Calcium in PDB 6wvw: Crystal Structure of the R59P-SNAP25 Containing Snare Complex

The structure of Crystal Structure of the R59P-SNAP25 Containing Snare Complex, PDB code: 6wvw was solved by Q.Zhou, K.I.White, A.T.Brunger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.29 / 2.11
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	48.761, 45.899, 109.066, 90, 94.41, 90
R / Rfree (%)	20 / 24.4

The binding sites of Calcium atom in the Crystal Structure of the R59P-SNAP25 Containing Snare Complex (pdb code 6wvw). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of the R59P-SNAP25 Containing Snare Complex, PDB code: 6wvw:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of the R59P-SNAP25 Containing Snare Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of the R59P-SNAP25 Containing Snare Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca301 b:23.5 occ:1.00 OE1 B:GLU238 2.6 24.6 1.0 O B:HOH401 2.8 21.4 1.0 CD B:GLU238 3.5 24.2 1.0 OE2 B:GLU238 3.6 23.3 1.0 HD1 B:TYR235 3.9 28.9 1.0 O B:HOH419 4.2 25.2 1.0 HA B:TYR235 4.3 23.2 1.0 O B:HOH407 4.5 21.9 1.0 CD1 B:TYR235 4.8 23.7 1.0 HG2 B:GLU234 4.8 21.7 1.0 CG B:GLU238 4.9 20.8 1.0 O B:HOH402 4.9 30.5 1.0 HB2 B:GLU238 4.9 24.0 1.0 HB2 B:TYR235 5.0 22.1 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of the R59P-SNAP25 Containing Snare Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of the R59P-SNAP25 Containing Snare Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca202 b:59.3 occ:1.00 O D:HOH343 2.5 38.4 1.0 O C:HOH314 2.5 33.0 1.0 OD1 C:ASP58 2.9 28.9 1.0 OE1 D:GLN177 2.9 22.0 1.0 O C:GLY54 3.1 23.3 1.0 HE22 D:GLN177 3.2 34.6 1.0 HA3 C:GLY54 3.3 23.1 1.0 CG C:ASP58 3.5 35.5 1.0 O D:HOH321 3.5 21.5 1.0 C C:GLY54 3.6 21.3 1.0 HA2 C:GLY54 3.6 23.1 1.0 OD2 C:ASP58 3.7 37.1 1.0 CA C:GLY54 3.7 18.9 1.0 CD D:GLN177 3.7 22.4 1.0 NE2 D:GLN177 3.7 28.5 1.0 HB2 C:LEU57 3.8 25.4 1.0 H C:ASP58 4.2 32.0 1.0 HD12 C:LEU57 4.5 21.3 1.0 HE21 D:GLN177 4.6 34.6 1.0 N C:GLU55 4.6 19.6 1.0 HG2 D:GLN174 4.6 21.0 1.0 N C:ASP58 4.6 26.3 1.0 CB C:LEU57 4.7 20.8 1.0 HA C:GLU55 4.7 30.1 1.0 CB C:ASP58 4.7 27.8 1.0 HB3 C:LEU57 4.8 25.4 1.0 HA C:ASP58 4.8 30.4 1.0 HB2 C:ASP58 4.9 33.8 1.0 OE2 C:GLU55 5.0 44.8 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of the R59P-SNAP25 Containing Snare Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of the R59P-SNAP25 Containing Snare Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca102 b:57.0 occ:1.00 O E:HOH227 2.6 34.3 1.0 OD1 E:ASP65 2.7 34.5 1.0 O E:HOH210 2.7 49.7 1.0 OD2 E:ASP65 2.7 34.6 1.0 O D:HOH323 2.7 48.0 1.0 CG E:ASP65 3.1 32.8 1.0 OE1 D:GLU183 3.9 57.0 1.0 OE2 D:GLU183 4.2 44.6 1.0 O E:HOH212 4.4 31.1 1.0 CD D:GLU183 4.5 55.0 1.0 CB E:ASP65 4.6 21.3 1.0 HB3 E:ASP65 4.9 26.0 1.0 HB2 E:ASP65 5.0 26.0 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of the R59P-SNAP25 Containing Snare Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of the R59P-SNAP25 Containing Snare Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca301 b:33.3 occ:1.00 O F:HOH403 2.4 25.5 1.0 O F:HOH427 2.4 30.4 1.0 OE1 F:GLU238 2.6 24.6 1.0 CD F:GLU238 3.5 22.6 1.0 OE2 F:GLU238 3.6 26.3 1.0 HA F:TYR235 4.3 23.7 1.0 HG2 F:GLU234 4.4 33.5 1.0 HD1 F:TYR235 4.4 38.2 1.0 O F:HOH411 4.6 23.8 1.0 O F:HOH418 4.6 25.2 1.0 HB2 F:GLU238 4.9 22.5 1.0 CG F:GLU238 4.9 23.4 1.0 OE1 F:GLU234 5.0 23.8 1.0

B.Alten, Q.Zhou, O.H.Shin, L.Esquivies, P.Y.Lin, K.I.White, R.Sun, W.K.Chung, L.M.Monteggia, A.T.Brunger, E.T.Kavalali. Role of Aberrant Spontaneous Neurotransmission in SNAP25-Associated Encephalopathies. Neuron V. 109 59 2021.
ISSN: ISSN 0896-6273
PubMed: 33147442
DOI: 10.1016/J.NEURON.2020.10.012