Sodium in PDB 5etp: E. Coli 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.05 Angstrom Resolution

Enzymatic activity of E. Coli 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.05 Angstrom Resolution

All present enzymatic activity of E. Coli 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.05 Angstrom Resolution:
2.7.6.3;

Protein crystallography data

The structure of E. Coli 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.05 Angstrom Resolution, PDB code: 5etp was solved by M.L.Dennis, T.S.Peat, J.D.Swarbrick, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	34.70 / 1.05
*Space group*	P 1 2₁ 1
*Cell size a, b, c (Å), α, β, γ (°)*	35.950, 57.770, 38.640, 90.00, 116.11, 90.00
*R / R_free (%)*	10.7 / 12.5

Other elements in 5etp:

The structure of E. Coli 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.05 Angstrom Resolution also contains other interesting chemical elements:

Bromine	(Br)	1 atom
Calcium	(Ca)	4 atoms
Chlorine	(Cl)	1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the E. Coli 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.05 Angstrom Resolution (pdb code 5etp). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the E. Coli 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.05 Angstrom Resolution, PDB code: 5etp:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 5etp

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Sodium Binding Sites List in 5etp

Sodium binding site 1 out of 3 in the E. Coli 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.05 Angstrom Resolution

Mono view

Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of E. Coli 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.05 Angstrom Resolution within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na206 b:20.4 occ:1.00	O	A:HOH409	2.2	30.0	1.0
	O	A:HOH539	2.2	19.4	1.0
	OD2	A:ASP139	2.3	9.1	1.0
	O	A:HOH406	2.3	10.7	1.0
	O	A:HOH528	2.5	12.2	1.0
	O	A:HOH465	2.6	18.8	1.0
	O	A:HOH321	2.7	21.4	1.0
	CG	A:ASP139	3.5	6.1	1.0
	CB	A:ASP139	4.0	5.7	1.0
	NZ	A:LYS119	4.1	7.4	1.0
	O	A:HOH545	4.3	16.1	1.0
	O	A:HOH322	4.4	14.7	1.0
	OD1	A:ASP139	4.5	5.8	1.0
	OE1	A:GLU141	4.9	9.6	1.0

Sodium binding site 2 out of 3 in 5etp

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Sodium Binding Sites List in 5etp

Sodium binding site 2 out of 3 in the E. Coli 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.05 Angstrom Resolution

Mono view

Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of E. Coli 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.05 Angstrom Resolution within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na207 b:29.5 occ:1.00	O	A:HOH509	2.2	30.0	1.0
	O	A:MET0	2.2	10.4	0.5
	O	A:MET0	2.2	10.4	0.5
	O	A:HOH327	2.2	30.0	1.0
	O	A:HOH454	3.0	24.2	1.0
	C	A:MET0	3.4	7.4	0.5
	C	A:MET0	3.4	7.4	0.5
	N	A:MET0	4.1	11.2	0.5
	N	A:MET0	4.1	11.2	0.5
	CA	A:MET0	4.2	9.4	0.5
	CA	A:MET0	4.2	9.4	0.5
	N	A:THR1	4.4	5.6	1.0
	O	A:HOH533	4.5	23.8	1.0
	CB	A:MET0	4.5	11.9	0.5
	CB	A:MET0	4.5	11.9	0.5
	CA	A:THR1	4.6	5.9	1.0
	O	A:HOH490	4.8	15.5	1.0
	O	A:HOH440	4.8	19.1	1.0

Sodium binding site 3 out of 3 in 5etp

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Sodium Binding Sites List in 5etp

Sodium binding site 3 out of 3 in the E. Coli 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.05 Angstrom Resolution

Mono view

Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of E. Coli 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.05 Angstrom Resolution within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na208 b:8.1 occ:1.00	O	A:HOH511	2.4	17.5	1.0
	O	A:HOH480	2.4	10.4	1.0
	O	A:HOH430	2.4	19.5	1.0
	O	A:HOH313	2.4	15.0	1.0
	OE1	A:GLU30	2.4	10.5	1.0
	O	A:SER63	2.7	8.3	1.0
	CD	A:GLU30	3.5	8.8	1.0
	C	A:SER63	3.6	5.1	1.0
	OE2	A:GLU30	3.8	10.7	1.0
	OG	A:SER63	4.0	7.9	1.0
	CB	A:SER63	4.0	6.3	1.0
	O	A:HOH426	4.2	11.2	1.0
	O	A:HOH341	4.3	13.4	1.0
	O	A:HOH447	4.3	15.5	1.0
	N	A:LEU64	4.3	4.3	1.0
	CA	A:LEU64	4.4	4.1	1.0
	CA	A:SER63	4.5	4.7	1.0
	O	A:HOH508	4.7	13.8	1.0
	CG	A:GLU30	4.8	7.6	1.0
	C	A:LEU64	5.0	4.2	1.0

Reference:

M.L.Dennis, N.P.Pitcher, M.D.Lee, A.J.Debono, Z.C.Wang, J.R.Harjani, R.Rahmani, B.Cleary, T.S.Peat, J.B.Baell, J.D.Swarbrick. Structural Basis For the Selective Binding of Inhibitors to 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase From Staphylococcus Aureus and Escherichia Coli. J.Med.Chem. V. 59 5248 2016.
ISSN: ISSN 0022-2623
PubMed: 27094768
DOI: 10.1021/ACS.JMEDCHEM.6B00002

Page generated: Mon Oct 7 20:51:15 2024

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