Calcium in PDB 7r2t: SYNJ2BP Complex with A Phosphorylated VANGL2 Peptide at the P-1 Position.

The structure of SYNJ2BP Complex with A Phosphorylated VANGL2 Peptide at the P-1 Position., PDB code: 7r2t 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)	46.89 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.1, 61.38, 145.31, 90, 90, 90
R / Rfree (%)	21.7 / 23.9

The binding sites of Calcium atom in the SYNJ2BP Complex with A Phosphorylated VANGL2 Peptide at the P-1 Position. (pdb code 7r2t). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the SYNJ2BP Complex with A Phosphorylated VANGL2 Peptide at the P-1 Position., PDB code: 7r2t:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in the SYNJ2BP Complex with A Phosphorylated VANGL2 Peptide at the P-1 Position.


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 Phosphorylated VANGL2 Peptide at the P-1 Position. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:117.4 occ:1.00 OE2 A:GLU136 2.8 102.9 1.0 O A:GLY133 2.9 113.6 1.0 C A:GLY133 3.9 114.7 1.0 CD A:GLU136 3.9 101.8 1.0 CA A:GLY133 4.1 116.4 1.0 O A:VAL134 4.4 102.9 1.0 OE1 A:GLU136 4.4 102.8 1.0

Calcium binding site 2 out of 5 in the SYNJ2BP Complex with A Phosphorylated VANGL2 Peptide at the P-1 Position.


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 Phosphorylated VANGL2 Peptide at the P-1 Position. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:82.8 occ:1.00 O A:ARG288 2.3 112.6 1.0 O A:HOH612 2.3 62.8 1.0 OE2 A:GLU330 2.4 92.2 1.0 O A:GLY290 2.4 79.9 1.0 O A:HOH622 2.5 60.3 1.0 OE1 A:GLU330 2.7 91.7 1.0 O A:GLY285 2.7 74.4 1.0 CD A:GLU330 2.9 88.4 1.0 N A:GLY290 3.3 87.1 1.0 C A:GLY290 3.3 81.0 1.0 C A:ARG288 3.5 102.4 1.0 C A:GLY285 3.6 71.0 1.0 CA A:GLY290 3.8 84.6 1.0 C A:LYS289 3.9 92.0 1.0 OG1 A:THR291 4.1 78.8 1.0 CA A:VAL286 4.1 70.8 1.0 CA A:LYS289 4.2 98.2 1.0 N A:VAL286 4.3 68.8 1.0 N A:LYS289 4.3 101.2 1.0 CG A:GLU330 4.3 84.3 1.0 O A:VAL286 4.4 77.1 1.0 C A:VAL286 4.5 74.5 1.0 N A:THR291 4.5 80.5 1.0 CA A:GLY285 4.5 70.5 1.0 N A:ARG288 4.6 90.3 1.0 CA A:ARG288 4.6 95.0 1.0 O A:LYS289 4.8 91.7 1.0 CA A:THR291 4.8 78.8 1.0

Calcium binding site 3 out of 5 in the SYNJ2BP Complex with A Phosphorylated VANGL2 Peptide at the P-1 Position.


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 Phosphorylated VANGL2 Peptide at the P-1 Position. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:54.9 occ:1.00 OD1 A:ASP405 2.2 86.5 1.0 O A:GLY363 2.3 49.9 1.0 O A:MET361 2.3 44.9 1.0 O A:GLY365 2.5 50.9 1.0 CG A:ASP405 2.9 81.3 1.0 OD2 A:ASP405 3.1 85.1 1.0 C A:MET361 3.3 44.0 1.0 C A:GLY363 3.5 52.2 1.0 C A:GLY365 3.7 53.4 1.0 CA A:MET361 3.9 46.8 1.0 N A:GLY363 3.9 53.1 1.0 C A:LYS362 4.1 52.3 1.0 N A:GLY365 4.2 55.4 1.0 C A:LYS364 4.2 59.2 1.0 CA A:GLY363 4.3 51.9 1.0 CB A:ASP405 4.3 72.5 1.0 O A:LYS362 4.3 55.1 1.0 OG1 A:THR366 4.4 56.3 1.0 N A:LYS362 4.4 44.8 1.0 CA A:GLY365 4.5 53.7 1.0 O A:LYS364 4.5 63.2 1.0 N A:LYS364 4.5 56.2 1.0 CB A:MET361 4.5 45.1 1.0 CA A:LYS364 4.7 58.4 1.0 N A:THR366 4.7 56.2 1.0 CA A:LYS362 4.7 48.9 1.0 CA A:THR366 4.8 55.2 1.0

Calcium binding site 4 out of 5 in the SYNJ2BP Complex with A Phosphorylated VANGL2 Peptide at the P-1 Position.


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 Phosphorylated VANGL2 Peptide at the P-1 Position. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca506 b:198.5 occ:1.00 O A:HOH609 2.7 66.2 1.0 NZ A:LYS287 2.7 74.4 1.0 CD A:LYS287 3.7 73.8 1.0 NH2 A:ARG279 3.7 67.8 1.0 CE A:LYS287 3.8 74.6 1.0 O A:HOH607 4.3 74.5 1.0 CZ A:ARG279 4.3 66.8 1.0 NE A:ARG279 4.4 65.8 1.0 CB A:ASP283 4.6 78.4 1.0 CD2 A:TYR282 4.7 71.2 1.0

Calcium binding site 5 out of 5 in the SYNJ2BP Complex with A Phosphorylated VANGL2 Peptide at the P-1 Position.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of SYNJ2BP Complex with A Phosphorylated VANGL2 Peptide at the P-1 Position. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca507 b:147.9 occ:1.00 CB A:SER304 4.1 53.6 1.0 N A:SER304 4.2 58.3 1.0 OG A:SER304 4.2 53.1 1.0 CB A:HIS307 4.3 50.9 1.0 CB A:ALA263 4.4 70.1 1.0 CG A:HIS307 4.5 52.0 1.0 ND1 A:HIS307 4.5 53.2 1.0 CA A:SER304 4.8 54.4 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.