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 / R_free (%)*	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

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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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