Sodium in PDB 2qd6: Hiv-1 Protease Mutant I50V with Potent Antiviral Inhibitor Grl-98065

Enzymatic activity of Hiv-1 Protease Mutant I50V with Potent Antiviral Inhibitor Grl-98065

All present enzymatic activity of Hiv-1 Protease Mutant I50V with Potent Antiviral Inhibitor Grl-98065:
3.4.23.16;

Protein crystallography data

The structure of Hiv-1 Protease Mutant I50V with Potent Antiviral Inhibitor Grl-98065, PDB code: 2qd6 was solved by Y.F.Wang, Y.Tie, P.I.Boross, J.Tozser, A.K.Ghosh, R.W.Harrison, I.T.Weber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	10.00 / 1.28
*Space group*	P 2₁ 2₁ 2
*Cell size a, b, c (Å), α, β, γ (°)*	58.294, 86.228, 46.006, 90.00, 90.00, 90.00
*R / R_free (%)*	15.5 / 20.2

Other elements in 2qd6:

The structure of Hiv-1 Protease Mutant I50V with Potent Antiviral Inhibitor Grl-98065 also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Hiv-1 Protease Mutant I50V with Potent Antiviral Inhibitor Grl-98065 (pdb code 2qd6). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Hiv-1 Protease Mutant I50V with Potent Antiviral Inhibitor Grl-98065, PDB code: 2qd6:

Sodium binding site 1 out of 1 in 2qd6

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Sodium Binding Sites List in 2qd6

Sodium binding site 1 out of 1 in the Hiv-1 Protease Mutant I50V with Potent Antiviral Inhibitor Grl-98065

Mono view

Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Hiv-1 Protease Mutant I50V with Potent Antiviral Inhibitor Grl-98065 within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na500 b:26.2 occ:1.00	O	A:HOH533	2.2	22.8	1.0
	O	A:ASP60	2.3	14.9	1.0
	O	A:HOH512	2.3	22.3	1.0
	O	A:HOH521	2.3	27.6	1.0
	O	A:HOH549	2.5	29.4	1.0
	O	A:HOH530	2.8	32.2	1.0
	C	A:ASP60	3.4	13.7	1.0
	N	A:ASP60	3.7	13.2	1.0
	CA	A:ASP60	4.0	14.1	1.0
	O	A:ARG41	4.2	17.6	1.0
	CB	A:ASP60	4.4	16.4	1.0
	CB	A:GLN61	4.4	18.0	1.0
	N	A:GLN61	4.4	14.0	1.0
	N	A:ARG41	4.5	22.1	1.0
	O	A:PRO39	4.6	24.0	1.0
	O	A:GLN61	4.6	18.8	1.0
	C	A:TYR59	4.7	10.8	1.0
	CD1	A:ILE62	4.7	17.0	1.0
	CA	A:GLY40	4.7	22.5	1.0
	CA	A:GLN61	4.8	14.5	1.0
	C	A:GLN61	4.8	14.4	1.0
	OE1	A:GLN61	4.8	42.8	1.0

Reference:

Y.F.Wang, Y.Tie, P.I.Boross, J.Tozser, A.K.Ghosh, R.W.Harrison, I.T.Weber. Potent New Antiviral Compound Shows Similar Inhibition and Structural Interactions with Drug Resistant Mutants and Wild Type Hiv-1 Protease. J.Med.Chem. V. 50 4509 2007.
ISSN: ISSN 0022-2623
PubMed: 17696515
DOI: 10.1021/JM070482Q

Page generated: Mon Oct 7 03:49:29 2024

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