Potassium in PDB 4kcu: Pyruvate Kinase (Pyk) From Trypanosoma Brucei Soaked with D-Malate

All present enzymatic activity of Pyruvate Kinase (Pyk) From Trypanosoma Brucei Soaked with D-Malate:
2.7.1.40;

The structure of Pyruvate Kinase (Pyk) From Trypanosoma Brucei Soaked with D-Malate, PDB code: 4kcu was solved by W.Zhong, H.P.Morgan, I.W.Mcnae, P.A.M.Michels, L.A.Fothergill-Gilmore, M.D.Walkinshaw, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	67.18 / 2.35
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	103.370, 108.270, 265.190, 90.00, 90.00, 90.00
R / Rfree (%)	16 / 20.6

The structure of Pyruvate Kinase (Pyk) From Trypanosoma Brucei Soaked with D-Malate also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Potassium atom in the Pyruvate Kinase (Pyk) From Trypanosoma Brucei Soaked with D-Malate (pdb code 4kcu). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 2 binding sites of Potassium where determined in the Pyruvate Kinase (Pyk) From Trypanosoma Brucei Soaked with D-Malate, PDB code: 4kcu:
Jump to Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 in the Pyruvate Kinase (Pyk) From Trypanosoma Brucei Soaked with D-Malate


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Pyruvate Kinase (Pyk) From Trypanosoma Brucei Soaked with D-Malate within 5.0Å range: probe atom residue distance (Å) B Occ A:K1002 b:36.7 occ:1.00 OD1 A:ASP84 2.7 36.4 1.0 OD1 A:ASN52 2.7 32.7 1.0 O A:THR85 2.8 33.8 1.0 O A:HOH1101 2.8 30.2 1.0 OG A:SER54 2.9 38.5 1.0 O A:HOH1242 3.1 32.6 1.0 C A:THR85 3.7 33.0 1.0 CG A:ASP84 3.7 30.5 1.0 OG A:SER212 3.7 28.4 1.0 NZ A:LYS239 3.9 28.7 1.0 CG A:ASN52 3.9 33.7 1.0 CB A:SER54 3.9 35.5 1.0 O A:ASP84 3.9 30.0 1.0 NH2 A:ARG50 4.2 27.4 1.0 N A:LYS86 4.2 35.0 1.0 N A:SER54 4.2 38.5 1.0 CA A:LYS86 4.2 37.1 1.0 OE2 A:GLU89 4.2 46.4 1.0 C A:ASP84 4.2 30.8 1.0 CB A:ASP84 4.5 27.6 1.0 OD2 A:ASP84 4.5 33.9 1.0 ND2 A:ASN52 4.5 31.8 1.0 CA A:SER54 4.6 40.0 1.0 N A:THR85 4.6 29.5 1.0 O A:LYS86 4.6 33.6 1.0 O A:HOH1102 4.6 28.9 1.0 N A:PHE53 4.7 32.6 1.0 CA A:THR85 4.7 30.9 1.0 C A:LYS86 4.8 33.6 1.0 CB A:SER212 4.9 27.3 1.0 CB A:ASN52 5.0 30.6 1.0 CA A:ASP84 5.0 27.9 1.0 CA A:ASN52 5.0 31.3 1.0

Potassium binding site 2 out of 2 in the Pyruvate Kinase (Pyk) From Trypanosoma Brucei Soaked with D-Malate


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Pyruvate Kinase (Pyk) From Trypanosoma Brucei Soaked with D-Malate within 5.0Å range: probe atom residue distance (Å) B Occ B:K502 b:44.9 occ:1.00 O B:HOH601 2.6 32.6 1.0 OD1 B:ASN52 2.8 33.2 1.0 OD1 B:ASP84 2.9 37.1 1.0 O B:THR85 2.9 31.0 1.0 O B:HOH787 3.0 38.9 1.0 OG B:SER54 3.0 36.9 1.0 C B:THR85 3.7 30.9 1.0 NZ B:LYS239 3.8 31.0 1.0 CG B:ASP84 3.8 36.5 1.0 O B:ASP84 3.8 29.8 1.0 CG B:ASN52 3.8 31.9 1.0 CB B:SER54 4.0 34.7 1.0 OG B:SER212 4.0 31.5 1.0 NH2 B:ARG50 4.1 25.7 1.0 O B:HOH790 4.1 42.3 1.0 C B:ASP84 4.2 29.1 1.0 N B:LYS86 4.2 34.8 1.0 CA B:LYS86 4.2 35.7 1.0 N B:SER54 4.2 35.4 1.0 ND2 B:ASN52 4.3 30.7 1.0 CB B:ASP84 4.4 31.1 1.0 OD2 B:ASP84 4.6 39.3 1.0 N B:THR85 4.6 29.3 1.0 O B:LYS86 4.6 34.4 1.0 CA B:SER54 4.7 36.5 1.0 CA B:THR85 4.7 31.6 1.0 N B:PHE53 4.8 32.2 1.0 C B:LYS86 4.8 33.9 1.0 CB B:ASN52 4.9 27.0 1.0 CA B:ASP84 4.9 29.1 1.0 CA B:ASN52 5.0 28.6 1.0

W.Zhong, H.P.Morgan, M.W.Nowicki, I.W.Mcnae, M.Yuan, J.Bella, P.A.Michels, L.A.Fothergill-Gilmore, M.D.Walkinshaw. Pyruvate Kinases Have An Intrinsic and Conserved Decarboxylase Activity. Biochem.J. V. 458 301 2014.
ISSN: ISSN 0264-6021
PubMed: 24328825
DOI: 10.1042/BJ20130790