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

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

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

Protein crystallography data

The structure of Aminoglycoside Phosphotransferase (2'')-Ia in Complex with Gmppnp, Magnesium, and Dibekacin, PDB code: 6cav 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)*	89.94 / 2.60
*Space group*	P 1 2₁ 1
*Cell size a, b, c (Å), α, β, γ (°)*	89.990, 98.340, 93.220, 90.00, 105.24, 90.00
*R / R_free (%)*	19.2 / 24.4

Other elements in 6cav:

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

Chlorine binding site 1 out of 3 in 6cav

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Chlorine Binding Sites List in 6cav

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

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 Dibekacin within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Cl802 b:72.8 occ:1.00	NE2	A:GLN462	2.8	77.6	1.0
	NH1	A:ARG469	3.6	59.9	1.0
	CG	A:GLU466	4.0	74.2	1.0
	CD	A:GLN462	4.0	81.7	1.0
	CG2	A:ILE465	4.0	55.1	1.0
	CB	A:GLU466	4.1	68.3	1.0
	N	A:GLU466	4.1	61.1	1.0
	CA	A:GLU466	4.1	62.2	1.0
	CG	A:GLN462	4.4	83.3	1.0
	CD	A:ARG469	4.4	56.3	1.0
	CB	A:ILE465	4.5	56.1	1.0
	C	A:ILE465	4.6	57.6	1.0
	CZ	A:ARG469	4.6	57.1	1.0
	O	A:GLN462	4.7	67.7	1.0
	NE	A:ARG469	4.9	57.1	1.0

Chlorine binding site 2 out of 3 in 6cav

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Chlorine Binding Sites List in 6cav

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

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 Dibekacin within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:Cl802 b:85.2 occ:1.00	NE2	B:GLN462	2.9	90.1	1.0
	NH1	B:ARG469	3.2	61.3	1.0
	CG	B:GLU466	3.6	86.0	1.0
	CG2	B:ILE465	3.8	65.9	1.0
	CD	B:ARG469	4.0	56.8	1.0
	CD	B:GLN462	4.2	92.6	1.0
	CZ	B:ARG469	4.2	58.0	1.0
	N	B:GLU466	4.3	72.1	1.0
	CA	B:GLU466	4.4	74.9	1.0
	CB	B:ILE465	4.4	66.4	1.0
	NE	B:ARG469	4.5	57.0	1.0
	CB	B:GLU466	4.5	82.4	1.0
	C	B:ILE465	4.6	68.6	1.0
	CD	B:GLU466	4.6	94.9	1.0
	CG	B:GLN462	4.8	92.3	1.0
	O	B:ILE465	4.9	68.9	1.0

Chlorine binding site 3 out of 3 in 6cav

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Chlorine Binding Sites List in 6cav

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

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 Dibekacin within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
C:Cl802 b:69.3 occ:1.00	NE2	C:GLN462	3.2	67.8	1.0
	NH1	C:ARG469	3.3	48.3	1.0
	CA	C:GLU466	3.7	54.6	1.0
	CG	C:GLU466	3.8	67.6	1.0
	CB	C:GLU466	3.8	61.2	1.0
	N	C:GLU466	3.8	51.2	1.0
	CD	C:ARG469	4.0	44.0	1.0
	CG2	C:ILE465	4.1	46.7	1.0
	CZ	C:ARG469	4.3	45.1	1.0
	C	C:ILE465	4.3	48.2	1.0
	CD	C:GLN462	4.4	69.6	1.0
	NE	C:ARG469	4.5	43.6	1.0
	CB	C:ILE465	4.5	47.9	1.0
	O	C:ILE465	4.6	48.1	1.0
	O	C:GLN462	4.8	57.6	1.0
	CG	C:GLN462	4.8	70.6	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 12:19:28 2025

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