Calcium in PDB 4m00: Crystal Structure of the Ligand Binding Region of Staphylococcal Adhesion Srap

The structure of Crystal Structure of the Ligand Binding Region of Staphylococcal Adhesion Srap, PDB code: 4m00 was solved by Y.H.Yang, Y.L.Jiang, J.Zhang, L.Wang, Y.Chen, C.Z.Zhou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.54 / 2.05
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	118.018, 118.018, 136.407, 90.00, 90.00, 120.00
R / Rfree (%)	18.1 / 20.6

The binding sites of Calcium atom in the Crystal Structure of the Ligand Binding Region of Staphylococcal Adhesion Srap (pdb code 4m00). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of the Ligand Binding Region of Staphylococcal Adhesion Srap, PDB code: 4m00:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of the Ligand Binding Region of Staphylococcal Adhesion Srap


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 the Ligand Binding Region of Staphylococcal Adhesion Srap within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca801 b:20.7 occ:1.00 O A:TYR367 2.3 22.4 1.0 OD1 A:ASN369 2.3 24.9 1.0 O A:HOH901 2.4 20.2 1.0 OD2 A:ASP382 2.4 22.3 1.0 O A:HOH902 2.4 18.7 1.0 OD2 A:ASP365 2.4 19.6 1.0 OD1 A:ASP365 2.5 20.9 1.0 CG A:ASP365 2.8 20.4 1.0 CG A:ASP382 3.4 23.8 1.0 CG A:ASN369 3.5 27.3 1.0 C A:TYR367 3.5 23.7 1.0 OD1 A:ASP382 3.7 23.2 1.0 N A:ASN369 3.9 25.1 1.0 CB A:ASN369 4.2 25.7 1.0 CG2 A:VAL351 4.2 19.5 1.0 CB A:ASP365 4.3 19.2 1.0 CA A:TYR367 4.4 22.1 1.0 CA A:HIS368 4.4 24.4 1.0 N A:HIS368 4.5 23.2 1.0 CB A:TYR367 4.5 22.8 1.0 NZ A:LYS363 4.5 17.3 1.0 N A:TYR367 4.5 20.6 1.0 O A:HOH960 4.5 24.9 1.0 ND2 A:ASN369 4.6 27.1 1.0 C A:HIS368 4.6 26.4 1.0 O A:ASP330 4.6 19.8 1.0 CA A:ASN369 4.7 27.0 1.0 CD2 A:TYR367 4.7 24.8 1.0 CA A:ALA349 4.8 20.9 1.0 O A:ALA349 4.8 20.2 1.0 CB A:ASP382 4.8 23.6 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of the Ligand Binding Region of Staphylococcal Adhesion Srap


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 the Ligand Binding Region of Staphylococcal Adhesion Srap within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca802 b:22.3 occ:1.00 O A:LYS575 2.2 23.5 1.0 OD2 A:ASP645 2.2 26.3 1.0 OD1 A:ASN602 2.3 26.0 1.0 OD2 A:ASP573 2.4 23.4 1.0 OD1 A:ASP601 2.5 25.4 1.0 OD1 A:ASP573 2.5 18.4 1.0 OD2 A:ASP601 2.5 25.7 1.0 CG A:ASP573 2.8 19.8 1.0 CG A:ASP601 2.9 27.6 1.0 CG A:ASP645 3.4 25.7 1.0 C A:LYS575 3.4 24.1 1.0 CG A:ASN602 3.4 26.0 1.0 ND2 A:ASN602 4.0 25.3 1.0 CB A:ASP645 4.1 25.3 1.0 N A:GLY603 4.1 25.9 1.0 ND2 A:ASN649 4.1 22.7 1.0 N A:LYS575 4.2 24.2 1.0 CA A:LYS575 4.2 25.7 1.0 O A:HOH1474 4.2 45.4 1.0 CB A:ASP573 4.3 19.5 1.0 N A:ASN602 4.3 28.8 1.0 CB A:LYS575 4.4 29.6 1.0 CB A:ASP601 4.4 28.3 1.0 OD1 A:ASP645 4.4 24.7 1.0 CA A:GLY603 4.4 24.6 1.0 N A:ALA576 4.4 24.4 1.0 C A:ALA576 4.5 24.7 1.0 O A:HOH1223 4.6 41.2 1.0 CA A:ALA576 4.6 25.4 1.0 N A:PRO577 4.7 26.6 1.0 CB A:ASN602 4.7 27.1 1.0 CG A:ASN649 4.7 26.9 1.0 O A:HOH1006 4.7 33.3 1.0 CB A:ASN649 4.8 25.6 1.0 C A:ASN602 4.8 25.5 1.0 CD A:PRO577 4.8 27.4 1.0 CA A:ASN602 4.8 26.3 1.0 O A:ALA576 4.9 24.3 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of the Ligand Binding Region of Staphylococcal Adhesion Srap


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 the Ligand Binding Region of Staphylococcal Adhesion Srap within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca803 b:38.8 occ:1.00 OD2 A:ASP734 2.3 38.6 1.0 O A:THR663 2.3 45.6 1.0 OD1 A:ASN691 2.3 45.3 1.0 OD2 A:ASP690 2.5 40.5 1.0 OD1 A:ASP661 2.5 44.6 1.0 OD1 A:ASP690 2.5 38.3 1.0 OD2 A:ASP661 2.6 44.8 1.0 CG A:ASP690 2.9 41.4 1.0 CG A:ASP661 2.9 46.2 1.0 CG A:ASP734 3.4 38.1 1.0 CG A:ASN691 3.4 44.9 1.0 C A:THR663 3.5 46.6 1.0 CB A:ASP734 3.8 38.8 1.0 ND2 A:ASN691 3.9 45.1 1.0 ND2 A:ASN738 3.9 40.9 1.0 N A:SER692 4.3 45.3 1.0 CA A:THR663 4.3 47.2 1.0 N A:ASN691 4.3 43.3 1.0 O A:HOH1152 4.3 39.7 1.0 N A:THR663 4.3 46.0 1.0 CB A:ASP690 4.4 39.2 1.0 CB A:THR663 4.4 48.3 1.0 CB A:ASP661 4.4 47.1 1.0 N A:ALA664 4.4 44.7 1.0 OD1 A:ASP734 4.4 37.2 1.0 C A:ALA664 4.5 40.8 1.0 O A:HOH1271 4.5 50.2 1.0 CA A:ALA664 4.6 42.6 1.0 CB A:SER692 4.6 47.7 1.0 CB A:ASN691 4.7 43.7 1.0 O A:ALA664 4.7 42.0 1.0 OG A:SER692 4.7 49.9 1.0 N A:PRO665 4.7 39.1 1.0 CB A:ASN738 4.8 40.1 1.0 CG A:ASN738 4.8 43.8 1.0 CA A:ASN691 4.9 45.9 1.0 CA A:ASP690 5.0 43.2 1.0

Y.H.Yang, Y.L.Jiang, J.Zhang, L.Wang, X.H.Bai, S.J.Zhang, Y.M.Ren, N.Li, Y.H.Zhang, Z.Zhang, Q.Gong, Y.Mei, T.Xue, J.R.Zhang, Y.Chen, C.Z.Zhou. Structural Insights Into Srap-Mediated Staphylococcus Aureus Adhesion to Host Cells Plos Pathog. V. 10 04169 2014.
ISSN: ISSN 1553-7366
PubMed: 24901708
DOI: 10.1371/JOURNAL.PPAT.1004169