Calcium in PDB 7f8l: Crystal Structure of Bat Coronavirus RATG13 ORF8 Accessory Protein

The structure of Crystal Structure of Bat Coronavirus RATG13 ORF8 Accessory Protein, PDB code: 7f8l was solved by X.Chen, Z.Zhou, S.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.95 / 1.76
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	37.473, 49.454, 111.22, 90, 90, 90
R / Rfree (%)	18.1 / 22.6

The binding sites of Calcium atom in the Crystal Structure of Bat Coronavirus RATG13 ORF8 Accessory Protein (pdb code 7f8l). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Bat Coronavirus RATG13 ORF8 Accessory Protein, PDB code: 7f8l:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of Bat Coronavirus RATG13 ORF8 Accessory Protein


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Bat Coronavirus RATG13 ORF8 Accessory Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca201 b:21.3 occ:1.00 OD1 A:ASP34 2.3 15.7 1.0 O A:ASP35 2.4 15.4 1.0 O A:HOH407 2.4 32.1 1.0 O A:HOH399 2.4 30.7 1.0 C A:ASP35 3.4 12.3 1.0 O A:HOH333 3.5 42.5 1.0 CG A:ASP34 3.5 28.4 1.0 N A:ASP35 4.0 14.4 1.0 OD2 A:ASP34 4.1 27.6 1.0 O A:HOH394 4.1 30.0 1.0 CA A:ASP35 4.3 12.7 1.0 C A:ASP34 4.3 10.8 1.0 N A:PRO36 4.3 12.7 1.0 CA A:PRO36 4.3 10.7 1.0 O A:CYS37 4.5 21.6 1.0 CB A:ASP34 4.7 13.8 1.0 CA A:ASP34 4.7 14.0 1.0 CB A:ASP35 4.8 16.4 1.0 O A:ASP34 4.8 15.6 1.0 C A:PRO36 4.8 18.4 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Bat Coronavirus RATG13 ORF8 Accessory Protein


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Bat Coronavirus RATG13 ORF8 Accessory Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca202 b:22.1 occ:1.00 O A:HOH408 2.4 32.4 1.0 O A:HOH321 2.4 25.2 1.0 OD2 A:ASP35 2.4 17.7 1.0 O A:HOH310 2.4 15.6 1.0 O A:HOH413 2.5 32.9 1.0 CG A:ASP35 3.2 23.8 1.0 OG A:SER43 3.6 34.8 1.0 CB A:ASP35 3.8 16.4 1.0 OD1 A:ASP35 4.1 18.5 1.0 O A:HOH345 4.2 17.7 1.0 O A:PHE41 4.4 18.3 1.0 O A:HOH422 4.5 42.6 1.0 O A:ILE39 4.5 42.5 1.0 CB A:SER43 4.7 13.1 1.0 O A:HOH443 4.7 33.2 1.0 O A:PRO38 4.7 21.4 1.0 O A:HOH415 4.8 48.8 1.0 O A:CYS37 4.9 21.6 1.0 CD1 A:ILE39 5.0 36.0 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Bat Coronavirus RATG13 ORF8 Accessory Protein


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Bat Coronavirus RATG13 ORF8 Accessory Protein within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca201 b:67.0 occ:1.00 O B:HOH355 2.3 37.5 1.0 O B:HOH309 2.4 39.2 1.0 OD2 B:ASP35 2.7 32.6 1.0 O B:HOH376 2.8 41.6 1.0 CG B:ASP35 3.4 27.7 1.0 O B:PHE41 4.0 28.9 1.0 CB B:ASP35 4.0 23.5 1.0 O B:ILE39 4.0 53.8 1.0 OG B:SER43 4.0 24.3 1.0 O B:PRO38 4.1 31.7 1.0 OD1 B:ASP35 4.1 30.6 1.0 CA B:ILE39 4.5 55.1 1.0 C B:ILE39 4.5 50.5 1.0 O B:HOH378 4.6 50.4 1.0 O B:CYS37 4.8 29.0 1.0 CB B:CYS37 4.9 31.6 1.0 CB B:SER43 4.9 22.8 1.0 C B:PRO38 4.9 38.9 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Bat Coronavirus RATG13 ORF8 Accessory Protein


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Bat Coronavirus RATG13 ORF8 Accessory Protein within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca202 b:49.7 occ:1.00 O B:HOH305 2.2 38.5 1.0 OD1 B:ASP34 2.5 30.9 1.0 O B:HOH403 2.5 56.8 1.0 O B:ASP35 2.8 22.9 1.0 CG B:ASP34 3.4 30.2 1.0 OD2 B:ASP34 3.6 40.8 1.0 C B:ASP35 3.9 26.5 1.0 O B:HOH376 4.0 41.6 1.0 O B:HOH361 4.3 30.5 1.0 N B:ASP35 4.3 20.6 1.0 O B:CYS37 4.6 29.0 1.0 CA B:ASP35 4.6 20.1 1.0 CB B:ASP34 4.7 19.8 1.0 C B:ASP34 4.7 21.7 1.0 N B:PRO36 4.8 23.2 1.0 CA B:PRO36 4.8 25.4 1.0 CB B:ASP35 5.0 23.5 1.0 O B:HOH308 5.0 43.3 1.0

X.Chen, Z.Zhou, C.Huang, Z.Zhou, S.Kang, Z.Huang, G.Jiang, Z.Hong, Q.Chen, M.Yang, S.He, S.Liu, J.Chen, K.Li, X.Li, J.Liao, J.Chen, S.Chen. Crystal Structures of Bat and Human Coronavirus ORF8 Protein Ig-Like Domain Provide Insights Into the Diversity of Immune Responses. Front Immunol V. 12 07134 2021.
ISSN: ESSN 1664-3224
PubMed: 34975921
DOI: 10.3389/FIMMU.2021.807134