Calcium in PDB 5kj8: Structure of the CA2+-Bound Synaptotagmin-1 Snare Complex (Long Unit Cell Form) - From Synchrotron Diffraction

Protein crystallography data

The structure of Structure of the CA2+-Bound Synaptotagmin-1 Snare Complex (Long Unit Cell Form) - From Synchrotron Diffraction, PDB code: 5kj8 was solved by A.Y.Lyubimov, M.Uervirojnangkoorn, Q.Zhou, M.Zhao, N.K.Sauter, A.S.Brewster, W.I.Weis, A.T.Brunger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.64 / 4.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 68.790, 169.710, 286.790, 90.00, 90.00, 90.00
R / Rfree (%) 28.3 / 29.7

Calcium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Calcium atom in the Structure of the CA2+-Bound Synaptotagmin-1 Snare Complex (Long Unit Cell Form) - From Synchrotron Diffraction (pdb code 5kj8). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 14 binding sites of Calcium where determined in the Structure of the CA2+-Bound Synaptotagmin-1 Snare Complex (Long Unit Cell Form) - From Synchrotron Diffraction, PDB code: 5kj8:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 14 in 5kj8

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Calcium binding site 1 out of 14 in the Structure of the CA2+-Bound Synaptotagmin-1 Snare Complex (Long Unit Cell Form) - From Synchrotron Diffraction


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A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of the CA2+-Bound Synaptotagmin-1 Snare Complex (Long Unit Cell Form) - From Synchrotron Diffraction within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca101

b:1.0
occ:1.00
 OE1 D:GLN177 3.8 0.9 1.0
O C:GLY54 3.9 0.5 1.0
C C:GLY54 4.1 0.5 1.0
OE2 D:GLU170 4.3 0.4 1.0
CA C:GLY54 4.4 0.5 1.0
NE2 D:GLN177 4.6 0.9 1.0
CD D:GLN177 4.6 0.9 1.0
N C:GLU55 4.7 0.3 1.0
OE1 C:GLU55 4.9 0.3 1.0
CB C:ASP58 5.0 0.2 1.0
CG C:ASP58 5.0 0.2 1.0

Calcium binding site 2 out of 14 in 5kj8

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Calcium binding site 2 out of 14 in the Structure of the CA2+-Bound Synaptotagmin-1 Snare Complex (Long Unit Cell Form) - From Synchrotron Diffraction


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of the CA2+-Bound Synaptotagmin-1 Snare Complex (Long Unit Cell Form) - From Synchrotron Diffraction within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca102

b:0.8
occ:1.00
 OD1 C:ASP58 3.3 0.2 1.0
OE1 C:GLU61 4.1 0.3 1.0
OE2 C:GLU61 4.1 0.3 1.0
CD C:GLU61 4.3 0.3 1.0
CG C:ASP58 4.3 0.2 1.0
OE2 C:GLU62 4.5 0.5 1.0
OD2 C:ASP58 4.5 0.2 1.0
NH2 D:ARG180 4.9 0.7 1.0

Calcium binding site 3 out of 14 in 5kj8

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Calcium binding site 3 out of 14 in the Structure of the CA2+-Bound Synaptotagmin-1 Snare Complex (Long Unit Cell Form) - From Synchrotron Diffraction


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of the CA2+-Bound Synaptotagmin-1 Snare Complex (Long Unit Cell Form) - From Synchrotron Diffraction within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca501

b:1.0
occ:1.00
 OD2 E:ASP303 2.2 0.6 1.0
O E:TYR364 2.5 0.2 1.0
OD2 E:ASP363 2.5 0.5 1.0
OD1 E:ASP303 2.6 0.6 1.0
OD1 E:ASP363 2.6 0.5 1.0
CG E:ASP303 2.6 0.6 1.0
OD2 E:ASP309 2.7 0.5 1.0
CG E:ASP363 2.9 0.5 1.0
OD1 E:ASP365 3.3 0.8 1.0
C E:TYR364 3.4 0.2 1.0
CB E:ASP309 3.5 0.5 1.0
CG E:ASP309 3.5 0.5 1.0
N E:ASP309 3.5 0.5 1.0
CA E:CA502 3.7 0.6 1.0
CB E:ASP303 4.0 0.6 1.0
CA E:ASP309 4.1 0.5 1.0
N E:TYR364 4.1 0.2 1.0
N E:ASP365 4.2 0.8 1.0
C E:SER308 4.3 0.5 1.0
CA E:ASP365 4.3 0.8 1.0
CB E:ASP363 4.3 0.5 1.0
CA E:TYR364 4.4 0.2 1.0
C E:ASP363 4.4 0.5 1.0
CG E:ASP365 4.5 0.8 1.0
N E:ASP303 4.6 0.6 1.0
CA E:SER308 4.6 0.5 1.0
OD1 E:ASP309 4.7 0.5 1.0
CA E:ASP303 4.7 0.6 1.0
O E:ASP309 4.7 0.5 1.0
C E:ASP309 4.8 0.5 1.0
O E:ASP363 4.9 0.5 1.0
CA E:ASP363 4.9 0.5 1.0

Calcium binding site 4 out of 14 in 5kj8

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Calcium binding site 4 out of 14 in the Structure of the CA2+-Bound Synaptotagmin-1 Snare Complex (Long Unit Cell Form) - From Synchrotron Diffraction


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of the CA2+-Bound Synaptotagmin-1 Snare Complex (Long Unit Cell Form) - From Synchrotron Diffraction within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca502

b:0.6
occ:1.00
 N E:ASP303 2.6 0.6 1.0
OD1 E:ASP303 2.6 0.6 1.0
OD1 E:ASP365 2.6 0.8 1.0
OD2 E:ASP363 2.7 0.5 1.0
CB E:MET302 3.0 0.1 1.0
CA E:ASP303 3.2 0.6 1.0
C E:MET302 3.3 0.1 1.0
CG E:ASP303 3.3 0.6 1.0
CG E:ASP365 3.6 0.8 1.0
CA E:MET302 3.7 0.1 1.0
CG E:ASP363 3.7 0.5 1.0
CA E:CA501 3.7 1.0 1.0
OD2 E:ASP365 3.8 0.8 1.0
CB E:ASP303 3.8 0.6 1.0
O E:MET302 4.1 0.1 1.0
CG E:MET302 4.3 0.1 1.0
OD2 E:ASP303 4.3 0.6 1.0
OD1 E:ASP363 4.3 0.5 1.0
OD2 E:ASP371 4.4 0.9 1.0
C E:ASP303 4.6 0.6 1.0
CB E:ASP363 4.6 0.5 1.0
N E:MET302 4.8 0.1 1.0
CE E:MET302 4.9 0.1 1.0
CB E:ASP365 4.9 0.8 1.0

Calcium binding site 5 out of 14 in 5kj8

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Calcium binding site 5 out of 14 in the Structure of the CA2+-Bound Synaptotagmin-1 Snare Complex (Long Unit Cell Form) - From Synchrotron Diffraction


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of the CA2+-Bound Synaptotagmin-1 Snare Complex (Long Unit Cell Form) - From Synchrotron Diffraction within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca503

b:1.0
occ:1.00
 OD2 E:ASP172 2.2 0.5 1.0
O E:PHE231 2.2 0.6 1.0
OD1 E:ASP232 2.6 0.8 1.0
OD2 E:ASP230 2.7 0.6 1.0
CA E:CA504 2.7 0.8 1.0
OD1 E:ASP230 2.8 0.6 1.0
CG E:ASP230 2.9 0.6 1.0
CG E:ASP232 2.9 0.8 1.0
CG E:ASP172 2.9 0.5 1.0
OD2 E:ASP232 3.1 0.8 1.0
C E:PHE231 3.1 0.6 1.0
OD1 E:ASP172 3.7 0.5 1.0
CB E:ASP172 3.7 0.5 1.0
N E:ASP232 3.8 0.8 1.0
N E:PHE231 3.9 0.6 1.0
CA E:ASP232 3.9 0.8 1.0
C E:ASP230 3.9 0.6 1.0
CB E:ASP232 4.0 0.8 1.0
CB E:ASP230 4.0 0.6 1.0
O E:ASP230 4.1 0.6 1.0
N E:ASP172 4.1 0.5 1.0
CA E:PHE231 4.1 0.6 1.0
CA E:ASP230 4.5 0.6 1.0
CA E:ASP172 4.5 0.5 1.0
CB E:ASP178 4.7 0.2 1.0
O E:ASP178 4.7 0.2 1.0
OD2 E:ASP178 4.8 0.2 1.0
N E:ASP178 4.8 0.2 1.0
C E:LEU171 5.0 0.6 1.0

Calcium binding site 6 out of 14 in 5kj8

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Calcium binding site 6 out of 14 in the Structure of the CA2+-Bound Synaptotagmin-1 Snare Complex (Long Unit Cell Form) - From Synchrotron Diffraction


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of the CA2+-Bound Synaptotagmin-1 Snare Complex (Long Unit Cell Form) - From Synchrotron Diffraction within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca504

b:0.8
occ:1.00
 OD2 E:ASP178 2.5 0.2 1.0
CA E:CA503 2.7 1.0 1.0
CG E:ASP178 2.8 0.2 1.0
OD1 E:ASP172 2.9 0.5 1.0
OD2 E:ASP172 3.0 0.5 1.0
CB E:ASP178 3.1 0.2 1.0
CG E:ASP172 3.2 0.5 1.0
O E:PHE231 3.2 0.6 1.0
N E:ASP178 3.3 0.2 1.0
OD1 E:ASP178 3.5 0.2 1.0
OD1 E:ASP230 3.6 0.6 1.0
CA E:ASP178 3.8 0.2 1.0
C E:SER177 4.2 0.5 1.0
N E:ASP172 4.3 0.5 1.0
CG E:ASP230 4.3 0.6 1.0
OD2 E:ASP230 4.3 0.6 1.0
C E:PHE231 4.5 0.6 1.0
CB E:ASP172 4.5 0.5 1.0
CA E:SER177 4.6 0.5 1.0
O E:ASP178 4.6 0.2 1.0
C E:ASP178 4.7 0.2 1.0
O E:THR176 4.9 0.2 1.0

Calcium binding site 7 out of 14 in 5kj8

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Calcium binding site 7 out of 14 in the Structure of the CA2+-Bound Synaptotagmin-1 Snare Complex (Long Unit Cell Form) - From Synchrotron Diffraction


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Structure of the CA2+-Bound Synaptotagmin-1 Snare Complex (Long Unit Cell Form) - From Synchrotron Diffraction within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca501

b:81.6
occ:1.00
 O F:PHE231 2.8 0.1 1.0
OD1 F:ASP230 2.9 0.8 1.0
OD2 F:ASP178 3.0 0.7 1.0
CA F:CA504 3.2 0.8 1.0
OD2 F:ASP172 3.3 0.2 1.0
OD2 F:ASP230 3.4 0.8 1.0
CG F:ASP178 3.4 0.7 1.0
CG F:ASP230 3.5 0.8 1.0
CB F:ASP178 3.6 0.7 1.0
N F:ASP178 3.7 0.7 1.0
OD1 F:ASP232 4.0 0.1 1.0
C F:PHE231 4.0 0.1 1.0
OD1 F:ASP178 4.2 0.7 1.0
CG F:ASP172 4.2 0.2 1.0
CA F:ASP178 4.2 0.7 1.0
CB F:ASP172 4.3 0.2 1.0
CG F:ASP232 4.4 0.1 1.0
OD2 F:ASP232 4.4 0.1 1.0
CA F:CA502 4.5 0.1 1.0
N F:PHE231 4.6 0.1 1.0
C F:SER177 4.6 0.3 1.0
O F:ASP178 4.7 0.7 1.0
CA F:PHE231 4.8 0.1 1.0
CA F:SER177 4.9 0.3 1.0
N F:ASP232 4.9 0.1 1.0
CB F:ASP230 4.9 0.8 1.0
C F:ASP178 5.0 0.7 1.0
CA F:ASP232 5.0 0.1 1.0

Calcium binding site 8 out of 14 in 5kj8

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Calcium binding site 8 out of 14 in the Structure of the CA2+-Bound Synaptotagmin-1 Snare Complex (Long Unit Cell Form) - From Synchrotron Diffraction


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Structure of the CA2+-Bound Synaptotagmin-1 Snare Complex (Long Unit Cell Form) - From Synchrotron Diffraction within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca502

b:0.1
occ:1.00
 OD2 F:ASP172 2.1 0.2 1.0
OD2 F:ASP230 2.2 0.8 1.0
OD1 F:ASP172 2.6 0.2 1.0
CG F:ASP172 2.6 0.2 1.0
OD2 F:ASP232 2.6 0.1 1.0
OD1 F:ASP232 3.2 0.1 1.0
CG F:ASP230 3.3 0.8 1.0
CG F:ASP232 3.3 0.1 1.0
CB F:ASP230 3.9 0.8 1.0
OD2 F:ASP238 3.9 0.1 1.0
CB F:ASP172 4.0 0.2 1.0
OD1 F:ASP230 4.3 0.8 1.0
CB F:ASP238 4.4 0.1 1.0
CG F:ASP238 4.5 0.1 1.0
CA F:CA501 4.5 81.6 1.0
CD2 F:LEU171 4.6 0.9 1.0
N F:ASP172 4.7 0.2 1.0
CB F:ASP232 4.8 0.1 1.0
O F:ASP230 4.8 0.8 1.0
CB F:LEU171 4.8 0.9 1.0
CA F:ASP172 4.8 0.2 1.0

Calcium binding site 9 out of 14 in 5kj8

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Calcium binding site 9 out of 14 in the Structure of the CA2+-Bound Synaptotagmin-1 Snare Complex (Long Unit Cell Form) - From Synchrotron Diffraction


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Structure of the CA2+-Bound Synaptotagmin-1 Snare Complex (Long Unit Cell Form) - From Synchrotron Diffraction within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca503

b:0.7
occ:1.00
 OD2 F:ASP309 2.6 0.2 1.0
OD2 F:ASP303 2.8 0.4 1.0
O F:TYR364 2.9 0.9 1.0
OD2 F:ASP363 3.1 0.4 1.0
OD1 F:ASP363 3.2 0.4 1.0
CG F:ASP363 3.5 0.4 1.0
CG F:ASP309 3.6 0.2 1.0
N F:ASP309 3.6 0.2 1.0
CG F:ASP303 3.7 0.4 1.0
OD1 F:ASP365 3.8 0.6 1.0
CB F:ASP309 3.9 0.2 1.0
C F:TYR364 4.0 0.9 1.0
C F:SER308 4.1 0.5 1.0
CA F:SER308 4.2 0.5 1.0
CB F:ASP303 4.2 0.4 1.0
CA F:ASP309 4.4 0.2 1.0
O F:MET302 4.7 0.1 1.0
OD1 F:ASP309 4.7 0.2 1.0
OD1 F:ASP303 4.7 0.4 1.0
CA F:ASP365 4.8 0.6 1.0
N F:TYR364 4.8 0.9 1.0
N F:ASP365 4.8 0.6 1.0
CB F:MET302 4.9 0.1 1.0
N F:SER308 4.9 0.5 1.0
O F:SER308 4.9 0.5 1.0
CG F:ASP365 5.0 0.6 1.0
C F:MET302 5.0 0.1 1.0
CA F:TYR364 5.0 0.9 1.0

Calcium binding site 10 out of 14 in 5kj8

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Calcium binding site 10 out of 14 in the Structure of the CA2+-Bound Synaptotagmin-1 Snare Complex (Long Unit Cell Form) - From Synchrotron Diffraction


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Structure of the CA2+-Bound Synaptotagmin-1 Snare Complex (Long Unit Cell Form) - From Synchrotron Diffraction within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca504

b:0.8
occ:1.00
 O F:THR176 2.5 0.4 1.0
CA F:SER177 2.8 0.3 1.0
CB F:ASP172 3.1 0.2 1.0
CA F:CA501 3.2 81.6 1.0
C F:THR176 3.2 0.4 1.0
N F:SER177 3.4 0.3 1.0
O F:ASP172 3.5 0.2 1.0
C F:SER177 3.6 0.3 1.0
N F:ASP172 3.6 0.2 1.0
N F:ASP178 3.6 0.7 1.0
CA F:ASP172 3.8 0.2 1.0
CB F:SER177 3.9 0.3 1.0
OD2 F:ASP230 3.9 0.8 1.0
CG F:ASP172 3.9 0.2 1.0
OD2 F:ASP172 3.9 0.2 1.0
OD1 F:ASP230 4.0 0.8 1.0
OG F:SER177 4.0 0.3 1.0
C F:ASP172 4.1 0.2 1.0
O F:ALA170 4.1 0.8 1.0
CG F:ASP230 4.3 0.8 1.0
O F:SER177 4.5 0.3 1.0
CA F:THR176 4.6 0.4 1.0
CB F:LEU171 4.6 0.9 1.0
OD1 F:ASP178 4.6 0.7 1.0
CG F:ASP178 4.6 0.7 1.0
C F:LEU171 4.8 0.9 1.0
OD2 F:ASP178 4.8 0.7 1.0
N F:THR176 4.8 0.4 1.0
OD1 F:ASP172 4.9 0.2 1.0
CA F:ASP178 4.9 0.7 1.0

Reference:

A.Y.Lyubimov, M.Uervirojnangkoorn, O.B.Zeldin, Q.Zhou, M.Zhao, A.S.Brewster, T.Michels-Clark, J.M.Holton, N.K.Sauter, W.I.Weis, A.T.Brunger. Advances in X-Ray Free Electron Laser (Xfel) Diffraction Data Processing Applied to the Crystal Structure of the Synaptotagmin-1 / Snare Complex. Elife V. 5 2016.
ISSN: ESSN 2050-084X
PubMed: 27731796
DOI: 10.7554/ELIFE.18740
Page generated: Sat Dec 12 05:33:44 2020

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