Calcium in PDB 5zgm: Crystal Structure of Parvalbumin Spvi, the Major Allergens in Mustelus Griseus

The structure of Crystal Structure of Parvalbumin Spvi, the Major Allergens in Mustelus Griseus, PDB code: 5zgm was solved by R.Q.Yang, Y.L.Chen, T.C.Jin, M.J.Cao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.53 / 1.40
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	26.207, 43.289, 52.570, 65.97, 88.93, 88.61
R / Rfree (%)	16.2 / 18.6

The binding sites of Calcium atom in the Crystal Structure of Parvalbumin Spvi, the Major Allergens in Mustelus Griseus (pdb code 5zgm). 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 Parvalbumin Spvi, the Major Allergens in Mustelus Griseus, PDB code: 5zgm:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of Parvalbumin Spvi, the Major Allergens in Mustelus Griseus


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 Parvalbumin Spvi, the Major Allergens in Mustelus Griseus within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca201 b:6.2 occ:1.00 OD1 A:ASP52 2.3 7.6 1.0 OD1 A:ASP54 2.3 8.3 1.0 OE1 A:GLU60 2.3 7.7 1.0 O A:PHE58 2.4 7.3 1.0 OE1 A:GLU63 2.4 8.7 1.0 OG A:SER56 2.5 7.9 1.0 OE2 A:GLU63 2.6 9.7 1.0 CD A:GLU63 2.8 9.3 1.0 CD A:GLU60 3.3 7.5 1.0 CG A:ASP54 3.3 11.7 1.0 CG A:ASP52 3.4 7.4 1.0 OE2 A:GLU60 3.5 8.8 1.0 CB A:SER56 3.6 9.2 1.0 C A:PHE58 3.6 6.3 1.0 OD2 A:ASP54 3.7 12.8 1.0 N A:SER56 4.0 8.2 1.0 CA A:ASP52 4.1 5.9 1.0 OD2 A:ASP52 4.2 7.8 1.0 CB A:ASP52 4.2 7.4 1.0 N A:ASP54 4.2 7.1 1.0 N A:GLU60 4.3 6.6 1.0 CG A:GLU63 4.3 9.7 1.0 CA A:SER56 4.3 8.9 1.0 C A:ASP52 4.4 7.7 1.0 N A:PHE58 4.4 6.5 1.0 CA A:ILE59 4.4 6.8 1.0 N A:ILE59 4.5 6.2 1.0 N A:LYS53 4.5 8.2 1.0 CB A:ASP54 4.5 9.6 1.0 CA A:PHE58 4.6 5.2 1.0 CG A:GLU60 4.6 8.2 1.0 N A:GLN55 4.7 7.5 1.0 CA A:ASP54 4.7 8.5 1.0 C A:ASP54 4.8 9.3 1.0 N A:GLY57 4.9 6.7 1.0 C A:ILE59 4.9 6.6 1.0 C A:SER56 4.9 9.4 1.0 CB A:GLU60 4.9 7.1 1.0 O A:ASP52 5.0 8.5 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Parvalbumin Spvi, the Major Allergens in Mustelus Griseus


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 Parvalbumin Spvi, the Major Allergens in Mustelus Griseus within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca202 b:7.8 occ:1.00 OD1 A:ASP91 2.3 7.8 1.0 O A:LYS97 2.3 8.1 1.0 OD1 A:ASP93 2.4 11.3 1.0 O A:HOH328 2.4 14.0 1.0 OD1 A:ASP95 2.4 9.8 1.0 OE1 A:GLU102 2.5 8.6 1.0 OE2 A:GLU102 2.5 10.2 1.0 CD A:GLU102 2.9 8.8 1.0 CG A:ASP95 3.3 10.8 1.0 CG A:ASP93 3.3 18.3 1.0 CG A:ASP91 3.5 9.5 1.0 C A:LYS97 3.5 6.6 1.0 OD2 A:ASP95 3.6 12.0 1.0 OD2 A:ASP93 3.7 24.7 1.0 O A:HOH403 4.1 28.7 1.0 CA A:ASP91 4.2 9.4 1.0 N A:LYS97 4.3 6.3 1.0 N A:ASP95 4.3 8.7 1.0 OD2 A:ASP91 4.3 9.0 1.0 CB A:ASP91 4.3 8.8 1.0 CG A:GLU102 4.4 7.8 1.0 N A:ILE98 4.4 7.2 1.0 CA A:ILE98 4.4 6.0 1.0 N A:ASP93 4.4 9.2 1.0 N A:GLY99 4.4 7.4 1.0 CB A:ASP95 4.4 8.8 1.0 CA A:LYS97 4.5 6.9 1.0 C A:ASP91 4.5 9.7 1.0 CB A:ASP93 4.6 11.8 1.0 CG A:LYS97 4.7 5.2 1.0 N A:HIS94 4.7 7.9 1.0 N A:SER92 4.7 8.6 1.0 CA A:ASP95 4.8 9.5 1.0 N A:GLY96 4.8 8.0 1.0 CA A:ASP93 4.8 9.3 1.0 C A:ILE98 4.9 7.7 1.0 C A:ASP93 4.9 10.3 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Parvalbumin Spvi, the Major Allergens in Mustelus Griseus


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 Parvalbumin Spvi, the Major Allergens in Mustelus Griseus within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca201 b:9.2 occ:1.00 OD1 B:ASP91 2.3 9.7 1.0 O B:HOH343 2.4 13.3 1.0 O B:LYS97 2.4 8.8 1.0 OD1 B:ASP93 2.4 12.0 1.0 OD1 B:ASP95 2.4 11.3 1.0 OE1 B:GLU102 2.5 9.8 1.0 OE2 B:GLU102 2.5 11.8 1.0 CD B:GLU102 2.8 10.7 1.0 CG B:ASP95 3.3 14.3 1.0 CG B:ASP93 3.3 16.8 1.0 CG B:ASP91 3.4 10.6 1.0 C B:LYS97 3.5 7.1 1.0 OD2 B:ASP95 3.7 15.2 1.0 OD2 B:ASP93 3.8 24.1 1.0 CA B:ASP91 4.2 11.0 1.0 O B:HOH386 4.2 27.3 1.0 N B:ASP95 4.2 10.8 1.0 N B:LYS97 4.3 8.6 1.0 OD2 B:ASP91 4.3 10.7 1.0 CB B:ASP91 4.3 10.2 1.0 CG B:GLU102 4.4 9.9 1.0 N B:ILE98 4.4 8.2 1.0 N B:ASP93 4.4 9.8 1.0 CA B:ILE98 4.4 7.8 1.0 CB B:ASP95 4.5 12.8 1.0 N B:GLY99 4.5 6.4 1.0 CA B:LYS97 4.5 7.2 1.0 C B:ASP91 4.5 10.6 1.0 CB B:ASP93 4.6 14.0 1.0 N B:HIS94 4.6 8.4 1.0 CG B:LYS97 4.7 6.4 1.0 N B:SER92 4.7 9.0 1.0 CA B:ASP95 4.7 12.0 1.0 CA B:ASP93 4.8 11.5 1.0 N B:GLY96 4.8 9.1 1.0 C B:ASP93 4.8 9.0 1.0 O B:HOH328 4.9 26.3 1.0 C B:ILE98 4.9 6.8 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Parvalbumin Spvi, the Major Allergens in Mustelus Griseus


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 Parvalbumin Spvi, the Major Allergens in Mustelus Griseus within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca202 b:6.8 occ:1.00 OD1 B:ASP52 2.3 7.6 1.0 OD1 B:ASP54 2.3 10.3 1.0 OE1 B:GLU60 2.4 10.4 1.0 O B:PHE58 2.4 7.9 1.0 OE1 B:GLU63 2.4 9.4 1.0 OG B:SER56 2.5 9.0 1.0 OE2 B:GLU63 2.6 10.1 1.0 CD B:GLU63 2.9 9.1 1.0 CD B:GLU60 3.3 8.5 1.0 CG B:ASP54 3.3 12.5 1.0 CG B:ASP52 3.4 8.2 1.0 OE2 B:GLU60 3.5 8.7 1.0 CB B:SER56 3.6 10.1 1.0 C B:PHE58 3.6 6.9 1.0 OD2 B:ASP54 3.7 11.8 1.0 N B:SER56 4.0 9.3 1.0 CA B:ASP52 4.1 7.1 1.0 CB B:ASP52 4.2 7.7 1.0 N B:ASP54 4.2 8.9 1.0 OD2 B:ASP52 4.2 8.9 1.0 N B:GLU60 4.3 7.9 1.0 CA B:SER56 4.3 10.0 1.0 CG B:GLU63 4.3 10.0 1.0 C B:ASP52 4.4 9.8 1.0 N B:PHE58 4.4 7.1 1.0 CA B:ILE59 4.4 7.1 1.0 N B:ILE59 4.5 6.3 1.0 N B:LYS53 4.5 9.7 1.0 CB B:ASP54 4.5 9.6 1.0 CA B:PHE58 4.6 5.3 1.0 CG B:GLU60 4.6 9.8 1.0 N B:GLN55 4.7 7.6 1.0 CA B:ASP54 4.7 10.1 1.0 NE2 A:GLN43 4.7 11.1 1.0 C B:ASP54 4.8 10.7 1.0 NZ A:LYS39 4.8 10.9 1.0 C B:ILE59 4.9 7.2 1.0 N B:GLY57 4.9 8.7 1.0 C B:SER56 4.9 8.8 1.0 O B:ASP52 4.9 10.2 1.0 CB B:GLU60 5.0 8.8 1.0

R.Q.Yang, Y.L.Chen, F.Chen, H.Wang, Q.Zhang, G.M.Liu, T.Jin, M.J.Cao. Purification, Characterization, and Crystal Structure of Parvalbumins, the Major Allergens in Mustelus Griseus. J. Agric. Food Chem. V. 66 8150 2018.
ISSN: ESSN 1520-5118
PubMed: 29969026
DOI: 10.1021/ACS.JAFC.8B01889