Calcium in PDB 1nub: Helix C Deletion Mutant of Bm-40 Fs-Ec Domain Pair

The structure of Helix C Deletion Mutant of Bm-40 Fs-Ec Domain Pair, PDB code: 1nub was solved by E.Hohenester, T.Sasaki, R.Timpl, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	6.00 / 2.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	51.860, 88.140, 153.730, 90.00, 90.00, 90.00
R / Rfree (%)	25.5 / 30.6

The binding sites of Calcium atom in the Helix C Deletion Mutant of Bm-40 Fs-Ec Domain Pair (pdb code 1nub). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Helix C Deletion Mutant of Bm-40 Fs-Ec Domain Pair, PDB code: 1nub:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Helix C Deletion Mutant of Bm-40 Fs-Ec Domain Pair


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Helix C Deletion Mutant of Bm-40 Fs-Ec Domain Pair within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:33.3 occ:1.00 OE1 A:GLU234 2.3 29.4 1.0 O A:PRO225 2.4 30.9 1.0 OE2 A:GLU234 2.4 19.0 1.0 O A:TYR229 2.6 20.1 1.0 OD1 A:ASP227 2.6 45.3 1.0 CD A:GLU234 2.6 14.0 1.0 OD1 A:ASP222 2.7 35.9 1.0 CG A:ASP227 3.5 39.4 1.0 C A:PRO225 3.5 19.8 1.0 C A:TYR229 3.8 15.2 1.0 N A:PRO225 3.8 13.2 1.0 OD2 A:ASP227 3.9 68.2 1.0 CG A:ASP222 3.9 30.2 1.0 N A:ASP227 4.1 27.9 1.0 CD A:PRO225 4.1 10.1 1.0 C A:HIS224 4.1 20.0 1.0 CG A:GLU234 4.1 6.4 1.0 CA A:ASP222 4.2 16.3 1.0 CA A:PRO225 4.3 13.3 1.0 O A:HIS224 4.3 28.2 1.0 N A:GLN223 4.4 10.5 1.0 N A:TYR229 4.4 14.8 1.0 N A:ILE226 4.5 23.0 1.0 C A:ASP222 4.5 15.1 1.0 N A:HIS224 4.6 23.1 1.0 CA A:LEU230 4.6 8.0 1.0 CB A:ASP222 4.6 5.8 1.0 CB A:ASP227 4.6 17.1 1.0 N A:LEU230 4.6 11.2 1.0 CA A:ILE226 4.6 21.0 1.0 CA A:TYR229 4.7 13.5 1.0 CG A:PRO225 4.7 2.0 1.0 C A:ILE226 4.8 24.4 1.0 CA A:ASP227 4.8 25.9 1.0 N A:GLY228 4.8 24.2 1.0 OD2 A:ASP222 4.9 38.4 1.0 N A:SER231 4.9 15.5 1.0 CA A:HIS224 4.9 22.3 1.0 CD2 A:LEU230 4.9 6.7 1.0 C A:GLN223 4.9 24.6 1.0

Calcium binding site 2 out of 6 in the Helix C Deletion Mutant of Bm-40 Fs-Ec Domain Pair


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Helix C Deletion Mutant of Bm-40 Fs-Ec Domain Pair within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:34.3 occ:1.00 OE1 A:GLU268 2.3 33.9 1.0 O A:TYR263 2.4 30.5 1.0 OD1 A:ASP257 2.5 6.8 1.0 OD1 A:ASP261 2.5 22.4 1.0 OD1 A:ASP259 2.7 30.8 1.0 OE2 A:GLU268 2.7 34.5 1.0 CD A:GLU268 2.9 26.3 1.0 CG A:ASP261 3.4 18.5 1.0 C A:TYR263 3.6 27.1 1.0 CG A:ASP257 3.7 31.5 1.0 CG A:ASP259 3.7 29.5 1.0 OD2 A:ASP261 3.9 52.2 1.0 CA A:ASP257 4.1 17.4 1.0 OD2 A:ASP259 4.1 34.0 1.0 N A:ASP261 4.1 27.0 1.0 N A:TYR263 4.2 26.2 1.0 C A:ASP257 4.2 19.0 1.0 N A:ASP259 4.2 31.7 1.0 N A:LEU258 4.3 24.1 1.0 CG A:GLU268 4.3 24.2 1.0 N A:ASN260 4.4 36.0 1.0 CB A:ASP257 4.4 17.0 1.0 CA A:TYR263 4.4 23.5 1.0 CB A:ASP261 4.5 11.5 1.0 N A:ILE264 4.5 24.2 1.0 CA A:ILE264 4.5 15.9 1.0 OD2 A:ASP257 4.6 42.2 1.0 N A:ALA265 4.7 12.9 1.0 N A:LYS262 4.8 28.6 1.0 CA A:ASP261 4.8 24.9 1.0 O A:ASP257 4.8 27.6 1.0 CA A:ASP259 4.8 32.7 1.0 CB A:TYR263 4.8 10.1 1.0 CB A:ASP259 4.8 36.7 1.0 C A:ASP259 4.9 34.9 1.0 CD1 A:ILE264 5.0 2.1 1.0

Calcium binding site 3 out of 6 in the Helix C Deletion Mutant of Bm-40 Fs-Ec Domain Pair


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Helix C Deletion Mutant of Bm-40 Fs-Ec Domain Pair within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:11.2 occ:1.00 OE1 A:GLU246 2.4 16.7 1.0 O A:ILE243 2.4 10.3 1.0 O A:PRO241 2.5 24.0 1.0 CD A:GLU246 3.3 8.1 1.0 C A:PRO241 3.4 15.7 1.0 C A:ILE243 3.5 6.1 1.0 OE2 A:GLU246 3.7 31.1 1.0 CA A:PRO241 4.0 13.7 1.0 C A:LEU242 4.1 12.3 1.0 N A:MET245 4.1 12.5 1.0 N A:ILE243 4.2 8.9 1.0 CA A:PRO244 4.2 10.5 1.0 O A:LEU242 4.2 20.8 1.0 N A:LEU242 4.3 16.9 1.0 N A:PRO244 4.3 6.2 1.0 CA A:ILE243 4.5 7.6 1.0 N A:GLU246 4.5 12.6 1.0 CA A:LEU242 4.5 14.9 1.0 CG A:GLU246 4.6 10.5 1.0 O A:ALA240 4.6 19.6 1.0 C A:PRO244 4.6 19.6 1.0 CB A:GLU246 4.8 10.8 1.0

Calcium binding site 4 out of 6 in the Helix C Deletion Mutant of Bm-40 Fs-Ec Domain Pair


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Helix C Deletion Mutant of Bm-40 Fs-Ec Domain Pair within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca301 b:33.3 occ:1.00 OE1 B:GLU234 2.3 29.4 1.0 O B:PRO225 2.4 30.9 1.0 OE2 B:GLU234 2.4 19.0 1.0 O B:TYR229 2.6 20.1 1.0 OD1 B:ASP227 2.6 45.3 1.0 CD B:GLU234 2.6 14.0 1.0 OD1 B:ASP222 2.7 35.9 1.0 CG B:ASP227 3.5 39.4 1.0 C B:PRO225 3.5 19.8 1.0 C B:TYR229 3.8 15.2 1.0 N B:PRO225 3.8 13.2 1.0 OD2 B:ASP227 3.9 68.2 1.0 CG B:ASP222 3.9 30.2 1.0 N B:ASP227 4.1 27.9 1.0 CD B:PRO225 4.1 10.1 1.0 C B:HIS224 4.1 20.0 1.0 CG B:GLU234 4.1 6.4 1.0 CA B:ASP222 4.2 16.3 1.0 CA B:PRO225 4.3 13.3 1.0 O B:HIS224 4.3 28.2 1.0 N B:GLN223 4.4 10.5 1.0 N B:TYR229 4.4 14.8 1.0 N B:ILE226 4.5 23.0 1.0 C B:ASP222 4.5 15.1 1.0 N B:HIS224 4.6 23.1 1.0 CA B:LEU230 4.6 8.0 1.0 CB B:ASP222 4.6 5.8 1.0 CB B:ASP227 4.6 17.1 1.0 N B:LEU230 4.6 11.2 1.0 CA B:ILE226 4.6 21.0 1.0 CA B:TYR229 4.7 13.5 1.0 CG B:PRO225 4.7 2.0 1.0 C B:ILE226 4.8 24.4 1.0 CA B:ASP227 4.8 25.9 1.0 N B:GLY228 4.8 24.2 1.0 OD2 B:ASP222 4.9 38.4 1.0 N B:SER231 4.9 15.5 1.0 CA B:HIS224 4.9 22.3 1.0 CD2 B:LEU230 4.9 6.7 1.0 C B:GLN223 4.9 24.6 1.0

Calcium binding site 5 out of 6 in the Helix C Deletion Mutant of Bm-40 Fs-Ec Domain Pair


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Helix C Deletion Mutant of Bm-40 Fs-Ec Domain Pair within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca302 b:34.3 occ:1.00 OE1 B:GLU268 2.3 33.9 1.0 O B:TYR263 2.4 30.5 1.0 OD1 B:ASP257 2.5 6.8 1.0 OD1 B:ASP261 2.5 22.4 1.0 OD1 B:ASP259 2.7 30.8 1.0 OE2 B:GLU268 2.7 34.5 1.0 CD B:GLU268 2.9 26.3 1.0 CG B:ASP261 3.4 18.5 1.0 C B:TYR263 3.6 27.1 1.0 CG B:ASP257 3.7 31.5 1.0 CG B:ASP259 3.7 29.5 1.0 OD2 B:ASP261 3.9 52.2 1.0 CA B:ASP257 4.1 17.4 1.0 OD2 B:ASP259 4.1 34.0 1.0 N B:ASP261 4.1 27.0 1.0 N B:TYR263 4.2 26.2 1.0 C B:ASP257 4.2 19.0 1.0 N B:ASP259 4.2 31.7 1.0 N B:LEU258 4.3 24.1 1.0 CG B:GLU268 4.3 24.2 1.0 N B:ASN260 4.4 36.0 1.0 CB B:ASP257 4.4 17.0 1.0 CA B:TYR263 4.4 23.5 1.0 CB B:ASP261 4.5 11.5 1.0 N B:ILE264 4.5 24.2 1.0 CA B:ILE264 4.5 15.9 1.0 OD2 B:ASP257 4.6 42.2 1.0 N B:ALA265 4.7 12.9 1.0 N B:LYS262 4.8 28.6 1.0 CA B:ASP261 4.8 24.9 1.0 O B:ASP257 4.8 27.6 1.0 CA B:ASP259 4.8 32.7 1.0 CB B:TYR263 4.8 10.1 1.0 CB B:ASP259 4.8 36.7 1.0 C B:ASP259 4.9 34.9 1.0 CD1 B:ILE264 5.0 2.1 1.0

Calcium binding site 6 out of 6 in the Helix C Deletion Mutant of Bm-40 Fs-Ec Domain Pair


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Helix C Deletion Mutant of Bm-40 Fs-Ec Domain Pair within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca303 b:11.2 occ:1.00 OE1 B:GLU246 2.4 16.7 1.0 O B:ILE243 2.4 10.3 1.0 O B:PRO241 2.5 24.0 1.0 CD B:GLU246 3.3 8.1 1.0 C B:PRO241 3.4 15.7 1.0 C B:ILE243 3.5 6.1 1.0 OE2 B:GLU246 3.7 31.1 1.0 CA B:PRO241 4.0 13.7 1.0 C B:LEU242 4.1 12.3 1.0 N B:MET245 4.1 12.5 1.0 N B:ILE243 4.2 8.9 1.0 CA B:PRO244 4.2 10.5 1.0 O B:LEU242 4.2 20.8 1.0 N B:LEU242 4.3 16.9 1.0 N B:PRO244 4.3 6.2 1.0 CA B:ILE243 4.5 7.6 1.0 N B:GLU246 4.5 12.6 1.0 CA B:LEU242 4.5 14.9 1.0 CG B:GLU246 4.6 10.5 1.0 O B:ALA240 4.6 19.6 1.0 C B:PRO244 4.6 19.6 1.0 CB B:GLU246 4.8 10.8 1.0

T.Sasaki, E.Hohenester, W.Gohring, R.Timpl. Crystal Structure and Mapping By Site-Directed Mutagenesis of the Collagen-Binding Epitope of An Activated Form of Bm-40/Sparc/Osteonectin. Embo J. V. 17 1625 1998.
ISSN: ISSN 0261-4189
PubMed: 9501084
DOI: 10.1093/EMBOJ/17.6.1625