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: Fri Jul 12 19:34:49 2024

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy