Calcium in PDB 8ael: SYNJ2BP Complex with A Synthetic VANGL2 Peptide (3MER).

The structure of SYNJ2BP Complex with A Synthetic VANGL2 Peptide (3MER)., PDB code: 8ael was solved by K.Carrasco, A.Cousido Siah, G.Gogl, S.Betzi, A.Mcewen, C.Kostmann, G.Trave, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.53 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	59.67, 75.06, 108.92, 90, 90, 90
R / Rfree (%)	22.1 / 26.4

The binding sites of Calcium atom in the SYNJ2BP Complex with A Synthetic VANGL2 Peptide (3MER). (pdb code 8ael). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the SYNJ2BP Complex with A Synthetic VANGL2 Peptide (3MER)., PDB code: 8ael:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the SYNJ2BP Complex with A Synthetic VANGL2 Peptide (3MER).


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of SYNJ2BP Complex with A Synthetic VANGL2 Peptide (3MER). within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:77.5 occ:1.00 OE1 A:GLU136 2.5 38.7 0.6 O A:GLY133 2.7 53.5 1.0 O A:VAL134 2.7 48.7 1.0 OE2 A:GLU136 3.0 39.2 0.6 CD A:GLU136 3.2 38.9 0.6 C A:GLY133 3.8 52.0 1.0 C A:VAL134 3.9 47.1 1.0 N A:VAL134 4.5 51.0 1.0 CA A:GLY133 4.6 54.8 1.0 CA A:VAL134 4.6 48.3 1.0 CG A:GLU136 4.6 38.9 0.6 O A:HOH749 4.7 46.3 1.0 CB A:VAL134 4.8 46.4 1.0 N A:GLU136 4.8 39.2 0.4 N A:GLU136 4.8 39.3 0.6 CG A:GLU136 4.9 38.8 0.4 N A:ASP135 5.0 45.2 1.0

Calcium binding site 2 out of 4 in the SYNJ2BP Complex with A Synthetic VANGL2 Peptide (3MER).


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of SYNJ2BP Complex with A Synthetic VANGL2 Peptide (3MER). within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:45.6 occ:1.00 O A:LYS171 2.3 44.0 1.0 O A:LEU174 2.4 33.2 1.0 OE1 A:GLU179 2.6 37.9 1.0 O A:HOH627 2.9 41.5 1.0 C A:LEU174 3.5 33.3 1.0 C A:LYS171 3.5 42.2 1.0 CD A:GLU179 3.6 35.8 1.0 OE2 A:GLU179 3.9 37.2 1.0 CA A:SER175 4.0 35.2 1.0 N A:SER175 4.2 32.3 1.0 CB A:SER175 4.2 37.2 1.0 CA A:LYS171 4.4 40.8 1.0 N A:SER172 4.5 41.2 1.0 CA A:SER172 4.5 42.5 1.0 N A:LEU174 4.6 46.3 1.0 CA A:LEU174 4.7 36.2 1.0 C A:SER172 4.7 43.5 1.0 CG A:GLU179 4.8 31.5 1.0 O A:SER172 4.9 46.0 1.0 O A:LEU170 4.9 39.9 1.0

Calcium binding site 3 out of 4 in the SYNJ2BP Complex with A Synthetic VANGL2 Peptide (3MER).


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of SYNJ2BP Complex with A Synthetic VANGL2 Peptide (3MER). within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:50.0 occ:1.00 O A:HOH789 2.3 38.7 1.0 O A:GLY285 2.3 43.0 1.0 O A:ARG288 2.4 45.4 1.0 OE1 A:GLU330 2.4 45.2 1.0 O A:GLY290 2.5 49.6 1.0 OE2 A:GLU330 2.9 44.5 1.0 CD A:GLU330 3.0 43.7 1.0 C A:GLY285 3.2 42.1 1.0 C A:ARG288 3.5 48.9 1.0 C A:GLY290 3.6 51.3 1.0 N A:GLY290 3.8 53.8 1.0 N A:VAL286 4.0 43.2 1.0 CA A:VAL286 4.1 42.9 1.0 CA A:GLY285 4.1 40.6 1.0 C A:LYS289 4.2 54.0 1.0 OG1 A:THR291 4.2 51.6 1.0 CA A:GLY290 4.2 54.0 1.0 C A:VAL286 4.2 42.9 1.0 N A:ARG288 4.2 46.3 1.0 O A:VAL286 4.2 45.0 1.0 CG A:ARG288 4.3 55.0 1.0 CA A:LYS289 4.4 54.9 1.0 N A:LYS289 4.4 53.4 1.0 CA A:ARG288 4.4 48.9 1.0 CG A:GLU330 4.5 41.3 1.0 O A:HOH769 4.5 60.5 1.0 N A:THR291 4.7 51.6 1.0 O A:HOH618 4.8 37.2 1.0 N A:LYS287 4.9 42.5 1.0 CA A:THR291 4.9 50.3 1.0 O A:LYS289 4.9 55.8 1.0 CB A:ARG288 5.0 52.1 1.0

Calcium binding site 4 out of 4 in the SYNJ2BP Complex with A Synthetic VANGL2 Peptide (3MER).


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of SYNJ2BP Complex with A Synthetic VANGL2 Peptide (3MER). within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:35.6 occ:1.00 O A:GLY365 2.4 31.8 1.0 O A:MET361 2.4 28.5 1.0 OD2 A:ASP405 2.5 30.6 1.0 O A:GLY363 2.5 36.9 1.0 OD1 A:ASP405 2.6 30.1 1.0 CG A:ASP405 2.9 31.2 1.0 C A:MET361 3.4 30.4 1.0 C A:GLY365 3.5 32.1 1.0 C A:GLY363 3.7 36.3 1.0 CA A:MET361 3.9 28.5 1.0 N A:GLY365 4.0 30.7 1.0 N A:GLY363 4.2 36.9 1.0 C A:LYS362 4.3 36.6 1.0 O A:HOH724 4.3 43.9 1.0 OG1 A:THR366 4.3 33.5 1.0 CA A:GLY365 4.3 29.6 1.0 C A:LYS364 4.3 32.2 1.0 CB A:ASP405 4.4 32.4 1.0 N A:LYS362 4.4 31.3 1.0 O A:LYS362 4.4 39.0 1.0 CA A:GLY363 4.5 35.8 1.0 CB A:MET361 4.5 26.8 1.0 N A:THR366 4.6 32.1 1.0 N A:LYS364 4.6 36.3 1.0 CA A:LYS364 4.7 34.5 1.0 O A:LYS364 4.8 31.1 1.0 CA A:THR366 4.8 31.1 1.0 CA A:LYS362 4.8 33.2 1.0 O A:HOH626 4.9 21.9 1.0 O A:HOH665 4.9 31.7 1.0

K.Carrasco, A.Cousido Siah, G.Gogl, S.Betzi, A.Mcewen, C.Kostmann, G.Trave. SYNJ2BP Pdz Domain in Complex with A Synthetic VANGL2 Peptide. To Be Published.