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Calcium in PDB 2yoa: Synaptotagmin-1 C2B Domain with Phosphoserine

Protein crystallography data

The structure of Synaptotagmin-1 C2B Domain with Phosphoserine, PDB code: 2yoa was solved by A.Honigmann, G.Van Den Bogaart, E.Iraheta, H.J.Risselada, D.Milovanovic, V.Mueller, S.Muellar, U.Diederichsen, D.Fasshauer, H.Grubmuller, S.W.Hell, C.Eggeling, K.Kuhnel, R.Jahn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.50 / 1.50
Space group P 4 21 2
Cell size a, b, c (Å), α, β, γ (°) 97.000, 97.000, 89.010, 90.00, 90.00, 90.00
R / Rfree (%) 18.3 / 20.4

Calcium Binding Sites:

The binding sites of Calcium atom in the Synaptotagmin-1 C2B Domain with Phosphoserine (pdb code 2yoa). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the Synaptotagmin-1 C2B Domain with Phosphoserine, PDB code: 2yoa:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in 2yoa

Go back to Calcium Binding Sites List in 2yoa
Calcium binding site 1 out of 7 in the Synaptotagmin-1 C2B Domain with Phosphoserine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Synaptotagmin-1 C2B Domain with Phosphoserine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1001

b:7.4
occ:1.00
 O A:SEP1004 2.3 9.0 1.0
O A:TYR364 2.3 7.1 1.0
OD2 A:ASP309 2.4 7.4 1.0
OD2 A:ASP303 2.4 9.3 1.0
OD1 A:ASP363 2.4 7.4 1.0
OD1 A:ASP303 2.4 9.4 1.0
OD1 A:ASP365 2.4 8.8 1.0
CG A:ASP303 2.7 9.8 1.0
OD2 A:ASP363 3.0 8.8 1.0
CG A:ASP363 3.0 7.2 1.0
CG A:ASP309 3.4 7.1 1.0
C A:TYR364 3.4 7.1 1.0
C A:SEP1004 3.5 10.5 1.0
CG A:ASP365 3.6 9.1 1.0
CA A:CA1002 3.7 9.3 1.0
CB A:ASP309 3.9 6.9 1.0
N A:SEP1004 3.9 11.1 1.0
CA A:ASP365 4.0 7.7 1.0
N A:ASP365 4.1 6.8 1.0
N A:ASP309 4.1 6.1 1.0
O A:HOH2025 4.2 17.4 1.0
CA A:SEP1004 4.2 10.8 1.0
CB A:ASP303 4.3 10.2 1.0
OXT A:SEP1004 4.3 11.8 1.0
CB A:ASP365 4.4 7.8 1.0
N A:TYR364 4.5 6.8 1.0
CB A:ASP363 4.5 7.4 1.0
OD1 A:ASP309 4.5 8.4 1.0
C A:ASP363 4.5 7.1 1.0
OD2 A:ASP365 4.5 11.1 1.0
CA A:TYR364 4.6 7.2 1.0
O A:HOH2026 4.6 15.2 1.0
CA A:ASP309 4.7 6.5 1.0
O A:ASP363 4.8 7.8 1.0
C A:SER308 4.8 7.1 1.0
CA A:SER308 4.9 8.1 1.0
CA A:ASP363 5.0 7.1 1.0

Calcium binding site 2 out of 7 in 2yoa

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Calcium binding site 2 out of 7 in the Synaptotagmin-1 C2B Domain with Phosphoserine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Synaptotagmin-1 C2B Domain with Phosphoserine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1002

b:9.3
occ:1.00
 OD2 A:ASP363 2.3 8.8 1.0
O A:HOH2023 2.3 15.7 1.0
OD2 A:ASP371 2.3 13.0 1.0
O A:MET302 2.3 10.0 1.0
OD1 A:ASP303 2.3 9.4 1.0
OD1 A:ASP365 2.5 8.8 1.0
OD2 A:ASP365 2.6 11.1 1.0
CG A:ASP365 2.9 9.1 1.0
C A:MET302 3.4 9.8 1.0
CG A:ASP371 3.4 13.6 1.0
CG A:ASP303 3.5 9.8 1.0
CG A:ASP363 3.5 7.2 1.0
CA A:CA1001 3.7 7.4 1.0
O A:HOH2071 3.8 21.7 1.0
CA A:ASP303 4.0 10.8 1.0
N A:ASP303 4.1 10.0 1.0
O A:HOH2024 4.1 26.4 1.0
CB A:MET302 4.1 10.4 1.0
O A:HOH2025 4.1 17.4 1.0
OD1 A:ASP371 4.2 15.2 1.0
OD1 A:ASP363 4.2 7.4 1.0
CA A:CA1003 4.3 14.5 1.0
CB A:ASP371 4.3 14.2 1.0
CB A:ASP303 4.4 10.2 1.0
OD2 A:ASP303 4.4 9.3 1.0
CA A:MET302 4.4 9.3 1.0
CB A:ASP365 4.4 7.8 1.0
CB A:ASP363 4.6 7.4 1.0
O A:SEP1004 4.8 9.0 1.0

Calcium binding site 3 out of 7 in 2yoa

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Calcium binding site 3 out of 7 in the Synaptotagmin-1 C2B Domain with Phosphoserine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Synaptotagmin-1 C2B Domain with Phosphoserine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1003

b:14.5
occ:1.00
 O A:HOH2076 2.3 20.6 1.0
OD1 A:ASP371 2.3 15.2 1.0
OD2 A:ASP365 2.3 11.1 1.0
O A:HOH2071 2.3 21.7 1.0
O A:LYS369 2.3 13.6 1.0
O A:HOH2070 2.4 16.1 1.0
CG A:ASP371 3.2 13.6 1.0
OD2 A:ASP371 3.4 13.0 1.0
CG A:ASP365 3.5 9.1 1.0
C A:LYS369 3.6 13.8 1.0
CB A:ASP365 4.0 7.8 1.0
CA A:CA1002 4.3 9.3 1.0
N A:LYS369 4.3 13.7 1.0
O A:HOH2023 4.3 15.7 1.0
CA A:LYS369 4.4 13.9 1.0
C A:ASN370 4.5 14.7 1.0
OD1 A:ASP365 4.5 8.8 1.0
N A:ASN370 4.5 13.1 1.0
O A:HOH2079 4.5 24.6 1.0
N A:ASP371 4.6 14.0 1.0
CA A:ASN370 4.6 13.8 1.0
CB A:ASP371 4.6 14.2 1.0
O A:ILE367 4.6 13.5 1.0
O A:ASN370 4.7 16.9 1.0
CB A:LYS369 4.8 14.8 1.0
C A:GLY368 4.8 13.4 1.0
CA A:ASP371 5.0 14.0 1.0

Calcium binding site 4 out of 7 in 2yoa

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Calcium binding site 4 out of 7 in the Synaptotagmin-1 C2B Domain with Phosphoserine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Synaptotagmin-1 C2B Domain with Phosphoserine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1005

b:23.3
occ:1.00
 O A:HOH2027 3.0 17.0 1.0
CG A:ASP309 3.6 7.1 1.0
CD2 A:TYR364 3.6 10.7 1.0
OD2 A:ASP309 3.8 7.4 1.0
CA A:SEP1004 3.8 10.8 1.0
OD1 A:ASP309 3.8 8.4 1.0
CE2 A:TYR364 3.9 12.2 1.0
CB A:ASP309 3.9 6.9 1.0
CG A:LYS332 4.0 13.3 1.0
CE A:LYS366 4.1 18.2 1.0
N A:SEP1004 4.3 11.1 1.0
C A:SEP1004 4.5 10.5 1.0
CD A:LYS332 4.5 17.3 1.0
CG A:LYS366 4.6 13.4 1.0
O A:HOH2130 4.7 21.0 1.0
CB A:LYS332 4.7 9.9 1.0
O A:TYR364 4.8 7.1 1.0
CB A:SEP1004 4.8 11.6 1.0
CG A:TYR364 4.8 8.5 1.0
OG A:SEP1004 4.8 13.3 1.0
OXT A:SEP1004 4.9 11.8 1.0
CE A:LYS332 4.9 19.1 1.0
CA A:LYS332 5.0 9.0 1.0
O A:SEP1004 5.0 9.0 1.0
CD A:LYS366 5.0 15.9 1.0

Calcium binding site 5 out of 7 in 2yoa

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Calcium binding site 5 out of 7 in the Synaptotagmin-1 C2B Domain with Phosphoserine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Synaptotagmin-1 C2B Domain with Phosphoserine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1001

b:7.2
occ:1.00
 O B:TYR364 2.3 6.9 1.0
O B:SEP1004 2.3 9.5 1.0
OD1 B:ASP365 2.3 8.7 1.0
OD2 B:ASP303 2.4 8.9 1.0
OD1 B:ASP363 2.4 7.5 1.0
OD2 B:ASP309 2.4 6.5 1.0
OD1 B:ASP303 2.6 8.3 1.0
CG B:ASP303 2.8 9.1 1.0
OD2 B:ASP363 3.0 9.3 1.0
CG B:ASP363 3.0 7.2 1.0
C B:TYR364 3.4 7.7 1.0
C B:SEP1004 3.5 11.3 1.0
CG B:ASP309 3.5 6.9 1.0
CG B:ASP365 3.6 8.6 1.0
CA B:CA1002 3.8 8.3 1.0
N B:SEP1004 3.9 11.1 1.0
CB B:ASP309 3.9 6.5 1.0
CA B:ASP365 3.9 8.2 1.0
N B:ASP365 4.1 7.4 1.0
N B:ASP309 4.2 6.2 1.0
O B:HOH2029 4.2 21.6 1.0
CA B:SEP1004 4.2 11.4 1.0
OXT B:SEP1004 4.3 12.8 1.0
CB B:ASP303 4.3 8.9 1.0
CB B:ASP365 4.4 8.5 1.0
N B:TYR364 4.4 7.1 1.0
CB B:ASP363 4.5 6.8 1.0
O B:HOH2030 4.5 11.8 1.0
OD2 B:ASP365 4.5 8.7 1.0
C B:ASP363 4.5 7.1 1.0
OD1 B:ASP309 4.5 7.9 1.0
CA B:TYR364 4.6 7.6 1.0
CA B:ASP309 4.7 6.4 1.0
O B:ASP363 4.8 7.8 1.0
C B:SER308 4.9 6.5 1.0
O B:HOH2123 4.9 20.8 1.0
CA B:SER308 4.9 7.0 1.0
CA B:ASP363 5.0 6.8 1.0

Calcium binding site 6 out of 7 in 2yoa

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Calcium binding site 6 out of 7 in the Synaptotagmin-1 C2B Domain with Phosphoserine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Synaptotagmin-1 C2B Domain with Phosphoserine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1002

b:8.3
occ:1.00
 O B:HOH2027 2.3 15.0 1.0
OD2 B:ASP363 2.3 9.3 1.0
OD1 B:ASP303 2.3 8.3 1.0
O B:MET302 2.3 9.2 1.0
OD2 B:ASP371 2.3 12.7 1.0
OD2 B:ASP365 2.6 8.7 1.0
OD1 B:ASP365 2.6 8.7 1.0
CG B:ASP365 2.9 8.6 1.0
C B:MET302 3.4 8.8 1.0
CG B:ASP371 3.4 13.0 1.0
CG B:ASP303 3.5 9.1 1.0
CG B:ASP363 3.6 7.2 1.0
CA B:CA1001 3.8 7.2 1.0
O B:HOH2076 3.8 16.7 1.0
CA B:ASP303 4.1 8.9 1.0
N B:ASP303 4.1 8.6 1.0
O B:HOH2028 4.1 25.5 1.0
CB B:MET302 4.1 9.2 1.0
O B:HOH2029 4.2 21.6 1.0
OD1 B:ASP371 4.2 14.0 1.0
OD1 B:ASP363 4.2 7.5 1.0
CA B:CA1003 4.2 12.5 1.0
CB B:ASP371 4.3 12.9 1.0
O B:HOH2031 4.3 25.2 1.0
OD2 B:ASP303 4.4 8.9 1.0
CA B:MET302 4.4 8.6 1.0
CB B:ASP303 4.4 8.9 1.0
CB B:ASP365 4.4 8.5 1.0
CB B:ASP363 4.6 6.8 1.0
O B:SEP1004 4.9 9.5 1.0

Calcium binding site 7 out of 7 in 2yoa

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Calcium binding site 7 out of 7 in the Synaptotagmin-1 C2B Domain with Phosphoserine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Synaptotagmin-1 C2B Domain with Phosphoserine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1003

b:12.5
occ:1.00
 O B:HOH2076 2.3 16.7 1.0
O B:HOH2082 2.3 18.9 1.0
O B:HOH2075 2.3 13.6 1.0
OD1 B:ASP371 2.3 14.0 1.0
O B:LYS369 2.3 12.0 1.0
OD2 B:ASP365 2.4 8.7 1.0
CG B:ASP371 3.2 13.0 1.0
OD2 B:ASP371 3.4 12.7 1.0
C B:LYS369 3.5 12.4 1.0
CG B:ASP365 3.6 8.6 1.0
CB B:ASP365 4.0 8.5 1.0
N B:LYS369 4.2 13.1 1.0
O B:HOH2027 4.2 15.0 1.0
CA B:CA1002 4.2 8.3 1.0
O B:HOH2085 4.3 23.7 1.0
CA B:LYS369 4.4 13.2 1.0
C B:ASN370 4.5 13.0 1.0
N B:ASN370 4.5 11.5 1.0
N B:ASP371 4.5 12.6 1.0
O B:HOH2081 4.5 23.0 1.0
CB B:ASP371 4.6 12.9 1.0
CA B:ASN370 4.6 12.0 1.0
OD1 B:ASP365 4.6 8.7 1.0
O B:ILE367 4.6 13.3 1.0
CB B:LYS369 4.7 14.3 1.0
O B:ASN370 4.8 14.9 1.0
C B:GLY368 4.8 12.5 1.0
CA B:ASP371 4.9 12.5 1.0

Reference:

A.Honigmann, G.Van Den Bogaart, E.Iraheta, H.J.Risselada, D.Milovanovic, V.Mueller, S.Muellar, U.Diederichsen, D.Fasshauer, H.Grubmuller, S.W.Hell, C.Eggeling, K.Kuhnel, R.Jahn. Phosphatidylinositol 4,5-Bisphosphate Clusters Act As Molecular Beacons For Vesicle Recruitment Nat.Struct.Mol.Biol. V. 20 679 2013.
ISSN: ISSN 1545-9993
PubMed: 23665582
DOI: 10.1038/NSMB.2570
Page generated: Fri Jul 12 19:34:49 2024

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