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

Protein crystallography data

The structure of Structure of the CA2+-Bound Synaptotagmin-1 Snare Complex (Long Unit Cell Form), PDB code: 5ccg was solved by Q.Zhou, M.Zhao, A.Y.Lyubimov, M.Uervirojnangkoorn, O.B.Zeldin, 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) 19.97 / 3.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 69.603, 171.092, 291.879, 90.00, 90.00, 90.00
R / Rfree (%) 32.2 / 35.3

Calcium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 19;

Binding sites:

The binding sites of Calcium atom in the Structure of the CA2+-Bound Synaptotagmin-1 Snare Complex (Long Unit Cell Form) (pdb code 5ccg). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 19 binding sites of Calcium where determined in the Structure of the CA2+-Bound Synaptotagmin-1 Snare Complex (Long Unit Cell Form), PDB code: 5ccg:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 19 in 5ccg

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Calcium binding site 1 out of 19 in the Structure of the CA2+-Bound Synaptotagmin-1 Snare Complex (Long Unit Cell Form)


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Stereo pair view

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) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca101

b:24.3
occ:1.00
 CA A:CA102 3.8 22.8 1.0
CG A:GLU55 3.9 42.6 1.0
CD A:GLU55 3.9 40.2 1.0
OE1 A:GLU55 4.0 33.9 1.0
OE1 A:GLN58 4.1 30.2 1.0
CB A:GLU55 4.2 32.7 1.0
CE A:LYS59 4.3 22.8 1.0
OE2 A:GLU55 4.4 61.3 1.0
NZ A:LYS59 4.4 22.8 1.0
CA A:GLU55 4.8 28.1 1.0

Calcium binding site 2 out of 19 in 5ccg

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Calcium binding site 2 out of 19 in the Structure of the CA2+-Bound Synaptotagmin-1 Snare Complex (Long Unit Cell Form)


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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) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca102

b:22.8
occ:1.00
 OE1 A:GLU62 3.8 59.0 1.0
CA A:CA101 3.8 24.3 1.0
NZ A:LYS59 4.4 22.8 1.0
CG A:LYS59 4.5 23.0 1.0
OE1 A:GLN58 4.6 30.2 1.0
CB A:GLN58 5.0 32.4 1.0

Calcium binding site 3 out of 19 in 5ccg

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Calcium binding site 3 out of 19 in the Structure of the CA2+-Bound Synaptotagmin-1 Snare Complex (Long Unit Cell Form)


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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) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca101

b:22.8
occ:1.00
 OE1 D:GLN177 3.8 23.4 1.0
O C:GLY54 3.9 30.8 1.0
C C:GLY54 4.1 34.6 1.0
OE2 D:GLU170 4.1 25.8 1.0
CA C:GLY54 4.4 30.6 1.0
NE2 D:GLN177 4.5 29.9 1.0
CD D:GLN177 4.6 25.2 1.0
N C:GLU55 4.7 34.4 1.0
CB C:ASP58 4.9 32.7 1.0
OE2 C:GLU55 5.0 51.4 1.0

Calcium binding site 4 out of 19 in 5ccg

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Calcium binding site 4 out of 19 in the Structure of the CA2+-Bound Synaptotagmin-1 Snare Complex (Long Unit Cell Form)


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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) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca102

b:22.8
occ:1.00
 OE2 C:GLU61 2.7 27.3 1.0
OE1 C:GLU61 3.0 27.6 1.0
CD C:GLU61 3.1 25.7 1.0
OD1 C:ASP58 3.3 29.9 1.0
NH2 D:ARG180 3.7 67.1 1.0
OE2 C:GLU62 4.3 30.4 1.0
CG C:GLU61 4.4 23.8 1.0
CZ D:ARG180 4.5 64.7 1.0
CG C:ASP58 4.6 31.5 1.0
NE D:ARG180 4.7 49.0 1.0
CB C:GLU61 4.8 29.2 1.0

Calcium binding site 5 out of 19 in 5ccg

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Calcium binding site 5 out of 19 in the Structure of the CA2+-Bound Synaptotagmin-1 Snare Complex (Long Unit Cell Form)


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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) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca103

b:22.8
occ:1.00
 OD2 C:ASP41 4.1 38.6 1.0
CG C:GLU37 4.2 34.6 1.0
O E:HOH604 4.8 22.8 1.0
NZ E:LYS297 4.9 34.7 1.0

Calcium binding site 6 out of 19 in 5ccg

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Calcium binding site 6 out of 19 in the Structure of the CA2+-Bound Synaptotagmin-1 Snare Complex (Long Unit Cell Form)


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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) within 5.0Å range:

Calcium binding site 7 out of 19 in 5ccg

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Calcium binding site 7 out of 19 in the Structure of the CA2+-Bound Synaptotagmin-1 Snare Complex (Long Unit Cell Form)


Mono view


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca501

b:37.4
occ:1.00
 OD2 E:ASP309 2.5 45.0 1.0
O E:TYR364 2.5 49.2 1.0
OD1 E:ASP365 2.6 57.9 1.0
OD2 E:ASP363 3.1 48.1 1.0
CB E:ASP303 3.2 51.0 1.0
C E:TYR364 3.5 55.9 1.0
CG E:ASP303 3.5 46.4 1.0
CG E:ASP309 3.6 44.0 1.0
CA E:ASP365 3.7 71.6 1.0
CG E:ASP365 3.7 59.0 1.0
OD1 E:ASP363 3.7 47.0 1.0
OD2 E:ASP303 3.8 43.8 1.0
CG E:ASP363 3.8 46.3 1.0
N E:ASP365 3.9 66.6 1.0
OD1 E:ASP303 4.0 45.3 1.0
CB E:ASP309 4.2 42.6 1.0
CA E:CA504 4.2 46.8 1.0
CB E:ASP365 4.2 71.2 1.0
CA E:ASP303 4.3 54.2 1.0
N E:ASP303 4.6 52.4 1.0
OD1 E:ASP309 4.6 44.4 1.0
CA E:TYR364 4.7 50.8 1.0
OD2 E:ASP365 4.7 57.3 1.0
N E:TYR364 4.8 49.4 1.0
N E:ASP309 4.8 41.0 1.0
C E:ASP365 4.8 59.0 1.0
N E:LYS366 4.9 57.9 1.0

Calcium binding site 8 out of 19 in 5ccg

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Calcium binding site 8 out of 19 in the Structure of the CA2+-Bound Synaptotagmin-1 Snare Complex (Long Unit Cell Form)


Mono view


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca502

b:35.3
occ:1.00
 CB E:ASP172 2.0 62.6 1.0
OD2 E:ASP230 2.1 43.9 1.0
O E:PHE231 2.3 42.8 1.0
CG E:ASP172 2.6 56.8 1.0
CG E:ASP230 2.9 42.5 1.0
OD1 E:ASP230 3.0 42.1 1.0
OD1 E:ASP172 3.0 46.9 1.0
CA E:ASP172 3.1 56.2 1.0
OD1 E:ASP232 3.3 45.4 1.0
C E:PHE231 3.4 43.9 1.0
OD2 E:ASP172 3.5 53.0 1.0
N E:ASP172 3.7 53.5 1.0
N E:PHE231 3.7 40.8 1.0
CG E:ASP232 3.8 47.3 1.0
OD2 E:ASP232 4.0 49.1 1.0
CA E:PHE231 4.1 40.4 1.0
CB E:ASP230 4.3 40.1 1.0
C E:ASP172 4.4 72.2 1.0
N E:ASP232 4.4 40.6 1.0
C E:LEU171 4.4 51.2 1.0
N E:ASP178 4.6 43.0 1.0
CA E:ASP232 4.6 41.8 1.0
O E:ASP178 4.6 62.9 1.0
N E:MET173 4.7 59.4 1.0
C E:ASP230 4.7 37.0 1.0
O E:LEU171 4.7 50.1 1.0
OD2 E:ASP178 4.7 25.9 1.0
CB E:ASP232 4.8 45.0 1.0
CA E:CA503 4.8 22.8 1.0
CG E:ASP178 4.9 29.1 1.0
CB E:PHE231 4.9 41.3 1.0
CB E:ASP178 4.9 37.2 1.0
CA E:ASP230 4.9 37.2 1.0

Calcium binding site 9 out of 19 in 5ccg

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Calcium binding site 9 out of 19 in the Structure of the CA2+-Bound Synaptotagmin-1 Snare Complex (Long Unit Cell Form)


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca503

b:22.8
occ:1.00
 OD2 E:ASP172 2.5 53.0 1.0
OD2 E:ASP178 3.0 25.9 1.0
OD1 E:ASP172 3.1 46.9 1.0
CG E:ASP172 3.1 56.8 1.0
NE E:ARG233 4.0 44.7 1.0
CG E:ARG233 4.1 49.5 1.0
CG E:ASP178 4.2 29.1 1.0
O E:PHE231 4.3 42.8 1.0
CD E:ARG233 4.4 46.3 1.0
CB E:ASP172 4.5 62.6 1.0
N E:ARG233 4.6 45.0 1.0
N E:MET173 4.8 59.4 1.0
CA E:ASP232 4.8 41.8 1.0
CA E:CA502 4.8 35.3 1.0
OD1 E:ASP178 4.9 34.3 1.0
CD2 E:PHE231 4.9 39.1 1.0
NH1 E:ARG199 4.9 38.8 1.0
CZ E:ARG233 4.9 45.1 1.0

Calcium binding site 10 out of 19 in 5ccg

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Calcium binding site 10 out of 19 in the Structure of the CA2+-Bound Synaptotagmin-1 Snare Complex (Long Unit Cell Form)


Mono view


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca504

b:46.8
occ:1.00
 OD1 E:ASP365 2.8 57.9 1.0
N E:ASP303 2.9 52.4 1.0
OD2 E:ASP365 2.9 57.3 1.0
C E:MET302 3.0 52.8 1.0
CA E:ASP303 3.0 54.2 1.0
O E:MET302 3.1 53.3 1.0
OD2 E:ASP363 3.2 48.1 1.0
CG E:ASP365 3.3 59.0 1.0
CB E:MET302 3.6 54.3 1.0
CB E:ASP303 3.7 51.0 1.0
CA E:MET302 3.8 52.8 1.0
CA E:CA501 4.2 37.4 1.0
OD2 E:ASP371 4.3 53.1 1.0
CG E:ASP363 4.3 46.3 1.0
C E:ASP303 4.3 59.4 1.0
OD1 E:ASP303 4.7 45.3 1.0
CG E:ASP303 4.7 46.4 1.0
CB E:ASP365 4.7 71.2 1.0
N E:VAL304 4.8 64.2 1.0
CE E:MET302 4.8 58.7 1.0
CG E:MET302 4.9 51.5 1.0

Reference:

Q.Zhou, Y.Lai, T.Bacaj, M.Zhao, A.Y.Lyubimov, M.Uervirojnangkoorn, O.B.Zeldin, A.S.Brewster, N.K.Sauter, A.E.Cohen, S.M.Soltis, R.Alonso-Mori, M.Chollet, H.T.Lemke, R.A.Pfuetzner, U.B.Choi, W.I.Weis, J.Diao, T.C.Sudhof, A.T.Brunger. Architecture of the Synaptotagmin-Snare Machinery For Neuronal Exocytosis. Nature V. 525 62 2015.
ISSN: ESSN 1476-4687
PubMed: 26280336
DOI: 10.1038/NATURE14975
Page generated: Sun Jul 14 17:03:49 2024

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