Sodium in PDB 3h5b: Crystal Structure of Wild Type Hiv-1 Protease with Novel P1'-Ligand Grl-02031

Enzymatic activity of Crystal Structure of Wild Type Hiv-1 Protease with Novel P1'-Ligand Grl-02031

All present enzymatic activity of Crystal Structure of Wild Type Hiv-1 Protease with Novel P1'-Ligand Grl-02031:
3.4.23.16;

Protein crystallography data

The structure of Crystal Structure of Wild Type Hiv-1 Protease with Novel P1'-Ligand Grl-02031, PDB code: 3h5b was solved by Y.Tie, Y.F.Wang, I.T.Weber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	10.00 / 1.29
*Space group*	P 2₁ 2₁ 2
*Cell size a, b, c (Å), α, β, γ (°)*	58.111, 86.416, 45.970, 90.00, 90.00, 90.00
*R / R_free (%)*	14.2 / 18.1

Other elements in 3h5b:

The structure of Crystal Structure of Wild Type Hiv-1 Protease with Novel P1'-Ligand Grl-02031 also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Wild Type Hiv-1 Protease with Novel P1'-Ligand Grl-02031 (pdb code 3h5b). 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 Crystal Structure of Wild Type Hiv-1 Protease with Novel P1'-Ligand Grl-02031, PDB code: 3h5b:

Sodium binding site 1 out of 1 in 3h5b

Go back to

Sodium Binding Sites List in 3h5b

Sodium binding site 1 out of 1 in the Crystal Structure of Wild Type Hiv-1 Protease with Novel P1'-Ligand Grl-02031

Mono view

Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Wild Type Hiv-1 Protease with Novel P1'-Ligand Grl-02031 within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na501 b:25.4 occ:1.00	O	A:HOH1036	2.3	24.7	1.0
	O	A:HOH1139	2.3	27.6	0.5
	O	A:HOH1060	2.3	29.9	1.0
	O	A:ASP60	2.4	17.6	1.0
	O	A:HOH1073	2.4	25.8	1.0
	O	A:HOH1084	2.7	33.3	1.0
	C	A:ASP60	3.4	16.6	1.0
	N	A:ASP60	3.7	14.5	1.0
	CA	A:ASP60	4.0	15.8	1.0
	O	A:ARG41	4.2	20.2	1.0
	CB	A:ASP60	4.3	18.3	1.0
	N	A:GLN61	4.5	15.3	1.0
	CB	A:GLN61	4.5	18.8	1.0
	N	A:ARG41	4.6	26.5	1.0
	C	A:TYR59	4.7	12.7	1.0
	O	A:PRO39	4.7	23.9	1.0
	CD1	A:ILE62	4.7	18.4	1.0
	O	A:GLN61	4.8	20.0	1.0
	CA	A:GLY40	4.8	26.6	1.0
	CA	A:GLN61	4.9	15.3	1.0
	C	A:GLN61	4.9	15.3	1.0
	OE1	A:GLN61	4.9	47.4	1.0

Reference:

A.K.Ghosh, S.Leshchenko-Yashchuk, D.D.Anderson, A.Baldridge, M.Noetzel, H.B.Miller, Y.Tie, Y.F.Wang, Y.Koh, I.T.Weber, H.Mitsuya. Design of Hiv-1 Protease Inhibitors with Pyrrolidinones and Oxazolidinones As Novel P1'-Ligands to Enhance Backbone-Binding Interactions with Protease: Synthesis, Biological Evaluation, and Protein-Ligand X-Ray Studies. J.Med.Chem. V. 52 3902 2009.
ISSN: ISSN 0022-2623
PubMed: 19473017
DOI: 10.1021/JM900303M

Page generated: Mon Oct 7 10:21:43 2024

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