Potassium in PDB 6u1h: Thermus Thermophilus D-Alanine-D-Alanine Ligase in Complex with Adp, Phosphate, MG2+ and K+

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

The structure of Thermus Thermophilus D-Alanine-D-Alanine Ligase in Complex with Adp, Phosphate, MG2+ and K+, PDB code: 6u1h was solved by J.L.Pederick, J.B.Bruning, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.43 / 2.20
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	55.291, 68.616, 91.646, 69.55, 78.97, 66.10
R / Rfree (%)	21.8 / 26.5

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

Magnesium

(Mg)

5 atoms

The binding sites of Potassium atom in the Thermus Thermophilus D-Alanine-D-Alanine Ligase in Complex with Adp, Phosphate, MG2+ and K+ (pdb code 6u1h). 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, MG2+ and K+, PDB code: 6u1h:
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, 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, MG2+ and K+ within 5.0Å range: probe atom residue distance (Å) B Occ A:K404 b:27.4 occ:0.72 O A:LEU283 2.7 26.5 1.0 O A:HOH558 2.8 35.6 1.0 O A:HOH565 2.8 32.6 1.0 O A:HOH567 2.8 33.1 1.0 OE1 A:GLU282 2.9 28.2 1.0 O A:CYS113 3.0 28.2 1.0 OD1 A:ASN284 3.3 26.2 1.0 MG A:MG401 3.6 32.1 0.9 C A:LEU283 3.8 24.3 1.0 C A:CYS113 3.9 27.1 1.0 CD A:GLU282 4.0 32.9 1.0 CA A:MET114 4.1 28.4 1.0 CG A:ASN284 4.1 32.2 1.0 CA A:ASN284 4.2 25.9 1.0 O A:HOH530 4.3 23.4 1.0 N A:MET114 4.4 24.2 1.0 N A:ASN284 4.4 27.9 1.0 SD A:MET114 4.4 45.3 1.0 CB A:GLU282 4.5 20.8 1.0 CG A:GLU282 4.6 25.6 1.0 CB A:ASN284 4.7 24.9 1.0 N A:LEU283 4.7 23.5 1.0 CG A:MET114 4.8 40.9 1.0 C A:MET114 4.8 30.5 1.0 O A:THR157 4.8 34.4 1.0 O A:HOH545 4.9 19.2 1.0 O A:MET114 4.9 31.9 1.0 OE2 A:GLU282 4.9 25.4 1.0 NZ A:LYS116 4.9 32.1 1.0 CA A:LEU283 4.9 19.8 1.0 O1B A:ADP405 4.9 22.7 1.0 ND2 A:ASN284 4.9 27.6 1.0 CB A:CYS113 5.0 23.5 1.0

Potassium binding site 2 out of 2 in the Thermus Thermophilus D-Alanine-D-Alanine Ligase in Complex with Adp, Phosphate, 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, MG2+ and K+ within 5.0Å range: probe atom residue distance (Å) B Occ C:K404 b:29.1 occ:0.80 O C:HOH559 2.7 35.5 1.0 O C:LEU283 2.9 32.7 1.0 OE1 C:GLU282 2.9 34.2 1.0 O C:HOH567 2.9 27.8 1.0 O C:CYS113 3.0 26.9 1.0 O C:HOH520 3.2 34.7 1.0 OD1 C:ASN284 3.5 37.5 1.0 MG C:MG402 3.8 40.5 1.0 C C:CYS113 4.0 31.0 1.0 C C:LEU283 4.0 25.3 1.0 CA C:MET114 4.0 28.1 1.0 CD C:GLU282 4.1 32.8 1.0 SD C:MET114 4.2 42.6 1.0 CG C:ASN284 4.3 35.1 1.0 CA C:ASN284 4.4 21.0 1.0 O C:HOH543 4.4 20.4 1.0 CB C:GLU282 4.4 24.6 1.0 N C:MET114 4.4 25.6 1.0 N C:ASN284 4.6 25.0 1.0 O C:MET114 4.7 34.5 1.0 C C:MET114 4.7 28.0 1.0 O C:HOH525 4.7 33.6 1.0 O C:THR157 4.7 39.9 1.0 CG C:GLU282 4.8 25.7 1.0 NZ C:LYS116 4.8 37.1 1.0 CB C:ASN284 4.8 30.1 1.0 N C:LEU283 4.8 20.8 1.0 O1B C:ADP405 4.9 39.1 1.0 CG C:MET114 4.9 31.9 1.0 OE2 C:GLU282 4.9 31.6 1.0 O C:HOH519 5.0 26.4 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