Sodium in PDB 6cgf: Crystal Structure of Hiv-1 Y188L Mutant Reverse Transcriptase in Complex with Non-Nucleoside Inhibitor K-5A2

Enzymatic activity of Crystal Structure of Hiv-1 Y188L Mutant Reverse Transcriptase in Complex with Non-Nucleoside Inhibitor K-5A2

All present enzymatic activity of Crystal Structure of Hiv-1 Y188L Mutant Reverse Transcriptase in Complex with Non-Nucleoside Inhibitor K-5A2:
2.7.7.49; 2.7.7.7; 3.1.13.2; 3.1.26.13;

Protein crystallography data

The structure of Crystal Structure of Hiv-1 Y188L Mutant Reverse Transcriptase in Complex with Non-Nucleoside Inhibitor K-5A2, PDB code: 6cgf was solved by Y.Yang, L.A.Nguyen, Z.B.Smithline, T.A.Steitz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	42.07 / 1.94
*Space group*	C 1 2 1
*Cell size a, b, c (Å), α, β, γ (°)*	162.700, 72.704, 109.048, 90.00, 100.21, 90.00
*R / R_free (%)*	19.4 / 23.2

Other elements in 6cgf:

The structure of Crystal Structure of Hiv-1 Y188L Mutant Reverse Transcriptase in Complex with Non-Nucleoside Inhibitor K-5A2 also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Hiv-1 Y188L Mutant Reverse Transcriptase in Complex with Non-Nucleoside Inhibitor K-5A2 (pdb code 6cgf). 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 Hiv-1 Y188L Mutant Reverse Transcriptase in Complex with Non-Nucleoside Inhibitor K-5A2, PDB code: 6cgf:

Sodium binding site 1 out of 1 in 6cgf

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Sodium Binding Sites List in 6cgf

Sodium binding site 1 out of 1 in the Crystal Structure of Hiv-1 Y188L Mutant Reverse Transcriptase in Complex with Non-Nucleoside Inhibitor K-5A2

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 Hiv-1 Y188L Mutant Reverse Transcriptase in Complex with Non-Nucleoside Inhibitor K-5A2 within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na603 b:0.2 occ:1.00	CD1	A:ILE526	3.9	58.8	1.0
	O	A:HOH1013	4.1	84.5	1.0
	CD2	A:TRP426	4.2	63.0	1.0
	CE2	A:TRP426	4.2	64.3	1.0
	CE3	A:TRP426	4.3	66.0	1.0
	O	A:HOH989	4.4	75.9	1.0
	CZ2	A:TRP426	4.4	69.7	1.0
	CZ3	A:TRP426	4.4	67.9	1.0
	O	A:ASP511	4.4	54.2	1.0
	CH2	A:TRP426	4.4	70.4	1.0
	CG	A:TRP426	4.7	57.3	1.0
	NE1	A:TRP426	4.8	60.5	1.0
	OE2	A:GLU523	4.9	0.9	1.0
	OE1	A:GLU523	4.9	0.6	1.0

Reference:

Y.Yang, D.Kang, L.A.Nguyen, Z.B.Smithline, C.Pannecouque, P.Zhan, X.Liu, T.A.Steitz. Structural Basis For Potent and Broad Inhibition of Hiv-1 Rt By Thiophene[3,2-D]Pyrimidine Non-Nucleoside Inhibitors. Elife V. 7 2018.
ISSN: ESSN 2050-084X
PubMed: 30044217
DOI: 10.7554/ELIFE.36340

Page generated: Mon Aug 18 04:01:52 2025

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