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Potassium in PDB 6u1i: Thermus Thermophilus D-Alanine-D-Alanine Ligase in Complex with Adp, Phosphorylated D-Cycloserine, MG2+ and K+

Enzymatic activity of Thermus Thermophilus D-Alanine-D-Alanine Ligase in Complex with Adp, Phosphorylated D-Cycloserine, MG2+ and K+

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

Protein crystallography data

The structure of Thermus Thermophilus D-Alanine-D-Alanine Ligase in Complex with Adp, Phosphorylated D-Cycloserine, MG2+ and K+, PDB code: 6u1i 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) 25.83 / 2.30
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 55.369, 68.453, 91.747, 69.50, 78.86, 66.05
R / Rfree (%) 23.8 / 28

Other elements in 6u1i:

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

Magnesium (Mg) 2 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Thermus Thermophilus D-Alanine-D-Alanine Ligase in Complex with Adp, Phosphorylated D-Cycloserine, MG2+ and K+ (pdb code 6u1i). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total only one binding site of Potassium was determined in the Thermus Thermophilus D-Alanine-D-Alanine Ligase in Complex with Adp, Phosphorylated D-Cycloserine, MG2+ and K+, PDB code: 6u1i:

Potassium binding site 1 out of 1 in 6u1i

Go back to Potassium Binding Sites List in 6u1i
Potassium binding site 1 out of 1 in the Thermus Thermophilus D-Alanine-D-Alanine Ligase in Complex with Adp, Phosphorylated D-Cycloserine, 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, Phosphorylated D-Cycloserine, MG2+ and K+ within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K403

b:9.5
occ:0.72
 O C:HOH570 2.5 13.9 1.0
O C:LEU283 2.6 15.2 1.0
O C:HOH540 2.8 17.0 1.0
OE1 C:GLU282 2.9 15.7 1.0
O C:CYS113 2.9 14.1 1.0
O C:HOH548 3.3 19.1 1.0
OD1 C:ASN284 3.3 9.6 1.0
MG C:MG402 3.7 14.9 1.0
C C:LEU283 3.7 13.2 1.0
SD C:MET114 3.8 17.8 1.0
C C:CYS113 3.8 12.8 1.0
CG C:ASN284 3.9 14.2 1.0
CA C:MET114 4.0 13.8 1.0
CA C:ASN284 4.0 10.7 1.0
CD C:GLU282 4.1 17.4 1.0
O C:HOH532 4.3 8.8 1.0
N C:ASN284 4.3 11.7 1.0
N C:MET114 4.3 9.9 1.0
CB C:ASN284 4.5 11.6 1.0
NZ C:LYS116 4.6 14.6 1.0
CG C:MET114 4.7 22.5 1.0
OE2 C:GLU87 4.7 15.5 1.0
ND2 C:ASN284 4.7 15.1 1.0
CB C:GLU282 4.7 12.8 1.0
N C:LEU283 4.8 12.6 1.0
C C:MET114 4.8 15.3 1.0
O C:THR157 4.8 20.4 1.0
O C:HOH552 4.8 10.2 1.0
CG C:GLU282 4.9 15.4 1.0
CA C:LEU283 4.9 10.8 1.0
CB C:CYS113 4.9 8.3 1.0
CB C:MET114 4.9 13.1 1.0
O C:HOH542 4.9 10.6 1.0
O1B C:ADP404 4.9 12.2 0.9
OE2 C:GLU282 4.9 18.9 1.0
CA C:CYS113 5.0 11.6 1.0
O C:MET114 5.0 18.0 1.0

Reference:

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
Page generated: Mon Aug 12 17:43:17 2024

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