Sodium in PDB 2hwl: Crystal Structure of Thrombin in Complex with Fibrinogen Gamma' Peptide

All present enzymatic activity of Crystal Structure of Thrombin in Complex with Fibrinogen Gamma' Peptide:
3.4.21.5;

The structure of Crystal Structure of Thrombin in Complex with Fibrinogen Gamma' Peptide, PDB code: 2hwl was solved by A.O.Pineda, Z.W.Chen, F.Marino, F.S.Mathews, M.W.Mosesson, E.Di Cera, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 2.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	66.397, 81.523, 70.256, 90.00, 109.35, 90.00
R / Rfree (%)	21.4 / 24.9

The binding sites of Sodium atom in the Crystal Structure of Thrombin in Complex with Fibrinogen Gamma' Peptide (pdb code 2hwl). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Thrombin in Complex with Fibrinogen Gamma' Peptide, PDB code: 2hwl:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Thrombin in Complex with Fibrinogen Gamma' Peptide


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 Thrombin in Complex with Fibrinogen Gamma' Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Na802 b:51.3 occ:1.00 O B:ARG221A 2.2 53.6 1.0 O B:HOH1124 2.2 46.5 1.0 O B:HOH1134 2.4 55.2 1.0 O B:HOH1110 2.5 46.1 1.0 O B:LYS224 2.6 44.5 1.0 O B:HOH1085 2.7 39.8 1.0 C B:ARG221A 3.2 53.4 1.0 N B:ARG221A 3.7 51.2 1.0 C B:LYS224 3.7 43.6 1.0 O B:HOH1050 4.0 40.0 1.0 C B:ASP221 4.0 50.6 1.0 O B:HOH1051 4.0 42.1 1.0 N B:ASP222 4.1 53.2 1.0 CA B:ARG221A 4.1 52.8 1.0 O B:TYR184A 4.1 42.8 1.0 N B:LYS224 4.1 45.1 1.0 CA B:ASP222 4.2 54.0 1.0 CA B:ASP221 4.3 50.1 1.0 N B:GLY223 4.4 49.0 1.0 OD1 B:ASP221 4.4 48.6 1.0 CA B:LYS224 4.4 44.9 1.0 C B:ASP222 4.5 52.3 1.0 O B:ASP221 4.7 50.9 1.0 N B:TYR225 4.7 43.1 1.0 CB B:LYS224 4.8 44.8 1.0 CA B:TYR225 4.9 43.0 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Thrombin in Complex with Fibrinogen Gamma' Peptide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Thrombin in Complex with Fibrinogen Gamma' Peptide within 5.0Å range: probe atom residue distance (Å) B Occ D:Na801 b:40.6 occ:1.00 O D:HOH1038 2.4 34.0 1.0 O D:HOH1109 2.5 50.2 1.0 O D:LYS224 2.5 41.1 1.0 O D:HOH1034 2.6 38.2 1.0 O D:HOH1135 2.7 58.5 1.0 O D:ARG221A 2.7 55.2 1.0 C D:ARG221A 3.7 53.3 1.0 C D:LYS224 3.7 43.4 1.0 O D:HOH1086 3.7 39.8 1.0 O D:HOH1076 3.7 41.7 1.0 O D:HOH1061 3.8 48.2 1.0 O D:TYR184A 4.0 43.5 1.0 N D:ARG221A 4.1 49.9 1.0 C D:ASP221 4.2 48.4 1.0 N D:LYS224 4.2 47.0 1.0 CA D:ASP221 4.4 48.8 1.0 OD1 D:ASP221 4.4 44.2 1.0 N D:ASP222 4.4 53.7 1.0 CA D:ASP222 4.5 53.3 1.0 CA D:LYS224 4.5 44.9 1.0 CA D:ARG221A 4.5 52.5 1.0 N D:GLY223 4.6 48.4 1.0 N D:TYR225 4.6 41.5 1.0 O D:ASP221 4.6 47.5 1.0 CA D:TYR225 4.7 42.5 1.0 C D:ASP222 4.8 51.3 1.0 CB D:LYS224 4.9 45.5 1.0 CD1 D:TYR225 4.9 42.7 1.0

A.O.Pineda, Z.W.Chen, F.Marino, F.S.Mathews, M.W.Mosesson, E.Di Cera. Crystal Structure of Thrombin in Complex with Fibrinogen Gamma' Peptide. Biophys.Chem. V. 125 556 2007.
ISSN: ISSN 0301-4622
PubMed: 16962697
DOI: 10.1016/J.BPC.2006.08.005