Sodium in PDB 2z4o: Wild Type Hiv-1 Protease with Potent Antiviral Inhibitor Grl-98065

Enzymatic activity of Wild Type Hiv-1 Protease with Potent Antiviral Inhibitor Grl-98065

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

Protein crystallography data

The structure of Wild Type Hiv-1 Protease with Potent Antiviral Inhibitor Grl-98065, PDB code: 2z4o 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 / 1.60
*Space group*	P 2₁ 2₁ 2
*Cell size a, b, c (Å), α, β, γ (°)*	58.250, 85.832, 45.967, 90.00, 90.00, 90.00
*R / R_free (%)*	14.4 / 20.5

Other elements in 2z4o:

The structure of Wild Type Hiv-1 Protease 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 Wild Type Hiv-1 Protease with Potent Antiviral Inhibitor Grl-98065 (pdb code 2z4o). 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 Wild Type Hiv-1 Protease with Potent Antiviral Inhibitor Grl-98065, PDB code: 2z4o:

Sodium binding site 1 out of 1 in 2z4o

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Sodium Binding Sites List in 2z4o

Sodium binding site 1 out of 1 in the Wild Type Hiv-1 Protease 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 Wild Type Hiv-1 Protease with Potent Antiviral Inhibitor Grl-98065 within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na500 b:23.9 occ:1.00	O	A:HOH510	2.3	21.1	1.0
	O	A:HOH515	2.3	21.8	1.0
	O	A:HOH530	2.3	29.4	1.0
	O	A:ASP60	2.4	15.4	1.0
	O	A:HOH522	2.5	25.0	1.0
	O	A:HOH532	2.6	25.8	1.0
	C	A:ASP60	3.5	14.6	1.0
	N	A:ASP60	3.7	12.9	1.0
	CA	A:ASP60	4.1	14.2	1.0
	O	A:ARG41	4.1	18.4	1.0
	CB	A:ASP60	4.4	16.6	1.0
	N	A:ARG41	4.5	23.8	1.0
	N	A:GLN61	4.5	14.3	1.0
	CB	A:GLN61	4.5	17.7	1.0
	O	A:HOH580	4.6	36.9	1.0
	O	A:HOH614	4.6	39.3	1.0
	O	A:HOH605	4.6	25.4	0.5
	CD1	A:ILE62	4.6	15.5	1.0
	O	A:GLN61	4.7	17.4	1.0
	C	A:TYR59	4.7	10.7	1.0
	O	A:PRO39	4.7	20.5	1.0
	C	A:GLN61	4.8	14.7	1.0
	OE1	A:GLN61	4.8	37.3	1.0
	CA	A:GLN61	4.8	14.8	1.0
	CA	A:GLY40	4.9	23.3	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: Sun Aug 17 12:29:27 2025

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