Chlorine in PDB 1jak: Streptomyces Plicatus Beta-N-Acetylhexosaminidase in Complex with (2R, 3R,4S,5R)-2-Acetamido-3,4-Dihydroxy-5-Hydroxymethyl-Piperidinium Chloride (Ifg)

Enzymatic activity of Streptomyces Plicatus Beta-N-Acetylhexosaminidase in Complex with (2R, 3R,4S,5R)-2-Acetamido-3,4-Dihydroxy-5-Hydroxymethyl-Piperidinium Chloride (Ifg)

All present enzymatic activity of Streptomyces Plicatus Beta-N-Acetylhexosaminidase in Complex with (2R, 3R,4S,5R)-2-Acetamido-3,4-Dihydroxy-5-Hydroxymethyl-Piperidinium Chloride (Ifg):
3.2.1.52;

Protein crystallography data

The structure of Streptomyces Plicatus Beta-N-Acetylhexosaminidase in Complex with (2R, 3R,4S,5R)-2-Acetamido-3,4-Dihydroxy-5-Hydroxymethyl-Piperidinium Chloride (Ifg), PDB code: 1jak was solved by B.L.Mark, D.J.Vocadlo, D.Zhao, S.Knapp, S.G.Withers, M.N.James, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	44.10 / 1.75
*Space group*	P 6₁ 2 2
*Cell size a, b, c (Å), α, β, γ (°)*	132.767, 132.767, 177.024, 90.00, 90.00, 120.00
*R / R_free (%)*	17.6 / 19.2

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Streptomyces Plicatus Beta-N-Acetylhexosaminidase in Complex with (2R, 3R,4S,5R)-2-Acetamido-3,4-Dihydroxy-5-Hydroxymethyl-Piperidinium Chloride (Ifg) (pdb code 1jak). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Streptomyces Plicatus Beta-N-Acetylhexosaminidase in Complex with (2R, 3R,4S,5R)-2-Acetamido-3,4-Dihydroxy-5-Hydroxymethyl-Piperidinium Chloride (Ifg), PDB code: 1jak:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 1jak

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Chlorine Binding Sites List in 1jak

Chlorine binding site 1 out of 3 in the Streptomyces Plicatus Beta-N-Acetylhexosaminidase in Complex with (2R, 3R,4S,5R)-2-Acetamido-3,4-Dihydroxy-5-Hydroxymethyl-Piperidinium Chloride (Ifg)

Mono view

Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Streptomyces Plicatus Beta-N-Acetylhexosaminidase in Complex with (2R, 3R,4S,5R)-2-Acetamido-3,4-Dihydroxy-5-Hydroxymethyl-Piperidinium Chloride (Ifg) within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Cl606 b:9.1 occ:1.00	OH	A:TYR271	3.0	7.1	1.0
	O	A:HOH664	3.1	10.8	1.0
	CD	A:LYS275	3.7	10.4	1.0
	CE1	A:TYR271	3.7	7.0	1.0
	CZ	A:TYR271	3.8	7.9	1.0
	CG	A:LYS275	4.1	9.6	1.0
	CB	A:LYS275	4.5	9.1	1.0
	CA	A:GLY273	4.6	8.1	1.0
	CE	A:LYS275	4.8	11.0	1.0
	O	A:HOH1024	4.9	33.5	1.0
	CD1	A:TYR271	5.0	8.5	1.0

Chlorine binding site 2 out of 3 in 1jak

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Chlorine Binding Sites List in 1jak

Chlorine binding site 2 out of 3 in the Streptomyces Plicatus Beta-N-Acetylhexosaminidase in Complex with (2R, 3R,4S,5R)-2-Acetamido-3,4-Dihydroxy-5-Hydroxymethyl-Piperidinium Chloride (Ifg)

Mono view

Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Streptomyces Plicatus Beta-N-Acetylhexosaminidase in Complex with (2R, 3R,4S,5R)-2-Acetamido-3,4-Dihydroxy-5-Hydroxymethyl-Piperidinium Chloride (Ifg) within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Cl607 b:11.3 occ:1.00	O	A:HOH775	3.1	22.2	1.0
	NH1	A:ARG176	3.2	10.9	1.0
	NE	A:ARG179	3.2	7.9	1.0
	NH2	A:ARG179	3.4	8.7	1.0
	CZ	A:ARG179	3.7	10.3	1.0
	O	A:ASP175	3.7	8.8	1.0
	C	A:ASP175	3.8	7.7	1.0
	CD	A:ARG176	3.8	8.8	1.0
	CB	A:ASP175	3.9	10.6	1.0
	N	A:ARG176	3.9	6.3	1.0
	O	A:HOH653	4.0	13.2	1.0
	CA	A:ARG176	4.1	7.0	1.0
	CZ	A:ARG176	4.3	9.6	1.0
	CD	A:ARG179	4.3	6.4	1.0
	CA	A:ASP175	4.5	7.7	1.0
	CD1	A:ILE495	4.5	12.4	1.0
	NE	A:ARG176	4.5	8.9	1.0
	CG	A:ARG176	4.5	7.9	1.0
	O	A:HOH1073	4.7	30.8	1.0
	CG	A:ARG179	4.8	5.5	1.0
	O	A:ARG172	4.9	6.7	1.0
	CB	A:ARG176	4.9	8.1	1.0
	NH2	A:ARG121	4.9	9.3	1.0

Chlorine binding site 3 out of 3 in 1jak

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Chlorine Binding Sites List in 1jak

Chlorine binding site 3 out of 3 in the Streptomyces Plicatus Beta-N-Acetylhexosaminidase in Complex with (2R, 3R,4S,5R)-2-Acetamido-3,4-Dihydroxy-5-Hydroxymethyl-Piperidinium Chloride (Ifg)

Mono view

Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Streptomyces Plicatus Beta-N-Acetylhexosaminidase in Complex with (2R, 3R,4S,5R)-2-Acetamido-3,4-Dihydroxy-5-Hydroxymethyl-Piperidinium Chloride (Ifg) within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Cl608 b:14.8 occ:1.00	N	A:VAL276	3.3	6.8	1.0
	NZ	A:LYS275	3.4	9.8	1.0
	CA	A:LYS275	3.6	7.0	1.0
	CB	A:LYS275	3.7	9.1	1.0
	O	A:VAL276	3.9	8.1	1.0
	CG	A:LYS275	3.9	9.6	1.0
	C	A:LYS275	4.0	7.5	1.0
	CG2	A:VAL276	4.0	7.8	1.0
	CA	A:VAL276	4.3	5.7	1.0
	CE	A:LYS275	4.4	11.0	1.0
	O1	A:GOL602	4.5	18.0	1.0
	C	A:VAL276	4.6	6.7	1.0
	CB	A:VAL276	4.7	5.5	1.0
	CD	A:LYS275	4.7	10.4	1.0
	N	A:LYS275	5.0	7.4	1.0
	O	A:THR274	5.0	10.4	1.0

Reference:

B.L.Mark, D.J.Vocadlo, D.Zhao, S.Knapp, S.G.Withers, M.N.James. Biochemical and Structural Assessment of the 1-N-Azasugar Galnac-Isofagomine As A Potent Family 20 Beta-N-Acetylhexosaminidase Inhibitor. J.Biol.Chem. V. 276 42131 2001.
ISSN: ISSN 0021-9258
PubMed: 11522797
DOI: 10.1074/JBC.M107154200

Page generated: Fri Jul 19 22:56:36 2024

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