Calcium in PDB 4dy7: 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;

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 / Rfree (%)	22.3 / 26.8

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

Sodium

(Na)

1 atom

The binding sites of Calcium 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 Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structures of Protease Nexin-1 in Complex with S195A Thrombin, PDB code: 4dy7:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structures of Protease Nexin-1 in Complex with S195A Thrombin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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 A:Ca102 b:52.6 occ:1.00 O A:ARG15 2.2 33.1 1.0 OXT A:ACT101 2.3 45.3 1.0 OD2 A:ASP14L 2.4 28.9 1.0 O B:GLY133 2.4 29.6 1.0 O A:SER14I 2.5 23.2 1.0 O A:ACT101 2.8 44.5 1.0 C A:ACT101 2.9 45.8 1.0 C B:GLY133 3.3 29.4 1.0 CG A:ASP14L 3.3 26.1 1.0 C A:ARG15 3.4 33.4 1.0 C A:SER14I 3.7 25.1 1.0 OD1 A:ASP14L 3.7 27.9 1.0 OG A:SER14I 3.9 33.1 1.0 CA B:GLY133 3.9 26.6 1.0 N A:ARG15 4.0 34.6 1.0 OXT A:ARG15 4.2 31.4 1.0 N B:TYR134 4.2 27.7 1.0 CA A:SER14I 4.3 24.0 1.0 CA A:ARG15 4.3 34.5 1.0 CH3 A:ACT101 4.4 47.6 1.0 CD1 B:TYR134 4.5 30.5 1.0 N A:ASP14L 4.5 26.2 1.0 N A:GLY14M 4.5 31.3 1.0 CB A:ASP14L 4.6 25.6 1.0 CA B:TYR134 4.6 26.3 1.0 CG A:ARG15 4.6 32.5 1.0 CB A:SER14I 4.7 24.4 1.0 N A:TYR14J 4.7 25.2 1.0 C A:TYR14J 4.9 23.7 1.0 CA A:ASP14L 4.9 25.8 1.0 C A:GLY14M 5.0 31.9 1.0 CE1 B:TYR134 5.0 33.3 1.0 CA A:TYR14J 5.0 24.5 1.0

Calcium binding site 2 out of 2 in the Crystal Structures of Protease Nexin-1 in Complex with S195A Thrombin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structures of Protease Nexin-1 in Complex with S195A Thrombin within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca401 b:0.6 occ:1.00 O F:THR309 2.3 53.8 1.0 O F:GLY311 2.7 54.4 1.0 O F:ALA306 3.4 49.5 1.0 N F:GLY311 3.4 66.4 1.0 C F:THR309 3.4 53.4 1.0 C F:GLY311 3.7 60.4 1.0 OG1 F:THR309 4.0 44.8 1.0 OE2 F:GLU104 4.0 66.3 1.0 C F:THR310 4.0 61.9 1.0 CA F:GLY311 4.1 64.0 1.0 CA F:THR310 4.1 57.6 1.0 N F:THR310 4.2 56.4 1.0 C F:ALA306 4.2 40.9 1.0 CA F:THR309 4.5 48.2 1.0 CB F:THR309 4.7 42.4 1.0 CA F:ALA306 4.7 40.5 1.0 N F:THR309 4.7 47.5 1.0 N F:SER312 4.8 58.1 1.0 O F:THR310 4.9 72.7 1.0 CB F:ALA306 4.9 38.2 1.0 CD F:GLU104 5.0 62.7 1.0

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