Sodium in PDB 4dy7: Crystal Structures of Protease Nexin-1 in Complex with S195A Thrombin

Enzymatic activity of Crystal Structures of Protease Nexin-1 in Complex with S195A Thrombin

All present enzymatic activity of Crystal Structures of Protease Nexin-1 in Complex with S195A Thrombin:
3.4.21.5;

Protein crystallography data

The structure of Crystal Structures of Protease Nexin-1 in Complex with S195A Thrombin, PDB code: 4dy7 was solved by J.A.Huntington, W.Li, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	47.04 / 2.80
*Space group*	C 1 2 1
*Cell size a, b, c (Å), α, β, γ (°)*	191.960, 86.670, 101.890, 90.00, 94.44, 90.00
*R / R_free (%)*	22.3 / 26.8

Other elements in 4dy7:

The structure of Crystal Structures of Protease Nexin-1 in Complex with S195A Thrombin also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structures of Protease Nexin-1 in Complex with S195A Thrombin (pdb code 4dy7). 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 Structures of Protease Nexin-1 in Complex with S195A Thrombin, PDB code: 4dy7:

Sodium binding site 1 out of 1 in 4dy7

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Sodium Binding Sites List in 4dy7

Sodium binding site 1 out of 1 in the Crystal Structures of Protease Nexin-1 in Complex with S195A Thrombin

Mono view

Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structures of Protease Nexin-1 in Complex with S195A Thrombin within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:Na302 b:74.7 occ:1.00	O	B:ARG221A	2.6	44.9	1.0
	O	B:LYS224	3.0	40.3	1.0
	O	B:HOH424	3.1	44.7	1.0
	N	B:ARG221A	3.6	42.7	1.0
	C	B:ARG221A	3.6	45.4	1.0
	C	B:ASP221	3.7	46.8	1.0
	O	B:HOH414	3.8	43.4	1.0
	CA	B:ASP221	3.8	45.4	1.0
	C	B:LYS224	3.9	40.3	1.0
	OD1	B:ASP221	4.2	47.7	1.0
	CA	B:ARG221A	4.2	43.3	1.0
	O	B:HOH425	4.3	64.2	1.0
	O	B:ASP221	4.3	43.0	1.0
	O	B:GLY188	4.4	35.6	1.0
	O	B:TYR184A	4.5	33.6	1.0
	N	B:LYS224	4.6	41.8	1.0
	N	B:ASP221	4.6	37.6	1.0
	CA	B:LYS224	4.6	41.5	1.0
	N	B:ASP222	4.6	43.1	1.0
	N	B:TYR225	4.7	36.0	1.0
	CB	B:LYS224	4.8	43.6	1.0
	CB	B:ASP189	4.8	29.0	1.0
	OD2	B:ASP189	4.8	29.3	1.0
	CA	B:TYR225	4.8	34.6	1.0
	CB	B:ARG221A	5.0	45.5	1.0
	CG	B:ASP221	5.0	45.4	1.0
	CA	B:ASP222	5.0	38.2	1.0

Reference:

W.Li, J.A.Huntington. Crystal Structures of Protease Nexin-1 in Complex with Heparin and Thrombin Suggest A 2-Step Recognition Mechanism. Blood V. 120 459 2012.
ISSN: ISSN 0006-4971
PubMed: 22618708
DOI: 10.1182/BLOOD-2012-03-415869

Page generated: Sun Aug 17 19:04:46 2025

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