1.0 C2 A:PGA581 3.0 0.7 1.0 CG A:ASP339 3.1 40.2 1.0 O2P A:PGA581 3.6 0.3 1.0 OE1 A:GLU315 3.6 43.1 1.0 CB A:ASP339 3.8 39.3 1.0 O3P A:PGA581 3.9 0.9 1.0 CG A:GLU315 3.9 39.5 1.0 OD1 A:ASP339 4.1 35.8 1.0 O2 A:PGA581 4.2 0.7 1.0 CZ A:PHE287 4.4 41.0 1.0 N A:ASP339 4.4 38.8 1.0 CE A:LYS313 4.5 36.9 1.0 CE1 A:PHE287 4.6 40.6 1.0 NZ A:LYS313 4.6 34.1 1.0 CA A:ASP339 4.7 39.1 1.0 CB A:ALA336 4.8 38.5 1.0 CB A:GLU315 4.8 38.8 1.0

Manganese binding site 2 out of 4 in the Human Erythrocyte Pyruvate Kinase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Human Erythrocyte Pyruvate Kinase within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn587 b:64.3 occ:1.00 OE2 B:GLU315 1.8 41.2 1.0 OD2 B:ASP339 1.8 40.9 1.0 O1 B:PGA581 2.1 0.6 1.0 O1P B:PGA581 2.2 0.6 1.0 O4P B:PGA581 2.5 0.6 1.0 C1 B:PGA581 2.9 0.2 1.0 P B:PGA581 2.9 0.9 1.0 CD B:GLU315 3.0 42.5 1.0 CG B:ASP339 3.0 40.3 1.0 C2 B:PGA581 3.0 0.3 1.0 OE1 B:GLU315 3.8 42.9 1.0 CB B:ASP339 3.8 39.2 1.0 O2P B:PGA581 3.9 0.5 1.0 OD1 B:ASP339 4.0 36.0 1.0 O3P B:PGA581 4.0 0.5 1.0 O2 B:PGA581 4.1 0.3 1.0 CG B:GLU315 4.1 39.7 1.0 N B:ASP339 4.2 38.7 1.0 CZ B:PHE287 4.4 41.0 1.0 CA B:ASP339 4.6 39.1 1.0 CE1 B:PHE287 4.6 40.2 1.0 CE B:LYS313 4.7 36.7 1.0 NZ B:LYS313 4.7 34.3 1.0 CB B:ALA336 4.9 38.6 1.0 CB B:GLU315 5.0 38.8 1.0

Manganese binding site 3 out of 4 in the Human Erythrocyte Pyruvate Kinase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Human Erythrocyte Pyruvate Kinase within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn591 b:58.1 occ:1.00 OE2 C:GLU315 1.6 41.8 1.0 OD2 C:ASP339 1.7 40.3 1.0 O1 C:PGA581 2.1 0.4 1.0 O4P C:PGA581 2.3 0.9 1.0 O1P C:PGA581 2.3 0.7 1.0 P C:PGA581 2.8 0.9 1.0 CD C:GLU315 2.8 42.6 1.0 CG C:ASP339 3.0 40.3 1.0 C1 C:PGA581 3.0 0.7 1.0 C2 C:PGA581 3.2 0.5 1.0 OE1 C:GLU315 3.5 42.5 1.0 O2P C:PGA581 3.7 0.8 1.0 CB C:ASP339 3.9 39.2 1.0 OD1 C:ASP339 4.0 36.0 1.0 CG C:GLU315 4.0 39.7 1.0 O3P C:PGA581 4.1 0.8 1.0 CZ C:PHE287 4.1 40.8 1.0 O2 C:PGA581 4.2 0.7 1.0 CE1 C:PHE287 4.4 40.3 1.0 N C:ASP339 4.4 38.8 1.0 CE C:LYS313 4.5 36.8 1.0 NZ C:LYS313 4.6 33.9 1.0 CA C:ASP339 4.8 39.2 1.0 CB C:GLU315 4.8 38.9 1.0 CB C:ALA336 4.9 38.4 1.0 CE2 C:PHE287 4.9 41.9 1.0

Manganese binding site 4 out of 4 in the Human Erythrocyte Pyruvate Kinase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Human Erythrocyte Pyruvate Kinase within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn595 b:59.6 occ:1.00 OE2 D:GLU315 1.5 41.7 1.0 OD2 D:ASP339 1.8 40.6 1.0 O1 D:PGA581 2.0 0.1 1.0 O1P D:PGA581 2.4 0.5 1.0 O4P D:PGA581 2.5 0.0 1.0 CD D:GLU315 2.8 42.5 1.0 C1 D:PGA581 2.9 0.5 1.0 P D:PGA581 3.0 0.8 1.0 CG D:ASP339 3.1 40.3 1.0 C2 D:PGA581 3.2 0.4 1.0 OE1 D:GLU315 3.5 42.9 1.0 O2P D:PGA581 3.8 0.6 1.0 CG D:GLU315 3.9 39.6 1.0 CB D:ASP339 4.0 39.2 1.0 OD1 D:ASP339 4.0 35.9 1.0 O2 D:PGA581 4.1 0.4 1.0 CZ D:PHE287 4.2 40.5 1.0 O3P D:PGA581 4.3 0.3 1.0 CE D:LYS313 4.4 36.7 1.0 CE1 D:PHE287 4.4 40.1 1.0 NZ D:LYS313 4.5 33.7 1.0 N D:ASP339 4.6 39.0 1.0 CB D:ALA336 4.8 38.3 1.0 CB D:GLU315 4.8 38.9 1.0 O D:HOH2017 4.9 34.4 1.0 CA D:ASP339 4.9 39.0 1.0 CE2 D:PHE287 5.0 41.9 1.0

G.Valentini, L.R.Chiarelli, R.Fortin, M.Dolzan, A.Galizzi, D.J.Abraham, C.Wang, P.Bianchi, A.Zanella, A.Mattevi. Structure and Function of Human Erythrocyte Pyruvate Kinase. Molecular Basis of Nonspherocytic Hemolytic Anemia. J.Biol.Chem. V. 277 23807 2002.
ISSN: ISSN 0021-9258
PubMed: 11960989
DOI: 10.1074/JBC.M202107200