Calcium in PDB 8i4k: Structure of Wild-Type Azami Green From Galaxea Fascicularis

The structure of Structure of Wild-Type Azami Green From Galaxea Fascicularis, PDB code: 8i4k was solved by S.Otsubo, N.Takekawa, H.Imamura, K.Imada, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	72.50 / 1.84
Space group	I 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	83.13, 72.77, 213.843, 90, 99.48, 90
R / Rfree (%)	17.6 / 21.7

The binding sites of Calcium atom in the Structure of Wild-Type Azami Green From Galaxea Fascicularis (pdb code 8i4k). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Structure of Wild-Type Azami Green From Galaxea Fascicularis, PDB code: 8i4k:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Structure of Wild-Type Azami Green From Galaxea Fascicularis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Wild-Type Azami Green From Galaxea Fascicularis within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca301 b:34.2 occ:1.00 O D:GLU96 2.3 12.9 1.0 O B:GLU96 2.3 12.2 1.0 O D:HOH458 2.4 32.0 1.0 O D:HOH417 2.5 29.7 1.0 O B:HOH558 2.5 21.9 1.0 C B:GLU96 3.5 14.3 1.0 C D:GLU96 3.5 15.4 1.0 O B:HOH572 3.8 30.7 1.0 O D:HOH406 3.8 28.9 1.0 CA B:ASP97 4.2 12.6 1.0 CA D:ASP97 4.2 9.8 1.0 N B:ASP97 4.3 11.1 1.0 N D:ASP97 4.3 8.9 1.0 CA D:GLU96 4.4 8.0 1.0 CA B:GLU96 4.4 13.0 1.0 O B:HOH427 4.4 28.0 1.0 C B:ASP97 4.5 12.3 1.0 O B:HOH585 4.6 30.2 1.0 N B:GLY98 4.6 10.6 1.0 N D:GLY98 4.7 10.0 1.0 C D:ASP97 4.7 10.8 1.0 O D:HOH483 4.8 36.4 1.0 CB D:GLU96 4.8 10.2 1.0 CB B:GLU96 4.9 11.8 1.0

Calcium binding site 2 out of 3 in the Structure of Wild-Type Azami Green From Galaxea Fascicularis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Wild-Type Azami Green From Galaxea Fascicularis within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca301 b:32.6 occ:1.00 O C:GLU96 2.2 13.7 1.0 O A:GLU96 2.4 10.3 1.0 O C:HOH508 2.4 29.2 1.0 O A:HOH474 2.4 26.3 1.0 O C:HOH549 2.4 23.5 1.0 O A:HOH480 2.6 36.9 1.0 O C:HOH544 3.0 42.1 1.0 C C:GLU96 3.4 15.0 1.0 C A:GLU96 3.6 12.1 1.0 O C:HOH440 4.0 25.6 1.0 CA C:ASP97 4.2 11.6 1.0 N C:ASP97 4.2 9.9 1.0 O A:HOH314 4.2 26.7 1.0 CA C:GLU96 4.3 8.6 1.0 CA A:ASP97 4.3 13.5 1.0 O C:HOH562 4.4 33.1 1.0 N A:ASP97 4.4 9.2 1.0 CA A:GLU96 4.5 13.9 1.0 C C:ASP97 4.6 12.3 1.0 N C:GLY98 4.6 14.7 1.0 C A:ASP97 4.7 14.9 1.0 O A:HOH512 4.8 29.4 1.0 N A:GLY98 4.8 13.2 1.0 CB C:GLU96 4.8 15.0 1.0 CB A:GLU96 4.9 13.7 1.0 O A:HOH508 5.0 44.0 1.0

Calcium binding site 3 out of 3 in the Structure of Wild-Type Azami Green From Galaxea Fascicularis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of Wild-Type Azami Green From Galaxea Fascicularis within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca301 b:38.7 occ:1.00 O F:GLU96 2.2 20.0 1.0 O F:HOH478 2.5 34.0 1.0 O F:HOH458 2.6 27.3 1.0 O F:HOH482 2.9 34.4 1.0 C F:GLU96 3.4 16.1 1.0 CA F:ASP97 4.3 17.6 1.0 N F:ASP97 4.3 16.1 1.0 CA F:GLU96 4.3 15.3 1.0 O F:HOH429 4.4 26.4 1.0 N F:GLY98 4.6 19.3 1.0 C F:ASP97 4.6 17.9 1.0 CB F:GLU96 4.9 16.5 1.0

H.Imamura, S.Otsubo, M.Nishida, N.Takekawa, K.Imada. Red Fluorescent Proteins Engineered From Green Fluorescent Proteins. Proc.Natl.Acad.Sci.Usa V. 120 87120 2023.
ISSN: ESSN 1091-6490
PubMed: 37871160
DOI: 10.1073/PNAS.2307687120