Atomistry » Calcium » PDB 2yi1-2z8s » 2yoa
Atomistry »
  Calcium »
    PDB 2yi1-2z8s »
      2yoa »

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

Go back to Calcium Binding Sites List in 2yoa
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

Go back to Calcium Binding Sites List in 2yoa
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

Go back to Calcium Binding Sites List in 2yoa
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

Go back to Calcium Binding Sites List in 2yoa
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

Go back to Calcium Binding Sites List in 2yoa
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

Go back to Calcium Binding Sites List in 2yoa
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: Tue Jul 8 09:42:30 2025

Last articles

Cl in 8BMZ
Cl in 8BN0
Cl in 8BLJ
Cl in 8BMY
Cl in 8BM2
Cl in 8BM5
Cl in 8BK5
Cl in 8BL0
Cl in 8BL1
Cl in 8BK4
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy