Calcium in PDB 3sib: Crystal Structure of URE3-Binding Protein, Wild-Type

The structure of Crystal Structure of URE3-Binding Protein, Wild-Type, PDB code: 3sib was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.16 / 1.90
Space group	I 4 2 2
Cell size a, b, c (Å), α, β, γ (°)	99.699, 99.699, 107.034, 90.00, 90.00, 90.00
R / Rfree (%)	15.9 / 19

The structure of Crystal Structure of URE3-Binding Protein, Wild-Type also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Calcium atom in the Crystal Structure of URE3-Binding Protein, Wild-Type (pdb code 3sib). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of URE3-Binding Protein, Wild-Type, PDB code: 3sib:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of URE3-Binding Protein, Wild-Type


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 URE3-Binding Protein, Wild-Type within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca221 b:19.6 occ:1.00 OD1 A:ASP61 2.2 16.0 1.0 OD1 A:ASP63 2.3 17.9 1.0 OE1 A:GLU69 2.4 18.3 1.0 O A:THR67 2.4 18.0 1.0 OE2 A:GLU72 2.4 18.1 1.0 OE1 A:GLU72 2.5 16.6 1.0 OG A:SER65 2.5 19.5 1.0 CD A:GLU72 2.8 16.9 1.0 CG A:ASP63 3.3 22.1 1.0 CG A:ASP61 3.4 16.5 1.0 CD A:GLU69 3.4 18.1 1.0 CB A:SER65 3.5 21.0 1.0 C A:THR67 3.6 17.4 1.0 OD2 A:ASP63 3.6 23.4 1.0 OE2 A:GLU69 3.8 20.8 1.0 N A:SER65 4.0 21.3 1.0 O A:HOH322 4.1 24.9 1.0 OG1 A:THR67 4.2 18.3 1.0 OD2 A:ASP61 4.2 19.1 1.0 CA A:ASP61 4.2 16.7 1.0 CG A:GLU72 4.3 16.7 1.0 CB A:ASP61 4.3 16.8 1.0 CA A:SER65 4.3 20.9 1.0 CA A:LEU68 4.3 16.7 1.0 N A:THR67 4.4 19.9 1.0 N A:ASP63 4.4 20.3 1.0 N A:LEU68 4.4 17.8 1.0 N A:GLU69 4.5 16.8 1.0 C A:ASP61 4.5 18.0 1.0 CA A:THR67 4.6 18.7 1.0 CB A:ASP63 4.6 22.0 1.0 N A:ARG64 4.7 21.4 1.0 CG A:GLU69 4.7 19.3 1.0 N A:ARG62 4.8 18.7 1.0 CA A:ASP63 4.8 22.5 1.0 C A:LEU68 4.8 17.1 1.0 C A:ASP63 4.8 22.6 1.0 O A:HOH252 4.8 21.9 1.0 O A:HOH279 4.9 21.3 1.0 N A:GLY66 4.9 20.9 1.0 C A:SER65 4.9 21.4 1.0 O A:ASP61 5.0 19.9 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of URE3-Binding Protein, Wild-Type


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 URE3-Binding Protein, Wild-Type within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca222 b:18.5 occ:1.00 OD1 A:ASP97 2.2 18.8 1.0 OD1 A:ASP99 2.3 22.6 1.0 O A:HIS103 2.3 18.5 1.0 O A:HOH242 2.4 9.2 1.0 OD1 A:ASN101 2.5 17.4 1.0 OE1 A:GLU108 2.6 16.0 1.0 OE2 A:GLU108 2.7 16.9 1.0 CD A:GLU108 3.0 16.4 1.0 CG A:ASP99 3.3 26.0 1.0 CG A:ASP97 3.3 19.0 1.0 CG A:ASN101 3.4 20.0 1.0 C A:HIS103 3.5 18.7 1.0 OD2 A:ASP99 3.6 29.4 1.0 ND2 A:ASN101 3.9 20.4 1.0 CA A:ASP97 4.0 16.9 1.0 CB A:ASP97 4.1 17.0 1.0 OD2 A:ASP97 4.2 20.2 1.0 N A:HIS103 4.3 19.2 1.0 C A:ASP97 4.4 17.6 1.0 N A:ASN101 4.4 22.8 1.0 N A:ILE104 4.4 17.4 1.0 N A:SER105 4.4 14.9 1.0 CA A:HIS103 4.4 18.8 1.0 N A:ASP99 4.5 23.2 1.0 CA A:ILE104 4.5 15.2 1.0 CG A:GLU108 4.5 15.4 1.0 N A:THR98 4.5 18.5 1.0 O A:HOH296 4.6 21.8 1.0 CB A:ASN101 4.6 21.7 1.0 CB A:ASP99 4.6 25.6 1.0 O A:HOH324 4.8 27.4 1.0 N A:PHE100 4.8 25.6 1.0 CB A:HIS103 4.8 19.5 1.0 CA A:ASP99 4.9 25.5 1.0 CA A:ASN101 4.9 22.1 1.0 C A:ILE104 4.9 16.0 1.0 C A:ASP99 5.0 26.1 1.0 O A:ASP97 5.0 19.1 1.0

Seattle Structural Genomics Center For Infectious Disease(Ssgcid), A.Gardberg, T.Edwards, B.Staker, P.Skubak, C.Gilchrist, L.Stewart. Crystal Structure of URE3-Binding Protein To Be Published.