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

Go back to

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

Go back to

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

Go back to

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: Fri Jul 26 23:29:33 2024

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1

	© Copyright 2008-2020 by atomistry.com
Home \| Site Map \| Copyright \| Contact us \| Privacy