Calcium in PDB 8c5h: NBSYT1 Anti-(Rat Synaptotagmin-1) Nanobody Bound to Target Cytosolic Domain of Synaptotagmin-1

The structure of NBSYT1 Anti-(Rat Synaptotagmin-1) Nanobody Bound to Target Cytosolic Domain of Synaptotagmin-1, PDB code: 8c5h was solved by M.Martinez-Carranza, P.Stenmark, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.26 / 1.68
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	52.41, 65.75, 66.91, 90, 90, 90
R / Rfree (%)	20.9 / 22.2

The binding sites of Calcium atom in the NBSYT1 Anti-(Rat Synaptotagmin-1) Nanobody Bound to Target Cytosolic Domain of Synaptotagmin-1 (pdb code 8c5h). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total only one binding site of Calcium was determined in the NBSYT1 Anti-(Rat Synaptotagmin-1) Nanobody Bound to Target Cytosolic Domain of Synaptotagmin-1, PDB code: 8c5h:

Calcium binding site 1 out of 1 in the NBSYT1 Anti-(Rat Synaptotagmin-1) Nanobody Bound to Target Cytosolic Domain of Synaptotagmin-1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of NBSYT1 Anti-(Rat Synaptotagmin-1) Nanobody Bound to Target Cytosolic Domain of Synaptotagmin-1 within 5.0Å range: probe atom residue distance (Å) B Occ S:Ca301 b:58.0 occ:1.00 O S:PHE231 2.3 42.4 1.0 OD1 S:ASP230 2.4 38.8 1.0 OD2 S:ASP178 2.5 39.1 1.0 OD1 S:ASP172 2.6 49.6 1.0 OD2 S:ASP230 2.7 40.7 1.0 CG S:ASP230 2.8 39.7 1.0 OD2 S:ASP172 3.0 49.4 1.0 CG S:ASP172 3.1 49.2 1.0 CG S:ASP178 3.5 38.4 1.0 C S:PHE231 3.5 43.2 1.0 CB S:ASP178 3.7 37.5 1.0 N S:ASP178 3.9 37.0 1.0 N S:PHE231 4.2 41.6 1.0 CB S:ASP230 4.3 39.2 1.0 CA S:ASP232 4.3 61.0 1.0 N S:ASP232 4.3 59.1 1.0 C S:ASP230 4.3 39.0 1.0 CB S:ASP232 4.4 61.7 1.0 CA S:ASP178 4.4 37.2 1.0 CA S:PHE231 4.5 42.0 1.0 O S:HOH413 4.5 50.2 1.0 OD1 S:ASP178 4.6 38.0 1.0 CB S:ASP172 4.6 51.5 1.0 C S:SER177 4.7 38.4 1.0 O S:ASP230 4.7 39.5 1.0 CA S:ASP230 4.8 38.2 1.0 CA S:SER177 4.8 38.8 1.0 OD1 S:ASP232 4.9 67.2 1.0

K.Queiroz Zetune Villa Real, N.Mougios, R.Rehm, S.Sograte-Idrissi, L.Albert, A.M.Rahimi, M.Maidorn, J.Hentze, M.Martinez-Carranza, H.Hosseini, K.A.Saal, N.Oleksiievets, M.Prigge, R.Tsukanov, P.Stenmark, E.F.Fornasiero, F.Opazo. A Versatile Synaptotagmin-1 Nanobody Provides Perturbation-Free Live Synaptic Imaging and Low Linkage-Error in Super-Resolution Microscopy. Small Methods 00218 2023.
ISSN: ESSN 2366-9608
PubMed: 37421204
DOI: 10.1002/SMTD.202300218