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Cadmium in PDB 7as6: 2.0 Angstrom Structure of Plant Extended Synaptotagmin 1, C2A Domain

Protein crystallography data

The structure of 2.0 Angstrom Structure of Plant Extended Synaptotagmin 1, C2A Domain, PDB code: 7as6 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) 42.23 / 2.00
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 70.937, 70.937, 116.309, 90, 90, 120
R / Rfree (%) 18.6 / 21.1

Other elements in 7as6:

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

Chlorine (Cl) 1 atom
Nickel (Ni) 2 atoms

Cadmium Binding Sites:

The binding sites of Cadmium atom in the 2.0 Angstrom Structure of Plant Extended Synaptotagmin 1, C2A Domain (pdb code 7as6). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 2 binding sites of Cadmium where determined in the 2.0 Angstrom Structure of Plant Extended Synaptotagmin 1, C2A Domain, PDB code: 7as6:
Jump to Cadmium binding site number: 1; 2;

Cadmium binding site 1 out of 2 in 7as6

Go back to Cadmium Binding Sites List in 7as6
Cadmium binding site 1 out of 2 in the 2.0 Angstrom Structure of Plant Extended Synaptotagmin 1, C2A Domain


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of 2.0 Angstrom Structure of Plant Extended Synaptotagmin 1, C2A Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd401

b:42.9
occ:1.00
OE2 A:GLU334 2.3 46.6 1.0
OD2 A:ASP276 2.4 41.4 1.0
O A:TRP333 2.4 40.0 1.0
OD2 A:ASP282 2.4 44.8 1.0
OD2 A:ASP332 2.4 42.5 1.0
OD1 A:ASP332 2.5 45.9 1.0
OD1 A:ASP276 2.8 56.5 1.0
CG A:ASP332 2.8 47.6 1.0
CG A:ASP276 2.9 54.5 1.0
CD A:GLU334 3.2 53.7 1.0
CG A:ASP282 3.4 40.9 1.0
C A:TRP333 3.6 42.0 1.0
CG A:GLU334 3.6 49.7 1.0
CB A:ASP282 3.8 43.0 1.0
N A:ASP282 3.9 38.7 1.0
OE1 A:GLU334 4.3 58.7 1.0
CB A:ASP332 4.3 49.9 1.0
N A:TRP333 4.3 38.3 1.0
O A:HOH511 4.4 54.6 1.0
CB A:ASP276 4.4 54.6 1.0
N A:GLU334 4.4 43.8 1.0
CA A:ASP282 4.5 40.5 1.0
OD1 A:ASP282 4.5 42.1 1.0
CA A:GLU334 4.5 45.3 1.0
CA A:TRP333 4.5 42.8 1.0
C A:ALA281 4.6 42.0 1.0
C A:ASP332 4.6 42.6 1.0
CB A:GLU334 4.7 46.6 1.0
CA A:ALA281 4.7 45.8 1.0
NZ A:LYS275 4.8 60.4 1.0
CA A:ASP332 4.9 42.0 1.0
O A:HOH516 5.0 52.8 1.0

Cadmium binding site 2 out of 2 in 7as6

Go back to Cadmium Binding Sites List in 7as6
Cadmium binding site 2 out of 2 in the 2.0 Angstrom Structure of Plant Extended Synaptotagmin 1, C2A Domain


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of 2.0 Angstrom Structure of Plant Extended Synaptotagmin 1, C2A Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd402

b:42.9
occ:0.33
NE2 A:HIS303 2.3 36.4 1.0
O A:HOH512 2.4 36.0 1.0
CD2 A:HIS303 3.2 36.5 1.0
CE1 A:HIS303 3.4 32.1 1.0
CG A:HIS303 4.4 35.9 1.0
ND1 A:HIS303 4.4 33.7 1.0
O A:HOH523 4.4 36.8 1.0
O A:VAL301 4.6 33.6 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 12:43:30 2021

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