Calcium in PDB 7atp: 2.0 Angstrom Structure in Complex with Ca of Plant Extended Synaptotagmin 1, C2A Domain

Protein crystallography data

The structure of 2.0 Angstrom Structure in Complex with Ca of Plant Extended Synaptotagmin 1, C2A Domain, PDB code: 7atp was solved by J.L.Benavente, A.Albert, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.59 / 2.10
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 69.127, 69.127, 115.669, 90, 90, 120
R / Rfree (%) 20.7 / 26.9

Other elements in 7atp:

The structure of 2.0 Angstrom Structure in Complex with Ca of Plant Extended Synaptotagmin 1, C2A Domain also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Zinc (Zn) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the 2.0 Angstrom Structure in Complex with Ca of Plant Extended Synaptotagmin 1, C2A Domain (pdb code 7atp). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the 2.0 Angstrom Structure in Complex with Ca of Plant Extended Synaptotagmin 1, C2A Domain, PDB code: 7atp:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 7atp

Go back to Calcium Binding Sites List in 7atp
Calcium binding site 1 out of 2 in the 2.0 Angstrom Structure in Complex with Ca of Plant Extended Synaptotagmin 1, C2A Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of 2.0 Angstrom Structure in Complex with Ca of Plant Extended Synaptotagmin 1, C2A Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:55.5
occ:1.00
O A:HOH506 2.3 60.6 1.0
OD2 A:ASP276 2.3 64.6 1.0
OD1 A:ASP332 2.3 56.6 1.0
OE2 A:GLU334 2.4 70.8 1.0
OD2 A:ASP282 2.4 62.9 1.0
OD1 A:ASP276 2.5 71.5 1.0
O A:TRP333 2.6 50.3 1.0
CG A:ASP276 2.7 70.2 1.0
OD2 A:ASP332 3.0 69.0 1.0
CG A:ASP332 3.0 61.0 1.0
CG A:ASP282 3.5 59.3 1.0
CA A:CA402 3.5 66.3 1.0
CD A:GLU334 3.6 67.2 1.0
C A:TRP333 3.7 53.5 1.0
N A:ASP282 4.0 54.3 1.0
CB A:ASP282 4.1 49.6 1.0
CB A:ASP276 4.2 67.7 1.0
OE1 A:GLU334 4.3 72.5 1.0
CA A:GLU334 4.3 62.9 1.0
CB A:ASP332 4.4 60.1 1.0
C A:ASP332 4.5 57.5 1.0
OD1 A:ASP282 4.5 61.7 1.0
N A:GLU334 4.5 55.2 1.0
O A:ASP332 4.5 64.0 1.0
N A:TRP333 4.5 52.9 1.0
CA A:ALA281 4.6 62.3 1.0
C A:ALA281 4.6 59.4 1.0
CG A:GLU334 4.7 66.1 1.0
CA A:ASP282 4.7 46.3 1.0
CA A:TRP333 4.8 59.6 1.0
O A:HOH507 4.9 64.8 1.0
CA A:ASP332 5.0 50.2 1.0
CB A:GLU334 5.0 65.2 1.0

Calcium binding site 2 out of 2 in 7atp

Go back to Calcium Binding Sites List in 7atp
Calcium binding site 2 out of 2 in the 2.0 Angstrom Structure in Complex with Ca of Plant Extended Synaptotagmin 1, C2A Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of 2.0 Angstrom Structure in Complex with Ca of Plant Extended Synaptotagmin 1, C2A Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:66.3
occ:1.00
OE2 A:GLU340 2.2 80.8 1.0
OE1 A:GLU334 2.3 72.5 1.0
OD1 A:ASP276 2.3 71.5 1.0
O A:HOH507 2.4 64.8 1.0
O A:LYS275 2.5 68.8 1.0
OD2 A:ASP332 2.5 69.0 1.0
OE2 A:GLU334 2.8 70.8 1.0
CD A:GLU334 2.8 67.2 1.0
CD A:GLU340 3.4 81.9 1.0
C A:LYS275 3.4 74.2 1.0
CG A:ASP276 3.5 70.2 1.0
CA A:CA401 3.5 55.5 1.0
CG A:ASP332 3.6 61.0 1.0
CA A:ASP276 4.0 70.5 1.0
CG A:GLU340 4.0 73.1 1.0
N A:ASP276 4.1 73.0 1.0
CB A:LYS275 4.2 72.4 1.0
OD1 A:ASP332 4.3 56.6 1.0
OD2 A:ASP276 4.3 64.6 1.0
CG A:GLU334 4.3 66.1 1.0
CB A:ASP276 4.3 67.7 1.0
OE1 A:GLU340 4.4 86.2 1.0
CA A:LYS275 4.4 75.1 1.0
O A:HOH506 4.6 60.6 1.0
CB A:ASP332 4.7 60.1 1.0

Reference:

J.L.Benavente, A.Albert. 2.0 Angstrom Structure of Plant Extended Synaptotagmin 1, C2A Domain Life Sci Alliance 2021.
ISSN: ESSN 2575-1077
DOI: 10.26508/LSA.202101152
Page generated: Sat Aug 21 12:35:01 2021

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