Calcium in PDB 7r2m: SYNJ2BP Complex with A Synthetic VANGL2 Peptide (9MER).

The structure of SYNJ2BP Complex with A Synthetic VANGL2 Peptide (9MER)., PDB code: 7r2m 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)	47.66 / 2.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	60.27, 60.71, 143.15, 90, 92.88, 90
R / Rfree (%)	21.5 / 23.9

The binding sites of Calcium atom in the SYNJ2BP Complex with A Synthetic VANGL2 Peptide (9MER). (pdb code 7r2m). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 9 binding sites of Calcium where determined in the SYNJ2BP Complex with A Synthetic VANGL2 Peptide (9MER)., PDB code: 7r2m:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in the SYNJ2BP Complex with A Synthetic VANGL2 Peptide (9MER).


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 (9MER). within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca501 b:120.2 occ:1.00 O D:GLY133 2.3 86.5 1.0 O D:VAL134 3.0 83.9 1.0 C D:GLY133 3.1 87.2 1.0 CA D:GLY133 3.7 90.5 1.0 C D:VAL134 4.0 82.8 1.0 N D:VAL134 4.1 85.6 1.0 CA D:VAL134 4.5 83.1 1.0 OE2 D:GLU136 4.7 93.0 1.0 CB D:VAL134 4.9 81.3 1.0 CG D:GLU136 5.0 86.2 1.0

Calcium binding site 2 out of 9 in the SYNJ2BP Complex with A Synthetic VANGL2 Peptide (9MER).


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 (9MER). within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca502 b:126.7 occ:1.00 OE1 D:GLU179 3.1 81.6 1.0 O D:LYS171 3.4 79.7 1.0 O D:LEU174 3.7 69.3 1.0 OE2 D:GLU179 3.7 80.7 1.0 CD D:GLU179 3.8 76.5 1.0 CA D:SER175 4.7 61.9 1.0 C D:LYS171 4.7 78.4 1.0 CB D:SER175 4.8 65.5 1.0 C D:LEU174 4.8 64.5 1.0

Calcium binding site 3 out of 9 in the SYNJ2BP Complex with A Synthetic VANGL2 Peptide (9MER).


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 (9MER). within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca503 b:65.5 occ:1.00 O D:ARG288 2.5 65.8 1.0 O D:HOH619 2.5 70.2 1.0 OE1 D:GLU330 2.5 63.3 1.0 O D:GLY290 2.5 61.3 1.0 O D:HOH645 2.6 63.3 1.0 O D:GLY285 2.7 58.5 1.0 OE2 D:GLU330 2.8 63.2 1.0 CD D:GLU330 3.0 61.8 1.0 C D:GLY285 3.6 55.5 1.0 C D:GLY290 3.6 60.4 1.0 N D:GLY290 3.7 62.9 1.0 C D:ARG288 3.7 67.0 1.0 OG1 D:THR291 4.1 59.7 1.0 C D:LYS289 4.2 67.4 1.0 CA D:GLY290 4.2 61.2 1.0 CA D:VAL286 4.2 54.6 1.0 CA D:LYS289 4.2 71.6 1.0 N D:VAL286 4.3 53.9 1.0 O D:HOH643 4.4 63.6 1.0 O D:VAL286 4.4 60.3 1.0 C D:VAL286 4.4 58.7 1.0 N D:LYS289 4.4 70.7 1.0 CA D:GLY285 4.4 53.3 1.0 CG D:GLU330 4.5 57.8 1.0 CG D:ARG288 4.6 62.5 1.0 N D:ARG288 4.6 65.0 1.0 CA D:ARG288 4.7 65.1 1.0 N D:THR291 4.7 61.0 1.0 O D:LYS289 5.0 68.7 1.0

Calcium binding site 4 out of 9 in the SYNJ2BP Complex with A Synthetic VANGL2 Peptide (9MER).


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 (9MER). within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca504 b:53.2 occ:1.00 O D:GLY363 2.5 48.7 1.0 O D:MET361 2.5 42.3 1.0 OD2 D:ASP405 2.6 42.8 1.0 OD1 D:ASP405 2.6 46.0 1.0 O D:GLY365 2.8 46.2 1.0 CG D:ASP405 2.9 43.7 1.0 C D:MET361 3.6 42.0 1.0 C D:GLY363 3.7 47.4 1.0 C D:GLY365 3.8 44.8 1.0 N D:GLY365 4.0 48.5 1.0 N D:GLY363 4.2 44.3 1.0 CA D:MET361 4.2 41.2 1.0 C D:LYS362 4.3 45.4 1.0 CA D:GLY365 4.4 46.8 1.0 CB D:ASP405 4.4 43.4 1.0 CA D:GLY363 4.4 44.1 1.0 O D:LYS362 4.4 47.8 1.0 C D:LYS364 4.4 48.5 1.0 N D:LYS362 4.6 44.1 1.0 OG1 D:THR366 4.6 41.9 1.0 N D:LYS364 4.7 48.6 1.0 CA D:LYS364 4.8 48.9 1.0 CB D:MET361 4.8 40.2 1.0 CA D:LYS362 4.9 44.2 1.0 N D:THR366 4.9 42.7 1.0 O D:LYS364 5.0 48.7 1.0 CA D:ASP405 5.0 45.4 1.0

Calcium binding site 5 out of 9 in the SYNJ2BP Complex with A Synthetic VANGL2 Peptide (9MER).


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 Synthetic VANGL2 Peptide (9MER). within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca508 b:123.8 occ:1.00 O D:ARG328 2.8 58.4 1.0 O D:VAL331 2.8 55.5 1.0 OE1 D:GLU336 3.1 57.7 1.0 OE2 D:GLU336 3.4 55.9 1.0 CD D:GLU336 3.5 54.4 1.0 C D:VAL331 3.8 55.8 1.0 C D:ARG328 3.8 54.7 1.0 O D:HOH632 3.8 60.7 1.0 CB D:LYS332 3.8 62.1 1.0 CA D:LYS332 4.0 60.8 1.0 N D:LYS332 4.3 58.8 1.0 CA D:ARG328 4.3 51.5 1.0 CG D:GLU336 4.7 50.6 1.0 O D:ILE327 4.8 52.3 1.0 N D:VAL331 4.9 54.0 1.0 N D:LYS329 4.9 55.5 1.0 CA D:VAL331 5.0 54.2 1.0 CG D:LYS332 5.0 66.6 1.0

Calcium binding site 6 out of 9 in the SYNJ2BP Complex with A Synthetic VANGL2 Peptide (9MER).


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of SYNJ2BP Complex with A Synthetic VANGL2 Peptide (9MER). within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:103.4 occ:1.00 O A:VAL134 2.5 94.9 1.0 O A:GLY133 3.4 97.7 1.0 C A:VAL134 3.8 94.8 1.0 C A:GLY133 4.1 99.6 1.0 CA A:ASP135 4.5 91.1 1.0 N A:ASP135 4.6 93.2 1.0 N A:VAL134 4.6 99.5 1.0 N A:GLU136 4.7 87.5 1.0 CG A:GLU136 4.7 98.6 1.0 CA A:VAL134 4.7 96.1 1.0 CA A:GLY133 4.8 103.1 1.0

Calcium binding site 7 out of 9 in the SYNJ2BP Complex with A Synthetic VANGL2 Peptide (9MER).


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of SYNJ2BP Complex with A Synthetic VANGL2 Peptide (9MER). within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:91.6 occ:1.00 O A:HOH633 2.3 64.9 1.0 OE1 A:GLU330 2.5 73.9 1.0 O A:GLY285 2.7 72.0 1.0 O A:GLY290 2.7 75.7 1.0 O A:ARG288 2.9 88.4 0.6 OE2 A:GLU330 2.9 73.2 1.0 O A:ARG288 3.0 88.6 0.5 CD A:GLU330 3.1 71.5 1.0 N A:GLY290 3.4 81.9 1.0 C A:GLY290 3.6 76.9 1.0 C A:ARG288 3.6 89.1 0.5 C A:GLY285 3.7 67.2 1.0 C A:ARG288 3.7 89.2 0.6 C A:LYS289 3.9 82.9 1.0 CA A:GLY290 4.0 80.6 1.0 CA A:LYS289 4.0 85.0 1.0 N A:LYS289 4.3 89.2 1.0 O A:VAL286 4.4 72.6 1.0 OG1 A:THR291 4.5 70.6 1.0 CA A:VAL286 4.5 65.3 1.0 N A:VAL286 4.5 64.9 1.0 CA A:GLY285 4.5 64.7 1.0 CG A:ARG288 4.5 89.9 0.5 CG A:GLU330 4.6 68.8 1.0 C A:VAL286 4.6 69.4 1.0 N A:THR291 4.7 74.4 1.0 N A:ARG288 4.8 86.3 0.6 CA A:ARG288 4.8 89.0 0.5 N A:ARG288 4.8 86.3 0.5 CA A:ARG288 4.8 89.1 0.6 O A:LYS289 4.9 82.5 1.0 CG A:ARG288 4.9 90.0 0.6

Calcium binding site 8 out of 9 in the SYNJ2BP Complex with A Synthetic VANGL2 Peptide (9MER).


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of SYNJ2BP Complex with A Synthetic VANGL2 Peptide (9MER). within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:66.0 occ:1.00 O A:GLY365 2.5 57.4 1.0 OD2 A:ASP405 2.5 59.1 1.0 OD1 A:ASP405 2.5 61.0 1.0 O A:GLY363 2.5 57.8 1.0 O A:MET361 2.7 57.9 1.0 CG A:ASP405 2.8 58.3 1.0 C A:GLY365 3.5 55.9 1.0 C A:MET361 3.6 53.8 1.0 C A:GLY363 3.7 57.9 1.0 N A:GLY365 3.8 59.3 1.0 CA A:GLY365 4.1 57.1 1.0 CA A:MET361 4.2 51.5 1.0 N A:GLY363 4.3 56.0 1.0 CB A:ASP405 4.3 57.4 1.0 C A:LYS364 4.3 60.3 1.0 OG1 A:THR366 4.3 48.9 1.0 C A:LYS362 4.3 55.0 1.0 O A:LYS362 4.5 55.6 1.0 N A:LYS362 4.6 53.5 1.0 CA A:GLY363 4.6 55.9 1.0 N A:THR366 4.6 54.4 1.0 N A:LYS364 4.6 58.6 1.0 O A:HOH610 4.6 38.4 1.0 CA A:LYS364 4.7 60.0 1.0 CB A:MET361 4.8 48.9 1.0 CA A:THR366 4.9 53.5 1.0 CA A:LYS362 4.9 54.3 1.0 O A:LYS364 4.9 61.5 1.0 CA A:ASP405 4.9 59.1 1.0

Calcium binding site 9 out of 9 in the SYNJ2BP Complex with A Synthetic VANGL2 Peptide (9MER).


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of SYNJ2BP Complex with A Synthetic VANGL2 Peptide (9MER). within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca506 b:142.1 occ:1.00 O A:VAL331 2.7 75.3 1.0 O A:ARG328 3.2 76.1 1.0 CB A:LYS332 3.4 84.3 1.0 C A:VAL331 3.5 76.2 1.0 CA A:LYS332 3.9 81.3 1.0 N A:LYS332 4.1 78.6 1.0 C A:ARG328 4.3 72.1 1.0 CG A:LYS332 4.3 86.8 1.0 N A:VAL331 4.5 75.0 1.0 OE1 A:GLU336 4.5 70.7 1.0 CA A:VAL331 4.6 75.2 1.0 CD A:LYS332 4.6 90.6 1.0 CD A:GLU336 4.8 68.1 1.0 C A:GLU330 4.8 76.7 1.0 C A:LYS329 4.8 72.2 1.0 OE2 A:GLU336 4.9 67.5 1.0 O A:LYS329 5.0 72.5 1.0 N A:GLU330 5.0 72.0 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.