Calcium in PDB 5hj2: Integrin ALPHA2BETA1 I-Domain

The structure of Integrin ALPHA2BETA1 I-Domain, PDB code: 5hj2 was solved by K.L.Brown, S.Banerjee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	101.87 / 2.15
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	144.066, 144.066, 130.004, 90.00, 90.00, 90.00
R / Rfree (%)	23.4 / 28.4

The structure of Integrin ALPHA2BETA1 I-Domain also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Calcium atom in the Integrin ALPHA2BETA1 I-Domain (pdb code 5hj2). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Integrin ALPHA2BETA1 I-Domain, PDB code: 5hj2:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in the Integrin ALPHA2BETA1 I-Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Integrin ALPHA2BETA1 I-Domain within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca301 b:40.3 occ:1.00 O C:HOH406 2.3 13.3 1.0 OG C:SER19 2.3 28.1 1.0 O C:HOH458 2.4 29.4 1.0 O C:HOH447 2.6 28.8 1.0 O C:HOH432 2.6 29.9 1.0 OD1 C:ASP118 3.0 22.5 1.0 OG C:SER17 3.2 20.9 1.0 CB C:SER19 3.4 23.2 1.0 OG1 C:THR85 3.4 29.2 1.0 CG C:ASP118 3.9 22.4 1.0 OD2 C:ASP118 4.1 19.3 1.0 CB C:SER17 4.3 20.2 1.0 OD2 C:ASP15 4.5 21.1 1.0 CA C:GLY119 4.5 25.4 1.0 CA C:SER19 4.5 23.2 1.0 N C:SER19 4.6 22.5 1.0 N C:GLY119 4.6 17.7 1.0 O C:ASP118 4.7 21.5 1.0 C C:ASP118 4.7 18.1 1.0 CB C:THR85 4.7 24.0 1.0 OD1 C:ASP15 4.9 17.1 1.0

Calcium binding site 2 out of 5 in the Integrin ALPHA2BETA1 I-Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Integrin ALPHA2BETA1 I-Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:35.6 occ:1.00 O A:HOH433 2.3 29.0 1.0 OD1 A:ASP118 2.5 26.2 1.0 O A:HOH407 2.5 36.2 1.0 O A:HOH471 2.5 32.4 1.0 OG A:SER19 2.5 27.4 1.0 O A:HOH425 2.5 22.8 1.0 CG A:ASP118 3.4 28.3 1.0 CB A:SER19 3.5 24.7 1.0 OD2 A:ASP118 3.7 29.5 1.0 OG A:SER17 4.0 27.2 1.0 CA A:GLY119 4.0 26.7 1.0 O A:ASP118 4.0 24.8 1.0 C A:ASP118 4.1 24.2 1.0 N A:GLY119 4.1 24.3 1.0 OG1 A:THR85 4.3 24.3 1.0 CD2 A:TYR149 4.4 29.2 1.0 CB A:ASP118 4.7 19.4 1.0 OD2 A:ASP15 4.8 26.7 1.0 CA A:SER19 4.8 24.5 1.0 CG A:TYR149 4.8 27.7 1.0 CE2 A:TYR149 4.8 30.7 1.0 CA A:ASP118 4.9 20.8 1.0 N A:SER19 5.0 20.3 1.0

Calcium binding site 3 out of 5 in the Integrin ALPHA2BETA1 I-Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Integrin ALPHA2BETA1 I-Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca301 b:28.0 occ:1.00 OG B:SER19 2.2 25.8 1.0 O B:HOH444 2.4 23.1 1.0 O B:HOH458 2.4 28.9 1.0 OD1 B:ASP118 2.4 26.0 1.0 O B:HOH460 2.5 28.4 1.0 O B:HOH409 2.5 31.5 1.0 O B:HOH410 2.7 21.9 1.0 CB B:SER19 3.2 25.9 1.0 CG B:ASP118 3.4 21.4 1.0 OD2 B:ASP118 3.7 21.1 1.0 OG B:SER17 3.9 28.2 1.0 O B:HOH446 4.0 25.9 1.0 O B:ASP118 4.2 20.7 1.0 OG1 B:THR85 4.2 28.5 1.0 CA B:GLY119 4.2 25.5 1.0 C B:ASP118 4.3 19.4 1.0 N B:GLY119 4.4 16.8 1.0 CA B:SER19 4.5 25.0 1.0 CD2 B:TYR149 4.5 21.9 1.0 OD2 B:ASP15 4.7 27.3 1.0 N B:SER19 4.7 25.6 1.0 CG B:TYR149 4.7 21.9 1.0 CB B:ASP118 4.8 19.4 1.0 CB B:TYR149 5.0 18.9 1.0

Calcium binding site 4 out of 5 in the Integrin ALPHA2BETA1 I-Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Integrin ALPHA2BETA1 I-Domain within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca301 b:37.9 occ:1.00 O D:HOH421 2.2 27.2 1.0 OG D:SER19 2.2 36.1 1.0 O D:HOH436 2.3 34.5 1.0 OD1 D:ASP118 2.4 27.7 1.0 O D:HOH428 2.5 34.3 1.0 CB D:SER19 3.3 32.5 1.0 CG D:ASP118 3.3 30.4 1.0 OG D:SER17 3.4 31.4 1.0 OD2 D:ASP118 3.6 29.6 1.0 O D:ASP118 4.1 27.7 1.0 C D:ASP118 4.2 26.0 1.0 OG1 D:THR85 4.2 28.8 1.0 N D:GLY119 4.3 24.0 1.0 CA D:GLY119 4.3 22.6 1.0 OD2 D:ASP15 4.4 27.2 1.0 CA D:SER19 4.4 28.2 1.0 N D:SER19 4.5 26.7 1.0 CB D:SER17 4.6 25.4 1.0 CB D:ASP118 4.7 26.1 1.0 CA D:ASP118 4.9 25.4 1.0

Calcium binding site 5 out of 5 in the Integrin ALPHA2BETA1 I-Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Integrin ALPHA2BETA1 I-Domain within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca301 b:52.9 occ:1.00 OG E:SER19 2.3 60.4 1.0 O E:HOH411 2.4 40.7 1.0 OG E:SER17 2.8 53.9 1.0 CB E:SER19 3.0 54.3 1.0 OD1 E:ASP118 3.2 53.5 1.0 CB E:SER17 3.9 55.1 1.0 CG E:ASP118 4.2 55.5 1.0 OD2 E:ASP15 4.2 51.2 1.0 CA E:SER19 4.2 56.3 1.0 N E:SER19 4.3 56.5 1.0 CA E:GLY119 4.3 55.9 1.0 OD2 E:ASP118 4.5 60.4 1.0 N E:GLY119 4.5 54.1 1.0 C E:ASP118 4.7 58.0 1.0 O E:ASP118 4.8 60.7 1.0 CD2 E:TYR149 4.9 69.9 1.0 CB E:THR85 5.0 52.9 1.0

K.L.Brown, S.Banerjee, A.Feigley, H.Abe, T.S.Blackwell, A.Pozzi, B.G.Hudson, R.Zent. Salt-Bridge Modulates Differential Calcium-Mediated Ligand Binding to Integrin Alpha 1- and Alpha 2-I Domains. Sci Rep V. 8 2916 2018.
ISSN: ESSN 2045-2322
PubMed: 29440721
DOI: 10.1038/S41598-018-21231-1