Sodium in PDB 1oyt: Complex of Recombinant Human Thrombin with A Designed Fluorinated Inhibitor

Enzymatic activity of Complex of Recombinant Human Thrombin with A Designed Fluorinated Inhibitor

All present enzymatic activity of Complex of Recombinant Human Thrombin with A Designed Fluorinated Inhibitor:
3.4.21.5;

Protein crystallography data

The structure of Complex of Recombinant Human Thrombin with A Designed Fluorinated Inhibitor, PDB code: 1oyt was solved by D.W.Banner, J.A.Olsen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	19.30 / 1.67
*Space group*	C 1 2 1
*Cell size a, b, c (Å), α, β, γ (°)*	70.693, 71.479, 72.802, 90.00, 100.53, 90.00
*R / R_free (%)*	n/a / n/a

Other elements in 1oyt:

The structure of Complex of Recombinant Human Thrombin with A Designed Fluorinated Inhibitor also contains other interesting chemical elements:

Fluorine	(F)	1 atom
Calcium	(Ca)	1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Complex of Recombinant Human Thrombin with A Designed Fluorinated Inhibitor (pdb code 1oyt). 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 Complex of Recombinant Human Thrombin with A Designed Fluorinated Inhibitor, PDB code: 1oyt:

Sodium binding site 1 out of 1 in 1oyt

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Sodium Binding Sites List in 1oyt

Sodium binding site 1 out of 1 in the Complex of Recombinant Human Thrombin with A Designed Fluorinated Inhibitor

Mono view

Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Complex of Recombinant Human Thrombin with A Designed Fluorinated Inhibitor within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
H:Na601 b:15.6 occ:1.00	O	H:HOH737	2.3	14.2	1.0
	O	H:HOH727	2.4	16.5	1.0
	O	H:ARG221A	2.4	15.4	1.0
	O	H:LYS224	2.5	12.9	1.0
	O	H:HOH724	2.5	12.6	1.0
	O	H:HOH729	2.8	15.4	1.0
	C	H:ARG221A	3.4	15.6	1.0
	C	H:LYS224	3.5	13.0	1.0
	N	H:LYS224	3.8	13.5	1.0
	N	H:ARG221A	3.9	15.1	1.0
	O	H:HOH728	4.0	12.4	1.0
	O	H:HOH746	4.0	18.2	1.0
	C	H:ASP221	4.0	15.1	1.0
	O	H:TYR184A	4.1	13.8	1.0
	N	H:GLY223	4.2	15.1	1.0
	CA	H:LYS224	4.2	12.9	1.0
	O	H:HOH718	4.2	12.5	1.0
	N	H:ASP222	4.2	15.3	1.0
	CA	H:ASP222	4.3	15.9	1.0
	CA	H:ARG221A	4.3	15.7	1.0
	CA	H:ASP221	4.3	14.8	1.0
	C	H:ASP222	4.5	15.5	1.0
	O	H:ASP221	4.5	15.3	1.0
	N	H:TYR225	4.5	12.0	1.0
	CB	H:LYS224	4.5	13.8	1.0
	OD1	H:ASP221	4.6	14.5	1.0
	O	H:HOH787	4.8	21.2	1.0
	CA	H:TYR225	4.8	11.6	1.0
	C	H:GLY223	4.8	14.0	1.0
	O	H:HOH740	5.0	16.4	1.0

Reference:

J.A.Olsen, D.W.Banner, P.Seiler, U.Obst-Sander, A.D'arcy, M.Stihle, K.Mueller, F.Diederich. A Fluorine Scan of Thrombin Inhibitors to Map the Fluorophilicity/Fluorophobicity of An Enzyme Active Site: Evidence For Cf...C=O Interactions. Angew.Chem.Int.Ed.Engl. V. 42 2507 2003.
ISSN: ISSN 1433-7851
PubMed: 12800172
DOI: 10.1002/ANIE.200351268

Page generated: Sun Oct 6 21:13:57 2024

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