Potassium in PDB 6mde: Mevalonate Kinase From Methanosarcina Mazei with Mevalonate Bound

All present enzymatic activity of Mevalonate Kinase From Methanosarcina Mazei with Mevalonate Bound:
2.7.1.36;

The structure of Mevalonate Kinase From Methanosarcina Mazei with Mevalonate Bound, PDB code: 6mde was solved by B.R.Miller, Y.Kung, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	56.66 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	54.050, 59.330, 191.100, 90.00, 90.00, 90.00
R / Rfree (%)	19.6 / 25

The binding sites of Potassium atom in the Mevalonate Kinase From Methanosarcina Mazei with Mevalonate Bound (pdb code 6mde). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 2 binding sites of Potassium where determined in the Mevalonate Kinase From Methanosarcina Mazei with Mevalonate Bound, PDB code: 6mde:
Jump to Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 in the Mevalonate Kinase From Methanosarcina Mazei with Mevalonate Bound


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Mevalonate Kinase From Methanosarcina Mazei with Mevalonate Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:K402 b:27.8 occ:1.00 O A:HOH698 3.2 43.5 1.0 O A:HOH691 3.3 29.3 1.0 C A:HIS59 3.4 18.1 1.0 N A:TYR61 3.4 22.4 1.0 CA A:HIS59 3.4 24.3 1.0 N A:VAL62 3.5 19.4 1.0 N A:PRO60 3.6 24.5 1.0 CD A:PRO60 3.7 20.5 1.0 CB A:TYR61 3.7 20.3 1.0 CG2 A:VAL62 3.7 13.6 1.0 O A:HIS59 3.8 20.3 1.0 O A:HOH542 4.0 37.8 1.0 CA A:TYR61 4.0 21.7 1.0 CD2 A:TYR61 4.1 18.8 1.0 CB A:HIS59 4.1 18.4 1.0 CB A:VAL62 4.2 27.9 1.0 C A:TYR61 4.3 19.0 1.0 C A:PRO60 4.3 22.9 1.0 CD2 A:HIS59 4.4 24.7 1.0 CG A:TYR61 4.4 19.6 1.0 O A:LYS58 4.4 29.0 1.0 CG A:PRO60 4.5 24.1 1.0 CA A:PRO60 4.5 26.3 1.0 CA A:VAL62 4.5 25.8 1.0 CG A:HIS59 4.6 21.1 1.0 N A:HIS59 4.6 23.8 1.0 CG1 A:VAL98 4.7 22.2 1.0 CG2 A:VAL98 4.9 19.2 1.0 C A:LYS58 5.0 29.1 1.0 O A:HOH562 5.0 29.1 1.0

Potassium binding site 2 out of 2 in the Mevalonate Kinase From Methanosarcina Mazei with Mevalonate Bound


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Mevalonate Kinase From Methanosarcina Mazei with Mevalonate Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:K502 b:69.9 occ:1.00 O B:PRO87 2.9 51.3 1.0 OG B:SER94 2.9 50.1 1.0 N B:GLY89 3.0 57.7 1.0 C2 B:GOL504 3.1 50.4 1.0 N B:SER94 3.1 37.2 1.0 O B:GLY89 3.2 37.2 1.0 CB B:SER94 3.2 33.0 1.0 N B:GLY93 3.4 36.3 1.0 O1 B:GOL504 3.5 47.7 1.0 C B:VAL88 3.5 55.6 1.0 CA B:VAL88 3.5 44.8 1.0 O3 B:GOL504 3.7 40.4 1.0 CA B:SER94 3.7 41.4 1.0 O2 B:GOL504 3.7 40.9 1.0 CB B:LEU92 3.7 36.3 1.0 C1 B:GOL504 3.8 58.0 1.0 CA B:GLY89 3.8 53.1 1.0 C B:GLY89 3.9 47.9 1.0 C B:PRO87 3.9 48.1 1.0 C B:LEU92 3.9 37.1 1.0 C3 B:GOL504 3.9 55.5 1.0 N B:LEU92 3.9 34.9 1.0 CA B:LEU92 4.0 38.4 1.0 C B:GLY93 4.1 33.4 1.0 N B:VAL88 4.2 52.4 1.0 CG2 B:ILE86 4.2 34.8 1.0 CA B:GLY93 4.2 37.8 1.0 O B:VAL88 4.4 43.7 1.0 CB B:VAL88 4.7 40.9 1.0 O B:LEU92 4.7 27.4 1.0 CG B:LEU92 4.8 39.8 1.0 C B:SER94 4.9 42.3 1.0 C B:GLY91 4.9 43.9 1.0 CG1 B:VAL88 4.9 45.4 1.0 N B:SER95 5.0 39.1 0.6 N B:SER95 5.0 39.1 0.4

B.R.Miller, Y.Kung. Structural Insight Into Substrate and Product Binding in An Archaeal Mevalonate Kinase. Plos One V. 13 08419 2018.
ISSN: ESSN 1932-6203
PubMed: 30521590
DOI: 10.1371/JOURNAL.PONE.0208419