Calcium in PDB 5xau: Crystal Structure of Integrin Binding Fragment of Laminin-511

The structure of Crystal Structure of Integrin Binding Fragment of Laminin-511, PDB code: 5xau was solved by M.Takizawa, T.Arimori, Y.Kitago, J.Takagi, K.Sekiguchi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.41 / 1.80
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	175.031, 121.618, 107.554, 90.00, 127.57, 90.00
R / Rfree (%)	20.2 / 23.7

The binding sites of Calcium atom in the Crystal Structure of Integrin Binding Fragment of Laminin-511 (pdb code 5xau). 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 Integrin Binding Fragment of Laminin-511, PDB code: 5xau:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Integrin Binding Fragment of Laminin-511


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 Integrin Binding Fragment of Laminin-511 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca3401 b:39.9 occ:1.00 O A:HOH3718 2.3 36.6 1.0 O A:LEU2866 2.3 28.5 1.0 O A:LEU2810 2.3 30.5 1.0 OD2 A:ASP2793 2.4 32.2 1.0 OD1 A:ASN2868 2.4 37.9 1.0 OD2 A:ASP3219 2.9 32.4 1.0 C A:LEU2866 3.4 29.7 1.0 CG A:ASP2793 3.4 32.9 1.0 C A:LEU2810 3.4 31.1 1.0 CG A:ASN2868 3.6 37.1 1.0 OD1 A:ASP2793 3.7 31.3 1.0 CG A:ASP3219 4.0 32.3 1.0 CA A:LEU2866 4.0 29.5 1.0 CA A:LEU2810 4.0 29.6 1.0 CB A:LEU2866 4.0 30.3 1.0 N A:ASN2868 4.1 32.5 1.0 N A:LEU2866 4.1 29.4 1.0 CB A:ASN2868 4.2 36.1 1.0 CB A:LEU2810 4.3 29.8 1.0 CB A:ASP3219 4.4 34.0 1.0 N A:LEU2867 4.4 28.6 1.0 N A:GLY2811 4.5 32.0 1.0 CB A:GLU2864 4.6 39.5 1.0 ND2 A:ASN2868 4.6 38.8 1.0 CB A:ASP2793 4.7 33.0 1.0 CA A:LEU2867 4.7 29.6 1.0 CA A:GLY2811 4.7 34.5 1.0 CA A:ASN2868 4.8 34.4 1.0 C A:LEU2867 4.9 30.5 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Integrin Binding Fragment of Laminin-511


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 Integrin Binding Fragment of Laminin-511 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca3401 b:27.6 occ:1.00 O D:LEU2810 2.3 25.2 1.0 OD2 D:ASP2793 2.3 26.8 1.0 OD2 D:ASP3219 2.3 27.1 1.0 O D:LEU2866 2.3 24.5 1.0 O D:HOH3710 2.4 28.8 1.0 OD1 D:ASN2868 2.4 33.7 1.0 CG D:ASP2793 3.3 26.8 1.0 C D:LEU2810 3.4 25.6 1.0 C D:LEU2866 3.4 26.2 1.0 CG D:ASP3219 3.4 27.1 1.0 CG D:ASN2868 3.5 36.0 1.0 OD1 D:ASP2793 3.6 26.9 1.0 O D:HOH3578 3.7 45.2 1.0 CB D:ASP3219 3.9 27.8 1.0 CA D:LEU2810 4.0 24.0 1.0 CA D:LEU2866 4.0 26.1 1.0 N D:LEU2866 4.1 26.0 1.0 CB D:LEU2866 4.1 26.6 1.0 CB D:ASN2868 4.1 34.4 1.0 N D:ASN2868 4.1 31.1 1.0 CB D:LEU2810 4.4 23.6 1.0 N D:GLY2811 4.4 27.2 1.0 N D:LEU2867 4.5 26.1 1.0 OD1 D:ASP3219 4.5 28.2 1.0 CB D:ASP2793 4.5 25.9 1.0 ND2 D:ASN2868 4.6 37.2 1.0 CB D:GLU2864 4.6 29.8 1.0 CA D:GLY2811 4.7 28.9 1.0 O D:HOH3745 4.7 53.7 1.0 CA D:ASN2868 4.8 33.8 1.0 CA D:LEU2867 4.8 28.2 1.0 C D:LEU2867 4.9 30.5 1.0 CG D:GLU2864 4.9 31.5 1.0

M.Takizawa, T.Arimori, Y.Taniguchi, Y.Kitago, E.Yamashita, J.Takagi, K.Sekiguchi. Mechanistic Basis For the Recognition of Laminin-511 By Alpha 6 Beta 1 Integrin. Sci Adv V. 3 01497 2017.
ISSN: ESSN 2375-2548
PubMed: 28879238
DOI: 10.1126/SCIADV.1701497