Calcium in PDB 5ffg: Crystal Structure of Integrin Alpha V Beta 6 Head

The structure of Crystal Structure of Integrin Alpha V Beta 6 Head, PDB code: 5ffg was solved by X.Dong, T.A.Springer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.99 / 2.25
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	215.590, 77.560, 59.070, 90.00, 101.46, 90.00
R / Rfree (%)	20.8 / 24.6

The binding sites of Calcium atom in the Crystal Structure of Integrin Alpha V Beta 6 Head (pdb code 5ffg). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of Integrin Alpha V Beta 6 Head, PDB code: 5ffg:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Crystal Structure of Integrin Alpha V Beta 6 Head


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 Alpha V Beta 6 Head within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2001 b:49.9 occ:1.00 O A:TYR290 2.3 69.0 1.0 OD1 A:ASN286 2.3 70.6 1.0 OD1 A:ASP284 2.3 79.4 1.0 O A:HOH2109 2.4 45.0 1.0 OD2 A:ASP292 2.4 69.6 1.0 OD1 A:ASP292 2.4 59.6 1.0 OD1 A:ASP288 2.5 85.8 1.0 CG A:ASP292 2.8 62.9 1.0 CG A:ASP288 3.3 75.0 1.0 CG A:ASN286 3.4 62.8 1.0 OD2 A:ASP288 3.4 65.9 1.0 C A:TYR290 3.4 62.4 1.0 CG A:ASP284 3.5 76.6 1.0 ND2 A:ASN286 3.9 70.8 1.0 CB A:TYR290 4.0 64.3 1.0 N A:ILE285 4.0 60.3 1.0 CA A:ASP284 4.1 68.9 1.0 CA A:TYR290 4.1 64.8 1.0 N A:TYR290 4.1 67.1 1.0 N A:ASN286 4.2 67.6 1.0 CB A:ASP284 4.2 71.2 1.0 CB A:ASP292 4.2 54.2 1.0 C A:ASP284 4.5 64.6 1.0 C A:ALA291 4.5 57.0 1.0 OD2 A:ASP284 4.5 79.0 1.0 N A:ALA291 4.5 61.5 1.0 N A:ASP292 4.6 57.2 1.0 CB A:ASN286 4.7 63.3 1.0 O A:ALA291 4.7 62.6 1.0 O A:GLN320 4.7 71.5 1.0 CB A:ASP288 4.8 71.1 1.0 N A:GLN320 4.8 55.4 1.0 N A:ASP288 4.8 77.2 1.0 CA A:ALA291 4.8 59.3 1.0 CA A:ASN286 4.9 67.1 1.0 CA A:ASP292 4.9 56.4 1.0 CG A:LEU319 5.0 64.2 1.0

Calcium binding site 2 out of 6 in the Crystal Structure of Integrin Alpha V Beta 6 Head


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 Alpha V Beta 6 Head within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2002 b:58.0 occ:1.00 O A:PHE355 2.3 72.3 1.0 OD1 A:ASP351 2.4 84.3 1.0 O A:HOH2127 2.4 51.1 1.0 OD1 A:ASP353 2.4 90.8 1.0 OD1 A:ASP349 2.4 72.8 1.0 OD1 A:ASP357 2.4 64.6 1.0 OD2 A:ASP357 2.5 70.0 1.0 CG A:ASP357 2.8 71.0 1.0 CG A:ASP351 3.3 72.2 1.0 CG A:ASP353 3.4 86.4 1.0 CG A:ASP349 3.5 73.9 1.0 C A:PHE355 3.5 73.1 1.0 OD2 A:ASP351 3.7 86.7 1.0 OD2 A:ASP353 3.8 80.8 1.0 ND2 A:ASN377 4.0 67.1 1.0 CA A:ASP349 4.1 77.8 1.0 N A:ASP351 4.1 72.9 1.0 N A:LEU350 4.1 69.6 1.0 OD2 A:ASP349 4.2 81.8 1.0 CB A:ASP357 4.3 68.7 1.0 C A:ASP349 4.3 74.9 1.0 N A:PHE355 4.3 79.7 1.0 CA A:PHE355 4.4 75.7 1.0 C A:ASN356 4.4 63.4 1.0 CB A:ASP349 4.4 73.3 1.0 N A:ASP353 4.5 78.3 1.0 N A:ASN356 4.5 67.1 1.0 O A:ASN356 4.5 62.6 1.0 N A:ASP357 4.6 62.7 1.0 N A:GLN352 4.6 77.2 1.0 CB A:ASP351 4.6 74.0 1.0 CB A:PHE355 4.6 69.1 1.0 CA A:ASN356 4.6 75.2 1.0 CB A:ASP353 4.7 82.4 1.0 CA A:ASP351 4.7 84.2 1.0 CB A:ASN377 4.8 63.0 1.0 N A:GLY378 4.9 61.7 1.0 C A:ASP351 4.9 77.4 1.0 CA A:ASP357 4.9 60.9 1.0 CG A:ASN377 4.9 63.8 1.0

Calcium binding site 3 out of 6 in the Crystal Structure of Integrin Alpha V Beta 6 Head


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 Integrin Alpha V Beta 6 Head within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2003 b:55.6 occ:1.00 O A:TYR420 2.3 87.4 1.0 O A:HOH2117 2.3 33.5 1.0 OD1 A:ASP414 2.3 84.0 1.0 OD1 A:ASP416 2.4 85.4 1.0 OD1 A:ASN418 2.4 85.4 1.0 OD1 A:ASP422 2.5 77.0 1.0 OD2 A:ASP422 2.5 82.1 1.0 CG A:ASP422 2.8 83.5 1.0 CG A:ASN418 3.3 87.2 1.0 C A:TYR420 3.4 82.1 1.0 CG A:ASP414 3.5 84.5 1.0 CG A:ASP416 3.5 86.9 1.0 OD2 A:ASP416 3.9 87.5 1.0 ND2 A:ASN418 4.0 86.6 1.0 N A:TYR420 4.1 84.0 1.0 CA A:ASP414 4.1 80.0 1.0 CA A:TYR420 4.1 84.5 1.0 CB A:ASN418 4.2 90.5 1.0 CB A:ASP414 4.3 85.7 1.0 CB A:ASP422 4.3 79.4 1.0 OD2 A:ASP414 4.3 86.9 1.0 N A:ASN418 4.3 91.2 1.0 CB A:TYR420 4.4 80.5 1.0 N A:ILE415 4.4 80.6 1.0 N A:ASP416 4.4 91.1 1.0 N A:PRO421 4.4 76.4 1.0 C A:PRO421 4.4 72.9 1.0 O A:ALA438 4.5 81.2 1.0 C A:ASP414 4.5 83.3 1.0 N A:ASP422 4.5 72.3 1.0 N A:ALA438 4.5 76.0 1.0 CA A:PRO421 4.6 78.4 1.0 CA A:ASN418 4.7 92.0 1.0 CB A:ASP416 4.7 88.8 1.0 CB A:ALA438 4.8 75.5 1.0 O A:PRO421 4.8 72.2 1.0 CA A:ASP422 4.9 74.7 1.0 N A:LYS417 4.9 90.2 1.0 N A:GLY419 4.9 90.0 1.0 CA A:ASP416 5.0 88.8 1.0

Calcium binding site 4 out of 6 in the Crystal Structure of Integrin Alpha V Beta 6 Head


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 Integrin Alpha V Beta 6 Head within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2004 b:62.0 occ:1.00 O A:ILE236 2.2 64.1 1.0 OD1 A:ASN232 2.3 68.2 1.0 O A:HOH2102 2.4 54.3 1.0 OD1 A:ASP230 2.4 79.1 1.0 OD1 A:ASP234 2.4 75.5 1.0 OD2 A:ASP238 2.4 58.6 1.0 OD1 A:ASP238 2.5 71.3 1.0 CG A:ASP238 2.7 70.7 1.0 C A:ILE236 3.4 65.5 1.0 CG A:ASN232 3.4 70.9 1.0 CG A:ASP230 3.5 81.0 1.0 CG A:ASP234 3.6 72.1 1.0 OD1 A:ASP257 3.9 0.5 1.0 ND2 A:ASN232 3.9 69.2 1.0 N A:ILE236 4.0 75.0 1.0 CA A:ILE236 4.0 70.9 1.0 CB A:ILE236 4.0 76.2 1.0 OD2 A:ASP234 4.1 70.1 1.0 N A:PHE231 4.1 60.3 1.0 CB A:ASP238 4.1 61.2 1.0 CA A:ASP230 4.2 61.5 1.0 N A:ASN232 4.2 61.5 1.0 N A:ASP238 4.3 62.1 1.0 OD2 A:ASP230 4.3 90.6 1.0 CB A:ASP230 4.3 64.6 1.0 C A:ASP237 4.5 68.7 1.0 N A:ASP237 4.5 65.4 1.0 N A:ASP234 4.6 74.7 1.0 CA A:ASP238 4.6 55.7 1.0 C A:ASP230 4.7 62.8 1.0 CB A:ASN232 4.7 72.8 1.0 CB A:ASP234 4.7 72.6 1.0 CA A:ASP237 4.8 62.1 1.0 CG2 A:ILE236 4.8 83.9 1.0 CA A:ASN232 4.9 69.1 1.0 O A:ASP237 4.9 73.0 1.0 N A:GLY233 4.9 67.1 1.0 N A:GLY258 4.9 57.4 1.0 N A:GLY235 5.0 73.3 1.0

Calcium binding site 5 out of 6 in the Crystal Structure of Integrin Alpha V Beta 6 Head


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Integrin Alpha V Beta 6 Head within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2001 b:39.4 occ:1.00 O B:HOH2165 2.2 30.1 1.0 OD1 B:ASP131 2.3 43.8 1.0 O B:HOH2120 2.3 39.1 1.0 O B:SER127 2.3 38.6 1.0 OD1 B:ASP130 2.4 52.8 1.0 O B:LYS338 2.4 46.1 1.0 CG B:ASP130 3.2 55.2 1.0 OD2 B:ASP130 3.2 55.4 1.0 CG B:ASP131 3.4 42.0 1.0 C B:SER127 3.6 40.9 1.0 C B:LYS338 3.6 48.9 1.0 OD2 B:ASP131 3.9 43.9 1.0 O B:HOH2105 3.9 32.4 1.0 CA B:MET128 4.2 32.8 1.0 N B:MET128 4.3 34.8 1.0 OD2 B:ASP254 4.3 52.1 1.0 N B:ASP131 4.3 47.6 1.0 N B:ASP339 4.4 40.9 1.0 CA B:ASP339 4.5 49.4 1.0 CA B:LYS338 4.5 48.4 1.0 CB B:ASP130 4.6 47.1 1.0 CA B:SER127 4.6 38.5 1.0 CB B:ASP131 4.6 38.8 1.0 C B:MET128 4.7 40.6 1.0 CB B:LYS338 4.8 53.1 1.0 N B:ASP130 4.8 50.1 1.0 SD B:MET128 4.9 82.2 1.0 CB B:SER127 4.9 33.5 1.0 N B:ASP129 5.0 46.3 1.0

Calcium binding site 6 out of 6 in the Crystal Structure of Integrin Alpha V Beta 6 Head


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Integrin Alpha V Beta 6 Head within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2002 b:53.6 occ:0.80 OD2 B:ASP123 2.2 44.0 1.0 OD1 B:ASP254 2.3 47.5 1.0 OE2 B:GLU223 2.4 29.1 1.0 OG B:SER125 2.4 46.4 1.0 O B:HOH2123 2.4 44.7 1.0 CG B:ASP123 2.9 39.1 1.0 OD1 B:ASP123 3.0 43.2 1.0 CB B:SER125 3.3 41.5 1.0 CD B:GLU223 3.3 35.5 1.0 CG B:ASP254 3.5 49.3 1.0 O B:HOH2126 3.6 38.0 1.0 OG B:SER127 3.6 42.2 1.0 OE1 B:GLU223 3.8 38.8 1.0 CB B:ALA255 3.9 39.9 1.0 OD2 B:ASP254 4.1 52.1 1.0 CB B:ASP123 4.1 29.8 1.0 CG B:MET128 4.3 32.0 1.0 N B:ASP254 4.3 25.9 1.0 N B:ALA255 4.4 43.3 1.0 C B:ASP254 4.5 26.8 1.0 CG B:GLU223 4.5 30.2 1.0 CA B:SER125 4.5 33.0 1.0 N B:SER125 4.6 30.7 1.0 OG B:SER253 4.6 40.2 1.0 CB B:ASP254 4.7 43.8 1.0 O B:HOH2142 4.7 57.7 1.0 CA B:ASP254 4.7 33.7 1.0 CA B:ALA255 4.8 43.5 1.0 O B:ILE219 4.8 66.2 1.0 O B:ASP254 4.9 37.4 1.0 SD B:MET128 5.0 82.2 1.0

X.Dong, B.Zhao, R.E.Iacob, J.Zhu, A.C.Koksal, C.Lu, J.R.Engen, T.A.Springer. Force Interacts with Macromolecular Structure in Activation of Tgf-Beta. Nature V. 542 55 2017.
ISSN: ESSN 1476-4687
PubMed: 28117447
DOI: 10.1038/NATURE21035