Calcium in PDB 1pz8: Modulation of Agrin Function By Alternative Splicing and CA2+ Binding

The structure of Modulation of Agrin Function By Alternative Splicing and CA2+ Binding, PDB code: 1pz8 was solved by J.Stetefeld, A.T.Alexandrescu, M.W.Maciejewski, M.Jenny, K.Rathgeb-Szabo, T.Schulthess, R.Landwehr, S.Frank, M.A.Ruegg, R.A.Kammerer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.35
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	76.847, 56.556, 84.586, 90.00, 99.75, 90.00
R / Rfree (%)	21.8 / 26

The binding sites of Calcium atom in the Modulation of Agrin Function By Alternative Splicing and CA2+ Binding (pdb code 1pz8). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Modulation of Agrin Function By Alternative Splicing and CA2+ Binding, PDB code: 1pz8:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Modulation of Agrin Function By Alternative Splicing and CA2+ Binding


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Modulation of Agrin Function By Alternative Splicing and CA2+ Binding within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca701 b:30.1 occ:1.00 O A:LEU90 2.5 9.2 1.0 O A:GLN140 2.5 15.0 1.0 OD1 A:ASP73 2.6 15.1 1.0 OD1 A:ASP142 3.1 24.3 1.0 CG A:ASP142 3.4 20.1 1.0 CG A:ASP73 3.5 11.6 1.0 C A:LEU90 3.6 10.2 1.0 OD2 A:ASP142 3.7 23.7 1.0 C A:GLN140 3.7 15.1 1.0 OD2 A:ASP73 3.9 10.3 1.0 N A:ASP142 4.1 15.4 1.0 CB A:ALA138 4.3 17.3 1.0 CA A:LEU90 4.3 9.5 1.0 CB A:ASP142 4.3 16.7 1.0 N A:GLY91 4.5 11.1 1.0 CB A:LEU90 4.5 9.8 1.0 CA A:LEU141 4.5 15.4 1.0 N A:LEU141 4.5 14.7 1.0 CA A:GLN140 4.6 15.8 1.0 CB A:GLN140 4.7 15.9 1.0 CA A:GLY91 4.7 11.8 1.0 C A:LEU141 4.7 15.2 1.0 CB A:ASP73 4.7 10.0 1.0 N A:GLN140 4.8 15.3 1.0 O A:HOH849 4.8 34.6 1.0 CA A:ASP142 4.8 16.7 1.0

Calcium binding site 2 out of 4 in the Modulation of Agrin Function By Alternative Splicing and CA2+ Binding


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Modulation of Agrin Function By Alternative Splicing and CA2+ Binding within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca702 b:37.8 occ:1.00 O B:LEU90 2.5 5.2 1.0 OD1 B:ASP73 2.6 11.5 1.0 O B:GLN140 2.6 16.1 1.0 OD2 B:ASP142 3.0 31.8 1.0 O B:HOH710 3.1 25.7 1.0 CG B:ASP73 3.6 6.0 1.0 CG B:GLN140 3.6 16.2 1.0 C B:LEU90 3.6 4.6 1.0 C B:GLN140 3.7 16.0 1.0 OD2 B:ASP73 3.9 7.4 1.0 CG B:ASP142 4.0 28.0 1.0 N B:ASP142 4.3 22.4 1.0 CA B:LEU90 4.4 4.3 1.0 CA B:GLN140 4.5 15.1 1.0 CB B:ASP142 4.5 24.5 1.0 CB B:GLN140 4.6 15.0 1.0 CB B:LEU90 4.6 4.7 1.0 N B:GLY91 4.6 5.9 1.0 N B:GLN140 4.7 13.3 1.0 N B:LEU141 4.7 17.6 1.0 CD B:GLN140 4.7 18.1 1.0 CA B:GLY91 4.7 6.5 1.0 CB B:ALA138 4.7 11.3 1.0 CB B:ASP73 4.8 4.2 1.0 CA B:LEU141 4.8 19.3 1.0 OD1 B:ASP142 4.8 30.8 1.0 NE2 B:GLN140 4.9 18.0 1.0 C B:LEU141 5.0 20.6 1.0

Calcium binding site 3 out of 4 in the Modulation of Agrin Function By Alternative Splicing and CA2+ Binding


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Modulation of Agrin Function By Alternative Splicing and CA2+ Binding within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca703 b:31.7 occ:1.00 O C:GLN140 2.3 11.7 1.0 O C:LEU90 2.5 6.3 1.0 OD1 C:ASP73 2.6 9.4 1.0 OD2 C:ASP142 2.7 10.8 1.0 CG C:ASP142 3.3 11.4 1.0 O C:HOH762 3.4 31.9 1.0 C C:GLN140 3.5 12.0 1.0 C C:LEU90 3.6 5.8 1.0 CG C:ASP73 3.6 8.0 1.0 OD1 C:ASP142 3.8 13.3 1.0 N C:ASP142 3.9 9.0 1.0 OD2 C:ASP73 4.0 9.3 1.0 CA C:LEU90 4.2 6.0 1.0 CB C:ASP142 4.3 9.4 1.0 N C:LEU141 4.3 11.4 1.0 CA C:LEU141 4.3 11.6 1.0 CB C:ALA138 4.3 14.3 1.0 CB C:LEU90 4.4 6.4 1.0 CA C:GLN140 4.5 12.9 1.0 C C:LEU141 4.6 10.4 1.0 N C:GLY91 4.6 6.6 1.0 N C:GLN140 4.6 12.6 1.0 CB C:GLN140 4.6 12.8 1.0 O C:HOH803 4.7 23.2 1.0 CA C:ASP142 4.8 9.5 1.0 CB C:ASP73 4.9 3.4 1.0 CA C:GLY91 4.9 7.1 1.0

Calcium binding site 4 out of 4 in the Modulation of Agrin Function By Alternative Splicing and CA2+ Binding


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Modulation of Agrin Function By Alternative Splicing and CA2+ Binding within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca704 b:33.1 occ:1.00 O D:GLN140 2.3 11.6 1.0 O D:LEU90 2.5 7.6 1.0 OD1 D:ASP73 2.6 9.9 1.0 OD2 D:ASP142 2.8 14.7 1.0 O D:HOH764 3.0 33.4 1.0 CG D:ASP142 3.5 16.0 1.0 C D:GLN140 3.5 11.7 1.0 C D:LEU90 3.6 7.3 1.0 CG D:ASP73 3.6 7.5 1.0 OD2 D:ASP73 3.9 11.8 1.0 O D:HOH792 3.9 33.6 1.0 OD1 D:ASP142 4.0 17.5 1.0 N D:ASP142 4.0 13.0 1.0 CA D:LEU90 4.3 7.4 1.0 CA D:LEU141 4.3 12.3 1.0 N D:LEU141 4.3 11.6 1.0 CB D:ASP142 4.4 13.8 1.0 CA D:GLN140 4.5 12.1 1.0 N D:GLY91 4.5 7.8 1.0 CB D:LEU90 4.5 8.1 1.0 C D:LEU141 4.6 12.6 1.0 CB D:ALA138 4.6 12.2 1.0 N D:GLN140 4.7 11.6 1.0 CA D:GLY91 4.7 7.5 1.0 CB D:GLN140 4.7 12.1 1.0 CA D:ASP142 4.9 13.7 1.0 CB D:ASP73 4.9 3.9 1.0

J.Stetefeld, A.T.Alexandrescu, M.W.Maciejewski, M.Jenny, K.Rathgeb-Szabo, T.Schulthess, R.Landwehr, S.Frank, M.A.Ruegg, R.A.Kammerer. Modulation of Agrin Function By Alternative Splicing and CA2+ Binding. Structure V. 12 503 2004.
ISSN: ISSN 0969-2126
PubMed: 15016366
DOI: 10.1016/J.STR.2004.02.001