Calcium in PDB 4kty: Fibrin-Stabilizing Factor with A Bound Ligand

All present enzymatic activity of Fibrin-Stabilizing Factor with A Bound Ligand:
2.3.2.13;

The structure of Fibrin-Stabilizing Factor with A Bound Ligand, PDB code: 4kty was solved by M.Stieler, A.Heine, G.Klebe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.80 / 1.98
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	56.761, 80.510, 102.844, 88.14, 76.70, 82.01
R / Rfree (%)	16.9 / 20.6

The binding sites of Calcium atom in the Fibrin-Stabilizing Factor with A Bound Ligand (pdb code 4kty). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Fibrin-Stabilizing Factor with A Bound Ligand, PDB code: 4kty:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Fibrin-Stabilizing Factor with A Bound Ligand


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Fibrin-Stabilizing Factor with A Bound Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca801 b:15.9 occ:1.00 OD1 A:ASN267 2.4 13.0 1.0 O A:ASN267 2.4 11.4 1.0 O A:HOH906 2.4 13.5 1.0 O A:ALA264 2.4 13.2 1.0 O A:LYS269 2.4 16.4 1.0 OD1 A:ASP271 2.5 19.8 1.0 OD2 A:ASP271 2.6 19.4 1.0 CG A:ASP271 2.8 20.0 1.0 CG A:ASN267 3.3 15.6 1.0 C A:ALA264 3.3 10.2 1.0 C A:ASN267 3.3 14.5 1.0 C A:LYS269 3.6 18.7 1.0 N A:LYS269 3.8 15.8 1.0 C A:ALA268 3.9 17.3 1.0 ND2 A:ASN267 4.0 14.2 1.0 CA A:ASN267 4.1 10.3 1.0 CA A:ALA264 4.1 10.9 1.0 CA A:LYS269 4.1 17.9 1.0 N A:MET265 4.2 10.2 1.0 N A:ALA268 4.2 14.6 1.0 CB A:ASN267 4.2 9.6 1.0 CA A:MET265 4.3 12.9 1.0 CB A:ASP271 4.3 16.3 1.0 O A:ALA268 4.3 18.0 1.0 N A:ASN267 4.3 11.4 1.0 N A:ASP271 4.4 19.1 1.0 O A:TYR407 4.4 16.1 1.0 OD2 A:ASP270 4.4 19.5 1.0 CB A:ALA264 4.4 10.2 1.0 CA A:ALA268 4.4 15.0 1.0 CB A:LYS269 4.5 22.7 1.0 C A:MET265 4.6 13.4 1.0 CB A:ASP270 4.6 21.3 1.0 N A:ASP270 4.7 19.5 1.0 N A:GLY273 4.7 19.8 1.0 CA A:ASP271 4.8 20.4 1.0 CA A:GLY273 4.8 14.8 1.0 O A:MET265 4.9 10.4 1.0 CG A:ASP270 5.0 22.0 1.0

Calcium binding site 2 out of 6 in the Fibrin-Stabilizing Factor with A Bound Ligand


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Fibrin-Stabilizing Factor with A Bound Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca802 b:29.7 occ:1.00 OD1 A:ASP345 2.3 33.5 1.0 OD2 A:ASP367 2.4 31.6 1.0 O A:GLN349 2.4 28.2 1.0 OD1 A:ASP343 2.4 26.0 1.0 OD1 A:ASN347 2.4 31.5 1.0 OD2 A:ASP351 2.5 32.4 1.0 CG A:ASP367 3.3 29.9 1.0 CG A:ASP345 3.4 37.7 1.0 CG A:ASN347 3.4 31.3 1.0 OD1 A:ASP367 3.5 29.4 1.0 CG A:ASP343 3.6 24.6 1.0 C A:GLN349 3.6 28.9 1.0 CG A:ASP351 3.6 39.0 1.0 ND2 A:ASN347 3.8 33.0 1.0 OD2 A:ASP345 3.8 42.9 1.0 N A:ASP351 3.9 34.8 1.0 OD2 A:ASP343 4.2 24.7 1.0 CB A:ASP351 4.2 39.0 1.0 N A:GLN349 4.3 28.5 1.0 N A:ASP345 4.4 30.9 1.0 CA A:MET350 4.5 29.1 1.0 CG A:GLN349 4.5 35.5 1.0 N A:MET350 4.5 27.1 1.0 CA A:GLN349 4.5 29.7 1.0 N A:ASN347 4.6 31.5 1.0 OD1 A:ASP351 4.6 40.8 1.0 CB A:ASP343 4.6 21.3 1.0 N A:ASN344 4.6 27.9 1.0 C A:MET350 4.6 31.8 1.0 O A:HOH1270 4.7 48.8 1.0 CB A:ASP367 4.7 29.1 1.0 CB A:ASP345 4.7 35.7 1.0 CA A:ASP343 4.7 21.7 1.0 CB A:ASN347 4.7 32.8 1.0 CA A:ASP351 4.7 38.0 1.0 CE A:MET350 4.7 22.4 1.0 CA A:ASP345 4.9 31.9 1.0 N A:LEU348 4.9 29.3 1.0 O A:HOH1314 4.9 42.6 1.0 C A:ASP345 4.9 32.8 1.0 N A:ALA346 5.0 34.1 1.0

Calcium binding site 3 out of 6 in the Fibrin-Stabilizing Factor with A Bound Ligand


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Fibrin-Stabilizing Factor with A Bound Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca803 b:20.8 occ:1.00 O A:HOH909 2.2 17.4 1.0 O A:ALA457 2.3 27.6 1.0 OE2 A:GLU490 2.3 33.8 1.0 OD1 A:ASN436 2.4 22.8 1.0 O A:HOH908 2.4 18.6 1.0 OE1 A:GLU485 2.5 31.0 1.0 OE2 A:GLU485 2.5 25.8 1.0 CD A:GLU485 2.9 27.1 1.0 CG A:ASN436 3.4 27.0 1.0 C A:ALA457 3.5 29.8 1.0 CD A:GLU490 3.5 31.6 1.0 ND2 A:ASN436 3.8 27.0 1.0 NH1 A:ARG491 4.1 33.2 0.7 CA A:THR458 4.2 27.3 1.0 NZ A:LYS482 4.2 20.4 1.0 O A:ASN436 4.2 21.4 1.0 N A:THR458 4.2 30.2 1.0 OE1 A:GLU490 4.3 34.6 1.0 O A:HOH1020 4.3 25.3 1.0 CG A:GLU485 4.4 25.4 1.0 OD1 A:ASP438 4.4 28.0 1.0 O A:HOH1060 4.5 19.2 1.0 CG A:GLU490 4.5 29.8 1.0 NH2 A:ARG491 4.5 36.7 0.3 CA A:ALA457 4.5 31.4 1.0 CE A:LYS482 4.6 31.0 1.0 CB A:ASN436 4.6 19.3 1.0 CA A:ASN436 4.7 20.2 1.0 C A:ASN436 4.7 20.4 1.0 O A:ILE460 4.7 21.6 1.0 C A:THR458 4.9 29.2 1.0 CB A:ALA457 5.0 30.2 1.0

Calcium binding site 4 out of 6 in the Fibrin-Stabilizing Factor with A Bound Ligand


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Fibrin-Stabilizing Factor with A Bound Ligand within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca801 b:15.7 occ:1.00 O B:ASN267 2.3 16.0 1.0 O B:ALA264 2.4 16.6 1.0 O B:HOH901 2.4 11.2 1.0 O B:LYS269 2.4 18.4 1.0 OD1 B:ASP271 2.4 18.8 1.0 OD1 B:ASN267 2.4 16.5 1.0 OD2 B:ASP271 2.6 16.3 1.0 CG B:ASP271 2.8 16.0 1.0 C B:ASN267 3.3 16.4 1.0 CG B:ASN267 3.3 17.8 1.0 C B:ALA264 3.4 17.1 1.0 C B:LYS269 3.5 18.5 1.0 N B:LYS269 3.8 17.8 1.0 C B:ALA268 3.9 20.8 1.0 ND2 B:ASN267 4.0 16.8 1.0 CA B:ASN267 4.1 17.0 1.0 N B:ALA268 4.1 17.0 1.0 CA B:LYS269 4.1 18.3 1.0 CA B:ALA264 4.2 20.4 1.0 N B:MET265 4.2 16.5 1.0 CB B:ASN267 4.3 18.4 1.0 CB B:ASP271 4.3 16.4 1.0 N B:ASN267 4.3 15.5 1.0 CA B:MET265 4.3 19.1 1.0 O B:ALA268 4.4 20.3 1.0 CA B:ALA268 4.4 18.6 1.0 N B:ASP271 4.4 17.5 1.0 OD2 B:ASP270 4.5 21.1 1.0 O B:TYR407 4.5 18.9 1.0 CB B:ASP270 4.5 17.8 1.0 CB B:ALA264 4.5 14.6 1.0 CB B:LYS269 4.6 22.6 1.0 N B:ASP270 4.6 18.5 1.0 C B:MET265 4.7 17.1 1.0 N B:GLY273 4.8 16.9 1.0 CA B:GLY273 4.9 16.0 1.0 CA B:ASP271 4.9 17.6 1.0 CG B:ASP270 4.9 23.0 1.0 CA B:ASP270 5.0 18.3 1.0 O B:MET265 5.0 15.2 1.0 O B:HOH915 5.0 14.3 1.0

Calcium binding site 5 out of 6 in the Fibrin-Stabilizing Factor with A Bound Ligand


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Fibrin-Stabilizing Factor with A Bound Ligand within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca802 b:26.6 occ:1.00 OD1 B:ASP345 2.4 33.7 1.0 OD1 B:ASN347 2.4 37.2 1.0 O B:GLN349 2.4 32.2 1.0 OD2 B:ASP351 2.4 31.5 1.0 OD2 B:ASP367 2.4 33.0 1.0 OD1 B:ASP343 2.5 26.9 1.0 CG B:ASP367 3.2 32.8 1.0 CG B:ASN347 3.4 34.4 1.0 OD1 B:ASP367 3.4 29.9 1.0 CG B:ASP345 3.5 34.8 1.0 C B:GLN349 3.6 29.4 1.0 CG B:ASP351 3.6 41.8 1.0 CG B:ASP343 3.6 26.2 1.0 ND2 B:ASN347 3.7 35.7 1.0 OD2 B:ASP345 4.0 38.0 1.0 N B:ASP351 4.1 33.8 1.0 OD2 B:ASP343 4.2 26.9 1.0 N B:GLN349 4.3 28.0 1.0 CG B:GLN349 4.4 33.4 1.0 CA B:MET350 4.4 31.7 1.0 CB B:ASP351 4.4 39.4 1.0 N B:ASP345 4.4 34.8 1.0 N B:MET350 4.4 33.9 1.0 OD1 B:ASP351 4.5 42.3 1.0 CA B:GLN349 4.5 32.3 1.0 O B:HOH1238 4.5 28.9 1.0 N B:ASN347 4.6 30.3 1.0 C B:MET350 4.6 33.0 1.0 CE B:MET350 4.6 26.9 1.0 CB B:ASP367 4.7 34.4 1.0 N B:ASN344 4.7 31.3 1.0 CB B:ASN347 4.7 33.7 1.0 CB B:ASP343 4.7 26.8 1.0 CA B:ASP343 4.7 24.8 1.0 CB B:ASP345 4.8 31.6 1.0 O B:HOH1342 4.9 43.0 1.0 N B:LEU348 4.9 26.3 1.0 CA B:ASP345 4.9 33.5 1.0 CA B:ASP351 4.9 37.9 1.0 C B:ASP345 5.0 33.0 1.0 CA B:ASN347 5.0 33.2 1.0 O B:HOH1271 5.0 36.5 1.0

Calcium binding site 6 out of 6 in the Fibrin-Stabilizing Factor with A Bound Ligand


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Fibrin-Stabilizing Factor with A Bound Ligand within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca803 b:22.9 occ:1.00 O B:HOH1307 2.2 21.5 1.0 OE2 B:GLU490 2.3 33.2 1.0 OE2 B:GLU485 2.4 31.4 1.0 O B:ALA457 2.4 33.4 1.0 OD1 B:ASN436 2.4 29.0 1.0 O B:HOH973 2.6 21.8 1.0 OE1 B:GLU485 2.6 36.3 1.0 CD B:GLU485 2.8 34.7 1.0 CG B:ASN436 3.3 28.5 1.0 CD B:GLU490 3.4 31.6 1.0 C B:ALA457 3.6 34.5 1.0 ND2 B:ASN436 3.6 27.7 1.0 OE1 B:GLU490 4.1 32.9 1.0 NH1 B:ARG491 4.3 34.6 1.0 CA B:THR458 4.3 34.6 1.0 O B:HOH1074 4.3 27.5 1.0 O B:ASN436 4.3 27.7 1.0 N B:THR458 4.4 35.1 1.0 CG B:GLU485 4.4 34.7 1.0 NZ B:LYS482 4.4 27.8 1.0 CG B:GLU490 4.4 30.7 1.0 OD1 B:ASP438 4.5 32.8 1.0 O B:HOH965 4.5 17.1 1.0 CA B:ALA457 4.6 35.4 1.0 CB B:ASN436 4.6 26.0 1.0 O B:ILE460 4.8 28.8 1.0 CA B:ASN436 4.8 26.1 1.0 C B:ASN436 4.9 26.8 1.0 CB B:ALA457 4.9 36.2 1.0

M.Stieler, J.Weber, M.Hils, P.Kolb, A.Heine, C.Buchold, R.Pasternack, G.Klebe. Structure of Active Coagulation Factor XIII Triggered By Calcium Binding: Basis For the Design of Next-Generation Anticoagulants. Angew.Chem.Int.Ed.Engl. V. 52 11930 2013.
ISSN: ISSN 1433-7851
PubMed: 24115223
DOI: 10.1002/ANIE.201305133