Sodium in PDB 3b7v: Hiv-1 Protease Complexed with Gem-Diol-Amine Tetrahedral Intermediate Nlltqi

Enzymatic activity of Hiv-1 Protease Complexed with Gem-Diol-Amine Tetrahedral Intermediate Nlltqi

All present enzymatic activity of Hiv-1 Protease Complexed with Gem-Diol-Amine Tetrahedral Intermediate Nlltqi:
3.4.23.16;

Protein crystallography data

The structure of Hiv-1 Protease Complexed with Gem-Diol-Amine Tetrahedral Intermediate Nlltqi, PDB code: 3b7v was solved by A.Y.Kovalevsky, A.A.Chumanevich, I.T.Weber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	10.00 / 1.46
*Space group*	P 2₁ 2₁ 2
*Cell size a, b, c (Å), α, β, γ (°)*	58.304, 86.121, 46.307, 90.00, 90.00, 90.00
*R / R_free (%)*	15.2 / 21.2

Other elements in 3b7v:

The structure of Hiv-1 Protease Complexed with Gem-Diol-Amine Tetrahedral Intermediate Nlltqi also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Hiv-1 Protease Complexed with Gem-Diol-Amine Tetrahedral Intermediate Nlltqi (pdb code 3b7v). 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 Complexed with Gem-Diol-Amine Tetrahedral Intermediate Nlltqi, PDB code: 3b7v:

Sodium binding site 1 out of 1 in 3b7v

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Sodium Binding Sites List in 3b7v

Sodium binding site 1 out of 1 in the Hiv-1 Protease Complexed with Gem-Diol-Amine Tetrahedral Intermediate Nlltqi

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 Complexed with Gem-Diol-Amine Tetrahedral Intermediate Nlltqi within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na901 b:22.5 occ:1.00	O	A:HOH1125	2.3	26.9	1.0
	O	A:ASP60	2.3	16.1	1.0
	O	A:HOH1010	2.3	20.3	1.0
	O	A:HOH1123	2.4	40.2	1.0
	O	A:HOH1023	2.5	22.0	1.0
	O	A:HOH1124	3.0	32.9	1.0
	C	A:ASP60	3.3	14.4	1.0
	N	A:ASP60	3.7	14.5	1.0
	CA	A:ASP60	4.0	14.7	1.0
	O	A:ARG41	4.3	16.9	1.0
	N	A:GLN61	4.4	15.1	1.0
	CB	A:GLN61	4.4	20.2	1.0
	CB	A:ASP60	4.4	16.0	1.0
	O	A:GLN61	4.6	20.5	1.0
	O	A:PRO39	4.6	20.5	1.0
	CD1	A:ILE62	4.7	16.9	1.0
	C	A:TYR59	4.7	10.8	1.0
	C	A:GLN61	4.7	16.0	1.0
	CA	A:GLN61	4.7	15.9	1.0
	N	A:ARG41	4.8	20.2	1.0
	O	A:HOH1117	4.8	51.2	1.0
	CA	A:GLY40	4.9	22.2	1.0

Reference:

A.Y.Kovalevsky, A.A.Chumanevich, F.Liu, J.M.Louis, I.T.Weber. Caught in the Act: the 1.5 A Resolution Crystal Structures of the Hiv-1 Protease and the I54V Mutant Reveal A Tetrahedral Reaction Intermediate. Biochemistry V. 46 14854 2007.
ISSN: ISSN 0006-2960
PubMed: 18052235
DOI: 10.1021/BI700822G

Page generated: Tue Dec 15 06:03:15 2020

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