Potassium in PDB 3hqn: Apo Crystal Structure of Leishmania Mexicana(Lmpyk)Pyruvate Kinase

All present enzymatic activity of Apo Crystal Structure of Leishmania Mexicana(Lmpyk)Pyruvate Kinase:
2.7.1.40;

The structure of Apo Crystal Structure of Leishmania Mexicana(Lmpyk)Pyruvate Kinase, PDB code: 3hqn was solved by H.P.Morgan, M.D.Walkinshaw, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.32 / 2.00
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	120.579, 167.333, 132.199, 90.00, 90.00, 90.00
R / Rfree (%)	16.9 / 20.9

The binding sites of Potassium atom in the Apo Crystal Structure of Leishmania Mexicana(Lmpyk)Pyruvate Kinase (pdb code 3hqn). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 4 binding sites of Potassium where determined in the Apo Crystal Structure of Leishmania Mexicana(Lmpyk)Pyruvate Kinase, PDB code: 3hqn:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in the Apo Crystal Structure of Leishmania Mexicana(Lmpyk)Pyruvate Kinase


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Apo Crystal Structure of Leishmania Mexicana(Lmpyk)Pyruvate Kinase within 5.0Å range: probe atom residue distance (Å) B Occ D:K502 b:43.4 occ:0.85 O D:GLN354 2.7 20.1 1.0 O D:LEU357 2.7 25.8 1.0 O D:HOH872 2.7 48.8 1.0 OE1 D:GLU359 2.9 42.7 1.0 OE2 D:GLU359 3.1 42.4 1.0 CD D:GLU359 3.3 40.0 1.0 O D:SER355 3.7 27.1 1.0 O D:HOH858 3.7 44.1 1.0 C D:GLN354 3.8 22.5 1.0 C D:LEU357 3.8 24.6 1.0 C D:SER355 3.9 23.9 1.0 N D:LEU357 4.0 22.3 1.0 CA D:SER355 4.1 24.3 1.0 CA D:LEU357 4.4 25.6 1.0 N D:SER355 4.5 20.1 1.0 N D:ALA356 4.6 20.6 1.0 C D:ALA356 4.6 22.9 1.0 CB D:LEU357 4.7 24.8 1.0 CG D:GLU359 4.8 26.4 1.0 NE2 D:HIS5 4.8 26.9 1.0 N D:ASN358 4.9 22.0 1.0 CG D:GLN354 4.9 24.1 1.0

Potassium binding site 2 out of 4 in the Apo Crystal Structure of Leishmania Mexicana(Lmpyk)Pyruvate Kinase


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Apo Crystal Structure of Leishmania Mexicana(Lmpyk)Pyruvate Kinase within 5.0Å range: probe atom residue distance (Å) B Occ D:K503 b:50.3 occ:0.92 OD1 D:ASP83 2.8 22.4 1.0 OD1 D:ASN51 2.8 21.9 1.0 O D:THR84 2.8 18.9 1.0 OG D:SER53 2.9 24.3 1.0 O3 D:GOL499 3.0 47.8 1.0 C3 D:GOL499 3.0 52.6 1.0 O D:HOH873 3.1 46.9 1.0 NZ D:LYS238 3.6 27.8 1.0 O D:ASP83 3.6 18.8 1.0 C D:THR84 3.7 19.4 1.0 CG D:ASP83 3.7 24.9 1.0 CG D:ASN51 3.8 21.9 1.0 OG D:SER211 4.0 26.3 1.0 N D:SER53 4.0 23.9 1.0 C D:ASP83 4.0 18.3 1.0 CB D:SER53 4.0 24.2 1.0 NH2 D:ARG49 4.1 23.6 1.0 CA D:LYS85 4.2 19.9 1.0 N D:LYS85 4.2 19.4 1.0 O D:HOH766 4.3 47.9 1.0 CB D:ASP83 4.4 18.6 1.0 N D:THR84 4.4 18.2 1.0 ND2 D:ASN51 4.5 24.9 1.0 C2 D:GOL499 4.5 55.9 1.0 OD2 D:ASP83 4.5 25.8 1.0 CA D:SER53 4.5 24.9 1.0 N D:PHE52 4.6 22.3 1.0 CA D:THR84 4.6 19.3 1.0 O D:LYS85 4.7 21.4 1.0 CA D:ASN51 4.8 20.5 1.0 C D:LYS85 4.8 19.3 1.0 CB D:ASN51 4.8 18.7 1.0 CA D:ASP83 4.8 18.2 1.0 C D:ASN51 4.9 21.1 1.0 C D:PHE52 5.0 22.3 1.0

Potassium binding site 3 out of 4 in the Apo Crystal Structure of Leishmania Mexicana(Lmpyk)Pyruvate Kinase


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Apo Crystal Structure of Leishmania Mexicana(Lmpyk)Pyruvate Kinase within 5.0Å range: probe atom residue distance (Å) B Occ A:K501 b:40.2 occ:0.86 O A:GLN354 2.7 16.9 1.0 OE1 A:GLU359 2.7 27.8 0.5 O A:LEU357 2.8 23.3 1.0 O A:HOH681 2.8 43.5 1.0 O A:HOH797 2.9 36.1 1.0 OE2 A:GLU359 2.9 25.8 0.5 CD A:GLU359 3.2 26.2 0.5 O A:HOH597 3.5 32.7 1.0 C A:GLN354 3.8 19.9 1.0 O A:SER355 3.9 24.1 1.0 C A:LEU357 3.9 20.9 1.0 C A:SER355 4.0 21.6 1.0 CA A:SER355 4.0 20.4 0.5 N A:LEU357 4.1 20.6 1.0 CA A:SER355 4.1 21.7 0.5 N A:SER355 4.4 19.4 1.0 CA A:LEU357 4.5 20.0 1.0 N A:ALA356 4.5 19.3 1.0 C A:ALA356 4.6 20.9 1.0 CB A:LEU357 4.6 19.0 1.0 CG A:GLU359 4.6 20.3 0.5 CG A:GLN354 4.8 23.2 1.0 O A:HOH748 4.8 52.1 1.0 NE2 A:HIS5 4.9 21.2 1.0 CG A:GLU359 4.9 22.2 0.5 N A:ASN358 4.9 20.8 1.0 CA A:ALA356 5.0 20.5 1.0

Potassium binding site 4 out of 4 in the Apo Crystal Structure of Leishmania Mexicana(Lmpyk)Pyruvate Kinase


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Apo Crystal Structure of Leishmania Mexicana(Lmpyk)Pyruvate Kinase within 5.0Å range: probe atom residue distance (Å) B Occ A:K502 b:44.6 occ:0.90 OD1 A:ASN51 2.7 25.5 1.0 O A:HOH678 2.8 27.8 1.0 OD1 A:ASP83 2.8 25.5 1.0 O A:THR84 2.9 19.6 1.0 OG A:SER53 2.9 23.8 1.0 O A:ASP83 3.7 20.9 1.0 CG A:ASP83 3.7 25.6 1.0 C A:THR84 3.7 22.8 1.0 CG A:ASN51 3.7 22.7 1.0 NZ A:LYS238 3.8 27.1 1.0 CB A:SER53 3.9 21.0 1.0 OG A:SER211 4.0 28.6 1.0 N A:SER53 4.0 20.6 1.0 NH2 A:ARG49 4.1 26.4 1.0 C A:ASP83 4.1 20.3 1.0 ND2 A:ASN51 4.3 23.8 1.0 CA A:LYS85 4.3 23.1 1.0 N A:LYS85 4.3 22.3 1.0 CB A:ASP83 4.4 18.2 1.0 OD2 A:ASP83 4.4 26.7 1.0 N A:THR84 4.5 21.5 1.0 CA A:SER53 4.5 21.9 1.0 N A:PHE52 4.6 20.2 1.0 O A:HOH541 4.7 38.6 1.0 CA A:THR84 4.7 21.4 1.0 O A:LYS85 4.8 23.5 1.0 CA A:ASN51 4.8 19.2 1.0 CB A:ASN51 4.8 19.2 1.0 CA A:ASP83 4.9 20.4 1.0 C A:ASN51 4.9 18.5 1.0 C A:LYS85 4.9 23.5 1.0 C A:PHE52 5.0 21.0 1.0

H.P.Morgan, I.W.Mcnae, M.W.Nowicki, V.Hannaert, P.A.M.Michels, L.A.Fothergill-Gilmore, M.D.Walkinshaw. The Allosteric Mechanism of Pryuvate Kinase From Leishmania Mexicana: A Rock and Lock Model J.Biol.Chem. V. 285 12892 2010.
ISSN: ISSN 0021-9258
PubMed: 20123988
DOI: 10.1074/JBC.M109.079905