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

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

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

Protein crystallography data

The structure of Aminoglycoside Phosphotransferase (2'')-Ia in Complex with Gmppnp, Magnesium, and Amikacin, PDB code: 6cgd 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)*	90.74 / 2.20
*Space group*	P 1 2₁ 1
*Cell size a, b, c (Å), α, β, γ (°)*	90.080, 100.220, 93.990, 90.00, 105.12, 90.00
*R / R_free (%)*	17.2 / 20.9

Other elements in 6cgd:

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

Chlorine binding site 1 out of 3 in 6cgd

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Chlorine Binding Sites List in 6cgd

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

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 Amikacin within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Cl802 b:77.7 occ:1.00	O	A:HOH1107	3.1	58.8	1.0
	NE2	A:GLN462	3.2	75.4	1.0
	NH1	A:ARG469	3.5	50.7	1.0
	CG2	A:ILE465	3.7	48.1	1.0
	CA	A:GLU466	3.7	55.2	1.0
	N	A:GLU466	3.8	50.4	1.0
	CD	A:ARG469	3.8	42.9	1.0
	CB	A:GLU466	4.0	64.2	1.0
	CG	A:GLU466	4.2	77.3	1.0
	C	A:ILE465	4.2	48.2	1.0
	CZ	A:ARG469	4.3	45.1	1.0
	CB	A:ILE465	4.3	49.0	1.0
	NE	A:ARG469	4.4	42.7	1.0
	CD	A:GLN462	4.5	75.8	1.0
	O	A:ILE465	4.5	44.1	1.0
	O	A:GLN462	4.7	59.6	1.0
	O	A:HOH1049	4.8	64.2	1.0
	CG	A:GLN462	4.9	73.4	1.0
	CA	A:ILE465	4.9	45.9	1.0

Chlorine binding site 2 out of 3 in 6cgd

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Chlorine Binding Sites List in 6cgd

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

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 Amikacin within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:Cl802 b:81.5 occ:1.00	NE2	B:GLN462	3.1	74.9	1.0
	O	B:HOH1107	3.3	60.2	1.0
	CG	B:GLU466	3.3	70.2	1.0
	NH1	B:ARG469	3.4	41.4	1.0
	CG2	B:ILE465	3.8	44.7	1.0
	CD	B:ARG469	3.9	38.3	1.0
	O	B:HOH1049	4.0	57.5	1.0
	CA	B:GLU466	4.1	55.8	1.0
	N	B:GLU466	4.1	50.4	1.0
	CB	B:GLU466	4.2	64.5	1.0
	CZ	B:ARG469	4.3	42.2	1.0
	CD	B:GLN462	4.4	71.8	1.0
	CD	B:GLU466	4.4	85.7	1.0
	C	B:ILE465	4.5	48.9	1.0
	NE	B:ARG469	4.5	40.9	1.0
	CB	B:ILE465	4.5	44.5	1.0
	O	B:ILE465	4.8	46.0	1.0
	CG	B:GLN462	4.8	70.7	1.0
	O	B:GLN462	4.9	59.5	1.0
	OE1	B:GLU466	5.0	80.2	1.0

Chlorine binding site 3 out of 3 in 6cgd

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Chlorine Binding Sites List in 6cgd

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

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 Amikacin within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
C:Cl802 b:68.1 occ:1.00	NE2	C:GLN462	3.2	59.6	1.0
	NH1	C:ARG469	3.5	34.7	1.0
	CA	C:GLU466	3.8	35.8	1.0
	N	C:GLU466	3.8	34.4	1.0
	CG2	C:ILE465	3.9	37.7	1.0
	CD	C:ARG469	3.9	30.4	1.0
	CB	C:GLU466	4.0	43.9	1.0
	CG	C:GLU466	4.2	54.7	1.0
	C	C:ILE465	4.3	35.4	1.0
	CD	C:GLN462	4.4	58.4	1.0
	CZ	C:ARG469	4.4	32.2	1.0
	CB	C:ILE465	4.4	37.4	1.0
	NE	C:ARG469	4.5	28.7	1.0
	O	C:GLN462	4.7	43.3	1.0
	O	C:ILE465	4.7	30.2	1.0
	CG	C:GLN462	4.7	55.2	1.0
	O	C:HOH1049	4.7	57.2	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: Sat Jul 12 12:23:09 2025

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