Calcium in PDB 2ykm: Crystal Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with A Difluoromethylbenzoxazole (Dfmb) Pyrimidine Thioether Derivative, A Non-Nucleoside Rt Inhibitor (Nnrti)

Enzymatic activity of Crystal Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with A Difluoromethylbenzoxazole (Dfmb) Pyrimidine Thioether Derivative, A Non-Nucleoside Rt Inhibitor (Nnrti)

All present enzymatic activity of Crystal Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with A Difluoromethylbenzoxazole (Dfmb) Pyrimidine Thioether Derivative, A Non-Nucleoside Rt Inhibitor (Nnrti):
2.7.7.49; 2.7.7.7; 3.1.26.13;

Protein crystallography data

The structure of Crystal Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with A Difluoromethylbenzoxazole (Dfmb) Pyrimidine Thioether Derivative, A Non-Nucleoside Rt Inhibitor (Nnrti), PDB code: 2ykm was solved by J.Boyer, E.Arnoult, M.Medebielle, J.Guillemont, T.Unge, J.Unge, D.Jochmans, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	30.00 / 2.90
*Space group*	C 2 2 2₁
*Cell size a, b, c (Å), α, β, γ (°)*	119.046, 155.576, 152.764, 90.00, 90.00, 90.00
*R / R_free (%)*	22 / 29

Other elements in 2ykm:

Fluorine

(F)

2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with A Difluoromethylbenzoxazole (Dfmb) Pyrimidine Thioether Derivative, A Non-Nucleoside Rt Inhibitor (Nnrti) (pdb code 2ykm). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total only one binding site of Calcium was determined in the Crystal Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with A Difluoromethylbenzoxazole (Dfmb) Pyrimidine Thioether Derivative, A Non-Nucleoside Rt Inhibitor (Nnrti), PDB code: 2ykm:

Calcium binding site 1 out of 1 in 2ykm

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Calcium Binding Sites List in 2ykm

Calcium binding site 1 out of 1 in the Crystal Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with A Difluoromethylbenzoxazole (Dfmb) Pyrimidine Thioether Derivative, A Non-Nucleoside Rt Inhibitor (Nnrti)

Mono view

Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with A Difluoromethylbenzoxazole (Dfmb) Pyrimidine Thioether Derivative, A Non-Nucleoside Rt Inhibitor (Nnrti) within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Ca1560 b:81.0 occ:1.00	OD1	A:ASP498	2.3	55.3	1.0
	OD1	A:ASP443	2.3	67.0	1.0
	OE1	A:GLN478	2.7	60.1	1.0
	O	A:HOH2154	3.1	87.5	1.0
	CG	A:ASP498	3.2	54.6	1.0
	OD2	A:ASP498	3.3	58.0	1.0
	O	A:GLY444	3.3	71.5	1.0
	NE2	A:GLN478	3.4	59.0	1.0
	CD	A:GLN478	3.4	60.9	1.0
	N	A:GLY444	3.5	67.5	1.0
	CG	A:ASP443	3.6	67.1	1.0
	O	A:HOH2147	3.7	53.0	1.0
	C	A:GLY444	4.1	71.3	1.0
	CA	A:GLY444	4.2	69.9	1.0
	OD2	A:ASP443	4.3	69.5	1.0
	CA	A:ASP443	4.4	64.5	1.0
	C	A:ASP443	4.5	65.7	1.0
	CB	A:ASP443	4.6	64.8	1.0
	CB	A:ASP498	4.6	51.7	1.0
	O	A:HOH2153	4.8	84.1	1.0
	C	A:ASP498	4.9	51.9	1.0
	CG	A:GLN478	4.9	60.9	1.0
	O	A:ASP498	5.0	52.7	1.0

Reference:

J.Boyer, E.Arnoult, M.Medebielle, J.Guillemont, J.Unge, D.Jochmans. Difluoromethylbenzoxazole Pyrimidine Thioether Derivatives: A Novel Class of Potent Non-Nucleoside Hiv-1 Reverse Transcriptase Inhibitors. J.Med.Chem. V. 54 7974 2011.
ISSN: ISSN 0022-2623
PubMed: 22017513
DOI: 10.1021/JM200766B

Page generated: Tue Jul 8 09:41:49 2025

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