Chlorine in PDB 6cgg: Aminoglycoside Phosphotransferase (2'')-Ia in Complex with Gmppnp, Magnesium, and Arbekacin

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

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

Protein crystallography data

The structure of Aminoglycoside Phosphotransferase (2'')-Ia in Complex with Gmppnp, Magnesium, and Arbekacin, PDB code: 6cgg 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)*	90.14 / 2.40
*Space group*	P 1 2₁ 1
*Cell size a, b, c (Å), α, β, γ (°)*	90.330, 99.780, 93.510, 90.00, 105.43, 90.00
*R / R_free (%)*	17.8 / 22.3

Other elements in 6cgg:

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

Magnesium

(Mg)

8 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Aminoglycoside Phosphotransferase (2'')-Ia in Complex with Gmppnp, Magnesium, and Arbekacin (pdb code 6cgg). 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 Arbekacin, PDB code: 6cgg:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 6cgg

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Chlorine Binding Sites List in 6cgg

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

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 Arbekacin within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Cl802 b:83.0 occ:1.00	NE2	A:GLN462	3.2	81.8	1.0
	CB	A:GLU466	3.5	72.8	1.0
	CA	A:GLU466	3.6	66.8	1.0
	NH1	A:ARG469	3.7	59.8	1.0
	N	A:GLU466	3.7	65.2	1.0
	CG	A:GLU466	3.9	77.4	1.0
	CG2	A:ILE465	3.9	62.9	1.0
	CD	A:ARG469	4.2	52.5	1.0
	C	A:ILE465	4.2	63.3	1.0
	CD	A:GLN462	4.3	85.2	1.0
	CB	A:ILE465	4.4	63.0	1.0
	O	A:GLN462	4.4	74.8	1.0
	CG	A:GLN462	4.5	84.2	1.0
	CZ	A:ARG469	4.5	55.8	1.0
	O	A:ILE465	4.7	59.6	1.0
	NE	A:ARG469	4.7	53.3	1.0
	OE1	A:GLU466	4.9	93.9	1.0
	CD	A:GLU466	5.0	85.3	1.0
	CA	A:ILE465	5.0	62.0	1.0

Chlorine binding site 2 out of 3 in 6cgg

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Chlorine Binding Sites List in 6cgg

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

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 Arbekacin within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:Cl802 b:98.3 occ:1.00	O	A:HOH1282	2.6	49.4	1.0
	NE2	B:GLN462	2.9	82.9	1.0
	NH1	B:ARG469	3.4	59.0	1.0
	CG2	B:ILE465	4.0	59.8	1.0
	CD	B:GLN462	4.1	83.9	1.0
	CZ	B:ARG469	4.6	56.9	1.0
	OE1	B:GLN462	4.8	82.2	1.0

Chlorine binding site 3 out of 3 in 6cgg

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Chlorine Binding Sites List in 6cgg

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

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 Arbekacin within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
C:Cl802 b:67.8 occ:1.00	NE2	C:GLN462	3.4	58.2	1.0
	NH1	C:ARG469	3.4	39.7	1.0
	CA	C:GLU466	3.7	48.5	1.0
	CB	C:GLU466	3.7	54.8	1.0
	N	C:GLU466	3.8	47.0	1.0
	CG2	C:ILE465	3.8	42.3	1.0
	CD	C:ARG469	3.9	36.7	1.0
	CG	C:GLU466	4.2	59.7	1.0
	C	C:ILE465	4.2	44.8	1.0
	CZ	C:ARG469	4.3	38.8	1.0
	CB	C:ILE465	4.4	43.8	1.0
	CD	C:GLN462	4.5	60.6	1.0
	NE	C:ARG469	4.5	37.6	1.0
	O	C:ILE465	4.6	42.2	1.0
	O	C:GLN462	4.6	54.0	1.0
	CG	C:GLN462	4.7	59.4	1.0
	CA	C:ILE465	4.9	44.4	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

Page generated: Fri Jul 26 23:29:33 2024

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