Sodium in PDB 6evv: X-Ray Structure of the Complex Between Human Alpha Thrombin and NU172, A Duplex/Quadruplex 26-Mer Dna Aptamer, in the Presence of Potassium Ions.

Enzymatic activity of X-Ray Structure of the Complex Between Human Alpha Thrombin and NU172, A Duplex/Quadruplex 26-Mer Dna Aptamer, in the Presence of Potassium Ions.

All present enzymatic activity of X-Ray Structure of the Complex Between Human Alpha Thrombin and NU172, A Duplex/Quadruplex 26-Mer Dna Aptamer, in the Presence of Potassium Ions.:
3.4.21.5;

Protein crystallography data

The structure of X-Ray Structure of the Complex Between Human Alpha Thrombin and NU172, A Duplex/Quadruplex 26-Mer Dna Aptamer, in the Presence of Potassium Ions., PDB code: 6evv was solved by R.Troisi, I.Russo Krauss, F.Sica, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	104.02 / 2.50
*Space group*	I 2 2 2
*Cell size a, b, c (Å), α, β, γ (°)*	67.875, 113.595, 208.034, 90.00, 90.00, 90.00
*R / R_free (%)*	16.9 / 20.5

Other elements in 6evv:

The structure of X-Ray Structure of the Complex Between Human Alpha Thrombin and NU172, A Duplex/Quadruplex 26-Mer Dna Aptamer, in the Presence of Potassium Ions. also contains other interesting chemical elements:

Potassium

(K)

1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the X-Ray Structure of the Complex Between Human Alpha Thrombin and NU172, A Duplex/Quadruplex 26-Mer Dna Aptamer, in the Presence of Potassium Ions. (pdb code 6evv). 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 X-Ray Structure of the Complex Between Human Alpha Thrombin and NU172, A Duplex/Quadruplex 26-Mer Dna Aptamer, in the Presence of Potassium Ions., PDB code: 6evv:

Sodium binding site 1 out of 1 in 6evv

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Sodium Binding Sites List in 6evv

Sodium binding site 1 out of 1 in the X-Ray Structure of the Complex Between Human Alpha Thrombin and NU172, A Duplex/Quadruplex 26-Mer Dna Aptamer, in the Presence of Potassium Ions.

Mono view

Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of X-Ray Structure of the Complex Between Human Alpha Thrombin and NU172, A Duplex/Quadruplex 26-Mer Dna Aptamer, in the Presence of Potassium Ions. within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
H:Na302 b:30.6 occ:1.00	O	H:HOH437	2.2	28.4	1.0
	O	H:HOH486	2.2	31.2	1.0
	O	H:ARG221	2.3	43.0	1.0
	O	H:HOH444	2.5	24.0	1.0
	O	H:LYS224	2.5	27.4	1.0
	O	H:HOH458	2.7	37.5	1.0
	C	H:ARG221	3.3	34.7	1.0
	C	H:LYS224	3.6	33.9	1.0
	O	H:HOH490	3.7	40.9	1.0
	N	H:ARG221	3.9	28.6	1.0
	O	H:HOH438	3.9	32.1	1.0
	O	H:TYR184A	4.0	34.8	1.0
	C	H:ASP221A	4.0	25.1	1.0
	N	H:LYS224	4.0	36.7	1.0
	O	H:HOH439	4.1	24.9	1.0
	N	H:ASP222	4.1	38.1	1.0
	CA	H:ARG221	4.2	29.6	1.0
	CA	H:ASP222	4.2	42.4	1.0
	CA	H:LYS224	4.3	37.0	1.0
	O	H:ASP221A	4.3	34.5	1.0
	N	H:GLY223	4.3	32.7	1.0
	CA	H:ASP221A	4.3	34.8	1.0
	OD1	H:ASP221A	4.4	40.8	1.0
	C	H:ASP222	4.6	33.7	1.0
	CB	H:LYS224	4.6	35.0	1.0
	N	H:TYR225	4.6	27.9	1.0
	NH1	H:ARG187	4.7	63.4	1.0
	O	H:HOH450	4.7	31.6	1.0
	CA	H:TYR225	4.9	32.3	1.0
	CD1	H:TYR225	4.9	42.1	1.0

Reference:

R.Troisi, V.Napolitano, V.Spiridonova, I.Russo Krauss, F.Sica. Several Structural Motifs Cooperate in Determining the Highly Effective Anti-Thrombin Activity of NU172 Aptamer. Nucleic Acids Res. V. 46 12177 2018.
ISSN: ESSN 1362-4962
PubMed: 30357392
DOI: 10.1093/NAR/GKY990

Page generated: Tue Dec 15 12:12:47 2020

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