Sodium in PDB 1de7: Interaction of Factor XIII Activation Peptide with Alpha-Thrombin: Crystal Structure of the Enzyme-Substrate Complex

All present enzymatic activity of Interaction of Factor XIII Activation Peptide with Alpha-Thrombin: Crystal Structure of the Enzyme-Substrate Complex:
3.4.21.5;

The structure of Interaction of Factor XIII Activation Peptide with Alpha-Thrombin: Crystal Structure of the Enzyme-Substrate Complex, PDB code: 1de7 was solved by C.Sadasivan, V.C.Yee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	54.070, 81.260, 85.460, 90.00, 101.62, 90.00
R / Rfree (%)	19.4 / 25.7

The binding sites of Sodium atom in the Interaction of Factor XIII Activation Peptide with Alpha-Thrombin: Crystal Structure of the Enzyme-Substrate Complex (pdb code 1de7). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Interaction of Factor XIII Activation Peptide with Alpha-Thrombin: Crystal Structure of the Enzyme-Substrate Complex, PDB code: 1de7:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Interaction of Factor XIII Activation Peptide with Alpha-Thrombin: Crystal Structure of the Enzyme-Substrate Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Interaction of Factor XIII Activation Peptide with Alpha-Thrombin: Crystal Structure of the Enzyme-Substrate Complex within 5.0Å range: probe atom residue distance (Å) B Occ H:Na1 b:16.2 occ:1.00 O H:HOH250 2.2 15.2 1.0 O H:LYS224 2.2 15.4 1.0 O H:HOH249 2.2 14.5 1.0 O H:HOH251 2.2 19.5 1.0 O H:ARG221A 2.2 18.9 1.0 O H:HOH252 2.2 24.6 1.0 C H:LYS224 3.3 17.5 1.0 C H:ARG221A 3.3 17.7 1.0 N H:LYS224 3.8 17.9 1.0 O H:HOH253 3.8 13.4 1.0 N H:ARG221A 3.9 18.3 1.0 O H:TYR184A 3.9 19.7 1.0 O H:HOH258 4.0 16.5 1.0 CA H:LYS224 4.0 17.5 1.0 C H:ASP221 4.1 18.5 1.0 N H:ASP222 4.1 19.1 1.0 O H:HOH289 4.2 14.6 1.0 CA H:ARG221A 4.3 20.2 1.0 N H:GLY223 4.3 16.8 1.0 CA H:ASP222 4.3 20.6 1.0 N H:TYR225 4.4 17.9 1.0 CA H:ASP221 4.4 18.1 1.0 O H:ASP221 4.5 19.1 1.0 CB H:LYS224 4.5 19.3 1.0 C H:ASP222 4.6 19.2 1.0 CA H:TYR225 4.7 16.7 1.0 C H:GLY223 4.7 17.0 1.0 OD1 H:ASP221 4.8 19.1 1.0 O H:HOH497 5.0 21.4 1.0 O H:HOH328 5.0 33.6 1.0

Sodium binding site 2 out of 2 in the Interaction of Factor XIII Activation Peptide with Alpha-Thrombin: Crystal Structure of the Enzyme-Substrate Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Interaction of Factor XIII Activation Peptide with Alpha-Thrombin: Crystal Structure of the Enzyme-Substrate Complex within 5.0Å range: probe atom residue distance (Å) B Occ K:Na2 b:23.6 occ:1.00 O K:HOH250 2.2 21.4 1.0 O K:HOH252 2.2 20.2 1.0 O K:LYS224 2.2 23.8 1.0 O K:ARG221A 2.2 25.1 1.0 O K:HOH249 2.2 25.2 1.0 O K:HOH251 2.2 24.3 1.0 C K:ARG221A 3.2 23.3 1.0 C K:LYS224 3.3 25.2 1.0 N K:ARG221A 3.7 26.8 1.0 N K:LYS224 3.9 23.2 1.0 O K:HOH417 3.9 26.4 1.0 O K:HOH281 3.9 20.1 1.0 O K:TYR184A 4.0 24.8 1.0 CA K:ARG221A 4.1 25.2 1.0 N K:ASP222 4.1 23.8 1.0 C K:ASP221 4.1 24.3 1.0 CA K:LYS224 4.1 24.5 1.0 CA K:ASP222 4.2 25.9 1.0 O K:HOH272 4.3 18.8 1.0 CA K:ASP221 4.4 24.5 1.0 N K:GLY223 4.4 25.0 1.0 N K:TYR225 4.4 24.3 1.0 OD1 K:ASP221 4.5 25.0 1.0 CB K:LYS224 4.6 23.7 1.0 C K:ASP222 4.6 26.7 1.0 CA K:TYR225 4.7 23.6 1.0 O K:ASP221 4.7 25.3 1.0 O K:HOH389 4.8 40.1 1.0 CD2 K:TYR225 4.9 23.2 1.0 C K:GLY223 4.9 23.8 1.0 CE2 K:TYR225 5.0 23.9 1.0

C.Sadasivan, V.C.Yee. Interaction of the Factor XIII Activation Peptide with Alpha -Thrombin. Crystal Structure of Its Enzyme-Substrate Analog Complex. J.Biol.Chem. V. 275 36942 2000.
ISSN: ISSN 0021-9258
PubMed: 10956659
DOI: 10.1074/JBC.M006076200