Potassium in PDB 6u1j: Thermus Thermophilus D-Alanine-D-Alanine Ligase in Complex with Adp, Phosphate, D-Ala-D-Ala, MG2+ and K+

All present enzymatic activity of Thermus Thermophilus D-Alanine-D-Alanine Ligase in Complex with Adp, Phosphate, D-Ala-D-Ala, MG2+ and K+:
6.3.2.4;

The structure of Thermus Thermophilus D-Alanine-D-Alanine Ligase in Complex with Adp, Phosphate, D-Ala-D-Ala, MG2+ and K+, PDB code: 6u1j was solved by J.L.Pederick, J.B.Bruning, A.P.Thompson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.85 / 2.20
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	59.613, 69.080, 93.792, 71.37, 80.24, 64.32
R / Rfree (%)	21.9 / 26.2

The structure of Thermus Thermophilus D-Alanine-D-Alanine Ligase in Complex with Adp, Phosphate, D-Ala-D-Ala, MG2+ and K+ also contains other interesting chemical elements:

Magnesium

(Mg)

4 atoms

The binding sites of Potassium atom in the Thermus Thermophilus D-Alanine-D-Alanine Ligase in Complex with Adp, Phosphate, D-Ala-D-Ala, MG2+ and K+ (pdb code 6u1j). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 2 binding sites of Potassium where determined in the Thermus Thermophilus D-Alanine-D-Alanine Ligase in Complex with Adp, Phosphate, D-Ala-D-Ala, MG2+ and K+, PDB code: 6u1j:
Jump to Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 in the Thermus Thermophilus D-Alanine-D-Alanine Ligase in Complex with Adp, Phosphate, D-Ala-D-Ala, MG2+ and K+


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Thermus Thermophilus D-Alanine-D-Alanine Ligase in Complex with Adp, Phosphate, D-Ala-D-Ala, MG2+ and K+ within 5.0Å range: probe atom residue distance (Å) B Occ A:K406 b:27.9 occ:0.68 O A:HOH544 2.6 38.4 1.0 O A:LEU283 2.7 31.2 1.0 O A:HOH526 2.7 30.4 1.0 OE1 A:GLU282 2.9 39.5 1.0 O A:CYS113 3.0 28.1 1.0 O A:HOH587 3.1 44.2 1.0 MG A:MG404 3.3 39.3 0.7 OD1 A:ASN284 3.4 38.5 1.0 C A:LEU283 3.8 29.9 1.0 CD A:GLU282 3.8 41.7 1.0 SD A:MET114 3.9 47.0 1.0 C A:CYS113 4.0 30.8 1.0 CA A:ASN284 4.1 27.8 1.0 CG A:ASN284 4.1 37.7 1.0 O A:HOH546 4.2 28.3 1.0 CA A:MET114 4.3 28.0 1.0 O A:HOH581 4.4 34.0 1.0 N A:ASN284 4.4 30.3 1.0 N A:MET114 4.5 29.9 1.0 OE2 A:GLU282 4.5 41.4 1.0 CB A:ASN284 4.6 34.3 1.0 CG A:GLU282 4.6 34.2 1.0 CB A:GLU282 4.7 38.5 1.0 OE2 A:GLU87 4.7 34.5 1.0 N A:LEU283 4.8 27.8 1.0 O3B A:ADP407 4.8 39.0 0.8 NZ A:LYS116 4.8 41.3 1.0 O A:THR157 4.9 39.9 1.0 CG A:MET114 4.9 41.4 1.0 O A:HOH541 4.9 23.0 1.0 CA A:LEU283 5.0 26.8 1.0 ND2 A:ASN284 5.0 33.8 1.0 CB A:CYS113 5.0 25.2 1.0

Potassium binding site 2 out of 2 in the Thermus Thermophilus D-Alanine-D-Alanine Ligase in Complex with Adp, Phosphate, D-Ala-D-Ala, MG2+ and K+


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Thermus Thermophilus D-Alanine-D-Alanine Ligase in Complex with Adp, Phosphate, D-Ala-D-Ala, MG2+ and K+ within 5.0Å range: probe atom residue distance (Å) B Occ C:K406 b:29.0 occ:0.79 O C:HOH558 2.7 29.9 1.0 O C:LEU283 2.7 30.1 1.0 O C:HOH535 2.9 37.4 1.0 OE1 C:GLU282 2.9 35.8 1.0 O C:HOH545 2.9 39.6 1.0 O C:CYS113 3.0 23.2 1.0 OD1 C:ASN284 3.2 36.8 1.0 MG C:MG404 3.5 32.2 0.7 SD C:MET114 3.8 38.5 1.0 C C:LEU283 3.9 30.5 1.0 CG C:ASN284 3.9 36.1 1.0 C C:CYS113 3.9 30.5 1.0 CD C:GLU282 4.0 35.0 1.0 CA C:MET114 4.0 27.8 1.0 CA C:ASN284 4.2 31.7 1.0 O C:HOH533 4.2 29.5 1.0 N C:MET114 4.4 26.7 1.0 N C:ASN284 4.4 29.4 1.0 CB C:ASN284 4.5 28.7 1.0 NZ C:LYS116 4.6 37.3 1.0 CB C:GLU282 4.6 37.4 1.0 ND2 C:ASN284 4.7 33.7 1.0 CG C:MET114 4.7 41.6 1.0 OE2 C:GLU87 4.7 34.6 1.0 O C:THR157 4.8 39.2 1.0 OE2 C:GLU282 4.8 36.7 1.0 O1B C:ADP407 4.8 34.3 0.9 C C:MET114 4.8 29.9 1.0 O C:HOH556 4.8 33.2 1.0 CG C:GLU282 4.9 32.1 1.0 N C:LEU283 4.9 28.9 1.0 O C:MET114 4.9 39.8 1.0 CE C:MET114 4.9 36.4 1.0 CB C:MET114 5.0 30.4 1.0

J.L.Pederick, A.P.Thompson, S.G.Bell, J.B.Bruning. D-Alanine-D-Alanine Ligase As A Model For the Activation of Atp-Grasp Enzymes By Monovalent Cations. J.Biol.Chem. 2020.
ISSN: ESSN 1083-351X
PubMed: 32335509
DOI: 10.1074/JBC.RA120.012936