Chlorine in PDB 6c5u: Aminoglycoside Phosphotransferase (2'')-Ia in Complex with Gmppnp, Magnesium, and Ribostamycin, Alternate Form

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

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

Protein crystallography data

The structure of Aminoglycoside Phosphotransferase (2'')-Ia in Complex with Gmppnp, Magnesium, and Ribostamycin, Alternate Form, PDB code: 6c5u 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)*	90.71 / 2.41
*Space group*	P 1 2₁ 1
*Cell size a, b, c (Å), α, β, γ (°)*	90.249, 100.280, 94.040, 90.00, 105.29, 90.00
*R / R_free (%)*	18 / 22.7

Other elements in 6c5u:

The structure of Aminoglycoside Phosphotransferase (2'')-Ia in Complex with Gmppnp, Magnesium, and Ribostamycin, Alternate Form 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 Ribostamycin, Alternate Form (pdb code 6c5u). 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 Ribostamycin, Alternate Form, PDB code: 6c5u:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 6c5u

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Chlorine Binding Sites List in 6c5u

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

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 Ribostamycin, Alternate Form within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Cl802 b:98.4 occ:1.00	NE2	A:GLN462	3.0	95.8	1.0
	O	A:HOH1107	3.3	84.3	1.0
	NH1	A:ARG469	3.5	71.8	1.0
	CG	A:GLU466	3.6	95.2	1.0
	CA	A:GLU466	3.6	76.5	1.0
	N	A:GLU466	3.7	72.9	1.0
	CB	A:GLU466	3.7	85.1	1.0
	CG2	A:ILE465	4.0	66.1	1.0
	CD	A:GLN462	4.2	98.0	1.0
	CD	A:ARG469	4.2	69.7	1.0
	C	A:ILE465	4.3	68.3	1.0
	CB	A:ILE465	4.4	66.8	1.0
	CG	A:GLN462	4.5	93.3	1.0
	CZ	A:ARG469	4.5	69.7	1.0
	O	A:GLN462	4.5	75.1	1.0
	O	A:ILE465	4.7	62.8	1.0
	NE	A:ARG469	4.8	67.8	1.0
	CD	A:GLU466	4.9	0.6	1.0
	CA	A:ILE465	5.0	67.1	1.0

Chlorine binding site 2 out of 3 in 6c5u

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Chlorine Binding Sites List in 6c5u

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

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 Ribostamycin, Alternate Form within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:Cl802 b:89.7 occ:1.00	NE2	B:GLN462	3.0	87.1	1.0
	CG	B:GLU466	3.3	92.0	1.0
	NH1	B:ARG469	3.3	65.3	1.0
	O	B:HOH1049	3.6	72.5	1.0
	CG2	B:ILE465	4.0	63.8	1.0
	CD	B:ARG469	4.1	61.0	1.0
	CA	B:GLU466	4.2	73.1	1.0
	N	B:GLU466	4.2	70.3	1.0
	CD	B:GLN462	4.2	85.7	1.0
	CB	B:GLU466	4.3	83.7	1.0
	CD	B:GLU466	4.3	0.1	1.0
	CZ	B:ARG469	4.4	64.6	1.0
	CB	B:ILE465	4.6	62.7	1.0
	NE	B:ARG469	4.7	61.0	1.0
	C	B:ILE465	4.7	65.3	1.0
	CG	B:GLN462	4.7	84.7	1.0
	OE1	B:GLU466	4.7	0.1	1.0

Chlorine binding site 3 out of 3 in 6c5u

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Chlorine Binding Sites List in 6c5u

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

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 Ribostamycin, Alternate Form within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
C:Cl802 b:76.2 occ:1.00	NE2	C:GLN462	3.3	70.9	1.0
	NH1	C:ARG469	3.4	51.8	1.0
	CA	C:GLU466	3.7	56.7	1.0
	N	C:GLU466	3.8	54.1	1.0
	CB	C:GLU466	3.8	64.4	1.0
	CG	C:GLU466	3.9	75.2	1.0
	CD	C:ARG469	4.0	44.6	1.0
	CG2	C:ILE465	4.0	53.1	1.0
	C	C:ILE465	4.3	51.4	1.0
	CZ	C:ARG469	4.3	47.6	1.0
	CD	C:GLN462	4.4	74.1	1.0
	CB	C:ILE465	4.5	52.8	1.0
	NE	C:ARG469	4.5	46.0	1.0
	O	C:ILE465	4.7	48.7	1.0
	O	C:GLN462	4.7	60.3	1.0
	CG	C:GLN462	4.7	71.8	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 23:18:45 2024

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