Calcium in PDB 7wbo: Crystal Structure of Sarcoplasmic Calcium-Binding Protein From Scylla Paramamosain

The structure of Crystal Structure of Sarcoplasmic Calcium-Binding Protein From Scylla Paramamosain, PDB code: 7wbo was solved by Y.Chen, T.Jin, G.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.52 / 1.60
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	81.121, 46.893, 64.474, 90, 125.35, 90
R / Rfree (%)	14.9 / 18.6

The structure of Crystal Structure of Sarcoplasmic Calcium-Binding Protein From Scylla Paramamosain also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Calcium atom in the Crystal Structure of Sarcoplasmic Calcium-Binding Protein From Scylla Paramamosain (pdb code 7wbo). 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 Sarcoplasmic Calcium-Binding Protein From Scylla Paramamosain, PDB code: 7wbo:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of Sarcoplasmic Calcium-Binding Protein From Scylla Paramamosain


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 Sarcoplasmic Calcium-Binding Protein From Scylla Paramamosain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca208 b:9.0 occ:1.00 O A:TYR24 2.3 8.8 1.0 OD1 A:ASP18 2.3 9.6 1.0 OD1 A:ASN22 2.3 11.6 1.0 OD1 A:ASP20 2.4 12.7 1.0 OD2 A:ASP29 2.4 8.9 1.0 O A:HOH330 2.5 12.0 1.0 OD1 A:ASP29 2.5 9.7 1.0 CG A:ASP29 2.8 10.0 1.0 CG A:ASN22 3.3 14.1 1.0 CG A:ASP20 3.3 15.2 1.0 CG A:ASP18 3.5 10.1 1.0 C A:TYR24 3.6 8.8 1.0 ND2 A:ASN22 3.7 15.4 1.0 OD2 A:ASP20 3.7 14.6 1.0 N A:ASN22 4.2 13.8 1.0 CA A:LEU25 4.3 8.2 1.0 OD2 A:ASP18 4.3 11.7 1.0 CA A:ASP18 4.3 10.1 1.0 N A:TYR24 4.3 10.8 1.0 CB A:ASP29 4.3 9.2 1.0 N A:LEU25 4.3 8.0 1.0 CB A:ASP18 4.4 10.5 1.0 CB A:ASN22 4.5 14.3 1.0 N A:ASP20 4.5 12.7 1.0 N A:ASN21 4.5 14.7 1.0 CA A:TYR24 4.6 9.5 1.0 CB A:ASP20 4.6 14.6 1.0 N A:ASP26 4.6 9.1 1.0 C A:ASP18 4.6 10.3 1.0 CA A:ASN22 4.7 13.5 1.0 OD1 A:ASP26 4.7 11.0 1.0 C A:ASP20 4.8 14.2 1.0 CD1 A:TYR24 4.8 11.8 1.0 N A:GLY23 4.8 12.2 1.0 C A:LEU25 4.8 9.1 1.0 CA A:ASP20 4.8 14.0 1.0 CD2 A:LEU25 4.9 8.9 1.0 C A:ASN22 4.9 12.9 1.0 O A:ASP18 4.9 11.1 1.0 N A:ILE19 4.9 11.8 1.0 CE1 A:TYR24 5.0 15.0 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Sarcoplasmic Calcium-Binding Protein From Scylla Paramamosain


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 Sarcoplasmic Calcium-Binding Protein From Scylla Paramamosain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca209 b:7.2 occ:1.00 O A:GLN76 2.3 7.7 1.0 OD1 A:ASN72 2.3 8.2 1.0 OD1 A:ASP70 2.3 7.1 1.0 O A:HOH411 2.4 11.2 1.0 OD1 A:ASP74 2.4 9.0 1.0 OE1 A:GLU81 2.4 7.9 1.0 OE2 A:GLU81 2.5 7.5 1.0 CD A:GLU81 2.8 7.6 1.0 CG A:ASP74 3.3 9.1 1.0 CG A:ASN72 3.4 8.9 1.0 C A:GLN76 3.5 7.4 1.0 CG A:ASP70 3.5 7.4 1.0 OD2 A:ASP74 3.7 11.5 1.0 ND2 A:ASN72 4.1 11.0 1.0 CA A:ASP70 4.2 7.1 1.0 N A:GLN76 4.2 8.2 1.0 N A:ASN72 4.2 8.0 1.0 N A:ASP74 4.3 8.8 1.0 OD2 A:ASP70 4.3 7.9 1.0 CA A:GLN76 4.3 8.1 1.0 CG A:GLU81 4.3 6.5 1.0 O A:HOH502 4.3 18.8 1.0 CA A:VAL77 4.4 6.8 1.0 N A:VAL77 4.4 6.4 1.0 CB A:ASP70 4.4 7.1 1.0 CB A:ASP74 4.5 8.7 1.0 C A:ASP70 4.5 7.7 1.0 O A:HOH342 4.5 13.6 1.0 CB A:ASN72 4.5 8.5 1.0 N A:PHE71 4.6 7.1 1.0 CB A:GLN76 4.6 9.7 1.0 N A:LYS73 4.6 9.8 1.0 CA A:ASN72 4.7 8.4 1.0 C A:ASN72 4.8 9.4 1.0 CA A:ASP74 4.8 8.6 1.0 N A:THR78 4.8 6.9 1.0 N A:GLY75 4.9 8.6 1.0 O A:ASP70 5.0 8.7 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Sarcoplasmic Calcium-Binding Protein From Scylla Paramamosain


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 Sarcoplasmic Calcium-Binding Protein From Scylla Paramamosain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca210 b:11.2 occ:1.00 OD1 A:ASP114 2.3 11.2 1.0 O A:LEU120 2.3 10.1 1.0 OD1 A:ASP118 2.4 14.2 1.0 OD1 A:ASN116 2.4 13.6 1.0 OE1 A:GLU125 2.4 9.7 1.0 O A:HOH480 2.4 14.2 1.0 OE2 A:GLU125 2.5 12.1 1.0 CD A:GLU125 2.8 10.3 1.0 CG A:ASN116 3.3 16.7 1.0 CG A:ASP118 3.3 18.9 1.0 CG A:ASP114 3.5 10.8 1.0 C A:LEU120 3.5 9.9 1.0 ND2 A:ASN116 3.7 19.3 1.0 OD2 A:ASP118 3.9 21.4 1.0 N A:LEU120 4.1 9.5 1.0 N A:ASP118 4.2 14.4 1.0 CA A:ASP114 4.2 11.5 1.0 CG A:GLU125 4.3 9.3 1.0 CB A:ASP114 4.3 10.8 1.0 OD2 A:ASP114 4.3 12.1 1.0 N A:ASN116 4.4 16.1 1.0 CA A:LEU120 4.4 8.9 1.0 CB A:ASP118 4.4 15.7 1.0 N A:VAL121 4.5 9.3 1.0 C A:ASP114 4.5 11.6 1.0 O A:HOH418 4.5 28.9 1.0 N A:GLY122 4.5 9.6 1.0 N A:GLY117 4.5 16.1 1.0 CA A:VAL121 4.5 8.9 1.0 CB A:ASN116 4.5 17.0 1.0 CA A:ASP118 4.7 14.3 1.0 CB A:LEU120 4.7 10.0 1.0 N A:GLY119 4.8 11.7 1.0 N A:ILE115 4.8 13.7 1.0 CA A:ASN116 4.8 16.5 1.0 C A:ASN116 4.8 16.9 1.0 CA A:CA211 4.8 21.0 1.0 O A:HOH399 4.8 27.7 1.0 O A:ASP114 4.9 12.3 1.0 C A:ASP118 4.9 12.7 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Sarcoplasmic Calcium-Binding Protein From Scylla Paramamosain


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 Sarcoplasmic Calcium-Binding Protein From Scylla Paramamosain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca211 b:21.0 occ:1.00 O A:HOH477 2.8 25.4 1.0 O A:HOH480 3.1 14.2 1.0 N A:GLU125 3.4 9.1 1.0 CA A:GLY122 3.4 8.8 1.0 C A:GLY122 3.4 9.3 1.0 CG A:GLU125 3.5 9.3 1.0 N A:ASP124 3.6 10.4 1.0 CB A:ASP124 3.6 12.1 1.0 CD A:GLU125 3.6 10.3 1.0 N A:GLY122 3.7 9.6 1.0 OE1 A:GLU125 3.8 9.7 1.0 O A:GLY122 3.8 9.1 1.0 CA A:ASP124 3.9 11.2 1.0 N A:VAL123 3.9 10.2 1.0 CB A:GLU125 4.0 9.6 1.0 C A:ASP124 4.1 9.8 1.0 OE2 A:GLU125 4.1 12.1 1.0 O A:HOH399 4.2 27.7 1.0 CA A:GLU125 4.3 8.9 1.0 CG A:ASP124 4.4 13.3 1.0 C A:VAL123 4.5 10.2 1.0 O A:HOH418 4.7 28.9 1.0 OD2 A:ASP124 4.7 18.4 1.0 CA A:VAL123 4.8 10.4 1.0 CA A:CA210 4.8 11.2 1.0 ND2 A:ASN116 4.9 19.3 1.0 C A:VAL121 5.0 9.2 1.0

Y.Chen, T.Jin. Crystal Structure of Sarcoplasmic Calcium-Binding Protein From Scylla Paramamosain To Be Published.