Chlorine in PDB 6cey: Aminoglycoside Phosphotransferase (2'')-Ia in Complex with Gmppnp, Magnesium, and Lividomycin Moieties

Enzymatic activity of Aminoglycoside Phosphotransferase (2'')-Ia in Complex with Gmppnp, Magnesium, and Lividomycin Moieties

All present enzymatic activity of Aminoglycoside Phosphotransferase (2'')-Ia in Complex with Gmppnp, Magnesium, and Lividomycin Moieties:
2.7.1.190;

Protein crystallography data

The structure of Aminoglycoside Phosphotransferase (2'')-Ia in Complex with Gmppnp, Magnesium, and Lividomycin Moieties, PDB code: 6cey was solved by S.J.Caldwell, A.M.Berghuis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	90.73 / 2.40
*Space group*	P 1 2₁ 1
*Cell size a, b, c (Å), α, β, γ (°)*	90.250, 100.240, 94.010, 90.00, 105.17, 90.00
*R / R_free (%)*	17.1 / 21.6

Other elements in 6cey:

The structure of Aminoglycoside Phosphotransferase (2'')-Ia in Complex with Gmppnp, Magnesium, and Lividomycin Moieties also contains other interesting chemical elements:

Magnesium

(Mg)

9 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Aminoglycoside Phosphotransferase (2'')-Ia in Complex with Gmppnp, Magnesium, and Lividomycin Moieties (pdb code 6cey). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Aminoglycoside Phosphotransferase (2'')-Ia in Complex with Gmppnp, Magnesium, and Lividomycin Moieties, PDB code: 6cey:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 6cey

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Chlorine Binding Sites List in 6cey

Chlorine binding site 1 out of 3 in the Aminoglycoside Phosphotransferase (2'')-Ia in Complex with Gmppnp, Magnesium, and Lividomycin Moieties

Mono view

Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Aminoglycoside Phosphotransferase (2'')-Ia in Complex with Gmppnp, Magnesium, and Lividomycin Moieties within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Cl802 b:77.8 occ:1.00	NE2	A:GLN462	3.3	79.0	1.0
	NH1	A:ARG469	3.4	62.7	1.0
	CA	A:GLU466	3.8	63.1	1.0
	CG2	A:ILE465	3.8	55.9	1.0
	N	A:GLU466	3.8	59.0	1.0
	CB	A:GLU466	3.9	71.7	1.0
	CG	A:GLU466	3.9	81.8	1.0
	CD	A:ARG469	4.0	54.9	1.0
	C	A:ILE465	4.3	56.1	1.0
	CZ	A:ARG469	4.3	58.0	1.0
	CB	A:ILE465	4.4	57.7	1.0
	CD	A:GLN462	4.4	82.9	1.0
	NE	A:ARG469	4.5	55.1	1.0
	O	A:ILE465	4.6	54.2	1.0
	O	A:GLN462	4.7	72.3	1.0
	CG	A:GLN462	4.7	81.6	1.0
	CA	A:ILE465	5.0	55.2	1.0

Chlorine binding site 2 out of 3 in 6cey

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Chlorine Binding Sites List in 6cey

Chlorine binding site 2 out of 3 in the Aminoglycoside Phosphotransferase (2'')-Ia in Complex with Gmppnp, Magnesium, and Lividomycin Moieties

Mono view

Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Aminoglycoside Phosphotransferase (2'')-Ia in Complex with Gmppnp, Magnesium, and Lividomycin Moieties within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:Cl802 b:82.1 occ:1.00	O	B:HOH1107	2.8	68.2	1.0
	NE2	B:GLN462	2.9	74.2	1.0
	O	B:HOH1049	3.1	61.7	1.0
	NH1	B:ARG469	3.2	56.0	1.0
	CG2	B:ILE465	3.5	51.2	1.0
	CD	B:ARG469	4.0	50.2	1.0
	CG	B:GLU466	4.0	77.1	1.0
	CD	B:GLN462	4.2	76.8	1.0
	CZ	B:ARG469	4.2	52.4	1.0
	CB	B:ILE465	4.3	52.6	1.0
	N	B:GLU466	4.4	59.1	1.0
	NE	B:ARG469	4.5	51.7	1.0
	CA	B:GLU466	4.6	64.3	1.0
	C	B:ILE465	4.7	55.7	1.0
	CG	B:GLN462	4.8	78.7	1.0
	CB	B:GLU466	4.8	72.7	1.0
	O	B:ILE465	5.0	59.5	1.0

Chlorine binding site 3 out of 3 in 6cey

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Chlorine Binding Sites List in 6cey

Chlorine binding site 3 out of 3 in the Aminoglycoside Phosphotransferase (2'')-Ia in Complex with Gmppnp, Magnesium, and Lividomycin Moieties

Mono view

Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Aminoglycoside Phosphotransferase (2'')-Ia in Complex with Gmppnp, Magnesium, and Lividomycin Moieties within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
C:Cl802 b:77.7 occ:1.00	NH1	C:ARG469	3.5	39.1	1.0
	NE2	C:GLN462	3.5	61.9	1.0
	CB	C:GLU466	3.8	54.9	1.0
	CA	C:GLU466	3.8	48.5	1.0
	CG	C:GLU466	3.9	65.1	1.0
	N	C:GLU466	3.9	45.4	1.0
	CD	C:ARG469	4.0	38.8	1.0
	CG2	C:ILE465	4.1	43.0	1.0
	CZ	C:ARG469	4.4	38.8	1.0
	C	C:ILE465	4.4	44.7	1.0
	NE	C:ARG469	4.6	36.6	1.0
	CD	C:GLN462	4.6	64.5	1.0
	CB	C:ILE465	4.6	44.1	1.0
	O	C:GLN462	4.7	57.3	1.0
	CG	C:GLN462	4.8	61.8	1.0
	O	C:ILE465	4.8	40.9	1.0

Reference:

S.J.Caldwell, A.M.Berghuis. Plasticity of Aminoglycoside Binding to Antibiotic Kinase Aph(2′′)-Ia. Antimicrob. Agents V. 62 2018CHEMOTHER..
ISSN: ESSN 1098-6596
PubMed: 29661878
DOI: 10.1128/AAC.00202-18

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