Potassium in PDB 4kcv: Pyruvate Kinase (Pyk) From Trypanosoma Brucei Soaked with 2- Oxoglutaric Acid

All present enzymatic activity of Pyruvate Kinase (Pyk) From Trypanosoma Brucei Soaked with 2- Oxoglutaric Acid:
2.7.1.40;

The structure of Pyruvate Kinase (Pyk) From Trypanosoma Brucei Soaked with 2- Oxoglutaric Acid, PDB code: 4kcv 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)	74.63 / 2.18
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	103.250, 108.010, 265.820, 90.00, 90.00, 90.00
R / Rfree (%)	15.8 / 19.3

The structure of Pyruvate Kinase (Pyk) From Trypanosoma Brucei Soaked with 2- Oxoglutaric Acid 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 2- Oxoglutaric Acid (pdb code 4kcv). 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 2- Oxoglutaric Acid, PDB code: 4kcv:
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 2- Oxoglutaric Acid


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 2- Oxoglutaric Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:K1002 b:37.5 occ:1.00 OD1 B:ASP84 2.7 21.2 1.0 OD1 B:ASN52 2.7 19.9 1.0 O B:HOH1209 2.9 32.2 1.0 O B:THR85 2.9 21.4 1.0 O B:HOH1129 2.9 21.7 1.0 OG B:SER54 3.1 35.7 1.0 CG B:ASP84 3.6 21.9 1.0 C B:THR85 3.7 21.3 1.0 O B:ASP84 3.7 18.5 1.0 CG B:ASN52 3.8 20.6 1.0 NZ B:LYS239 3.8 17.8 1.0 OG B:SER212 3.8 21.5 1.0 O B:HOH1425 3.8 43.3 1.0 CB B:SER54 3.9 29.8 1.0 O B:HOH1211 4.0 36.5 1.0 NH2 B:ARG50 4.1 15.8 1.0 C B:ASP84 4.1 20.1 1.0 N B:SER54 4.2 27.0 1.0 N B:LYS86 4.2 22.1 1.0 CA B:LYS86 4.2 24.2 1.0 OD2 B:ASP84 4.3 23.0 1.0 CB B:ASP84 4.4 20.1 1.0 ND2 B:ASN52 4.4 18.7 1.0 N B:THR85 4.5 19.2 1.0 O B:HOH1210 4.6 22.6 1.0 CA B:SER54 4.6 27.7 1.0 O B:LYS86 4.7 22.0 1.0 CA B:THR85 4.7 20.0 1.0 N B:PHE53 4.8 20.8 1.0 C B:LYS86 4.9 24.4 1.0 CA B:ASP84 4.9 18.8 1.0 CB B:ASN52 4.9 18.4 1.0 CA B:ASN52 4.9 18.9 1.0

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


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 2- Oxoglutaric Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:K1002 b:22.9 occ:1.00 OD1 A:ASN52 2.6 21.1 1.0 OD1 A:ASP84 2.8 21.3 1.0 O A:THR85 2.8 20.8 1.0 OG A:SER54 2.8 22.3 1.0 O A:HOH1135 2.8 20.1 1.0 O A:HOH1136 2.9 23.0 1.0 C A:THR85 3.6 22.4 1.0 CG A:ASP84 3.7 20.8 1.0 CG A:ASN52 3.7 22.1 1.0 OG A:SER212 3.7 21.2 1.0 CB A:SER54 3.8 22.6 1.0 O A:ASP84 3.9 19.8 1.0 NZ A:LYS239 4.0 19.0 1.0 N A:SER54 4.1 21.6 1.0 N A:LYS86 4.1 21.4 1.0 NH2 A:ARG50 4.1 19.7 1.0 CA A:LYS86 4.1 24.1 1.0 C A:ASP84 4.2 20.3 1.0 OE2 A:GLU89 4.2 29.5 1.0 ND2 A:ASN52 4.4 20.4 1.0 OD2 A:ASP84 4.5 21.5 1.0 CB A:ASP84 4.5 19.6 1.0 CA A:SER54 4.5 23.1 1.0 N A:THR85 4.5 20.3 1.0 O A:LYS86 4.5 21.8 1.0 O A:HOH1211 4.6 17.1 1.0 N A:PHE53 4.7 21.9 1.0 CA A:THR85 4.7 19.9 1.0 C A:LYS86 4.7 23.4 1.0 CB A:ASN52 4.9 20.9 1.0 CB A:SER212 4.9 18.2 1.0 CA A:ASN52 4.9 21.3 1.0 CA A:ASP84 5.0 19.2 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