Calcium in PDB 5ffo: Integrin Alpha V Beta 6 in Complex with Pro-Tgf-Beta

The structure of Integrin Alpha V Beta 6 in Complex with Pro-Tgf-Beta, PDB code: 5ffo was solved by X.Dong, B.Zhao, T.A.Springer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.72 / 3.49
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	81.440, 91.440, 131.030, 89.98, 86.25, 89.85
R / Rfree (%)	22.4 / 27.7

The structure of Integrin Alpha V Beta 6 in Complex with Pro-Tgf-Beta also contains other interesting chemical elements:

Manganese

(Mn)

6 atoms

The binding sites of Calcium atom in the Integrin Alpha V Beta 6 in Complex with Pro-Tgf-Beta (pdb code 5ffo). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Integrin Alpha V Beta 6 in Complex with Pro-Tgf-Beta, PDB code: 5ffo:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in the Integrin Alpha V Beta 6 in Complex with Pro-Tgf-Beta


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Integrin Alpha V Beta 6 in Complex with Pro-Tgf-Beta within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2001 b:0.8 occ:1.00 O A:TYR290 2.2 0.2 1.0 OD1 A:ASP292 2.3 0.4 1.0 OD1 A:ASP284 2.3 0.5 1.0 OD2 A:ASP292 2.4 0.7 1.0 OD1 A:ASN286 2.4 0.1 1.0 OD1 A:ASP288 2.4 0.8 1.0 CG A:ASP292 2.6 0.8 1.0 CG A:ASP288 3.2 0.2 1.0 OD2 A:ASP288 3.2 0.4 1.0 C A:TYR290 3.4 0.1 1.0 CG A:ASP284 3.5 0.6 1.0 CG A:ASN286 3.5 0.9 1.0 CA A:ASP284 3.9 1.0 1.0 ND2 A:ASN286 4.0 0.2 1.0 N A:ILE285 4.0 0.5 1.0 CB A:TYR290 4.1 0.4 1.0 CB A:ASP284 4.1 0.9 1.0 CA A:TYR290 4.1 0.8 1.0 CB A:ASP292 4.1 0.8 1.0 N A:TYR290 4.2 0.7 1.0 N A:ASN286 4.3 0.8 1.0 C A:ASP284 4.4 0.1 1.0 OD2 A:ASP284 4.5 0.2 1.0 C A:ALA291 4.5 0.4 1.0 N A:ASP292 4.5 0.5 1.0 N A:ALA291 4.5 0.8 1.0 O A:GLN320 4.6 0.2 1.0 CB A:ASP288 4.6 0.1 1.0 N A:ASP288 4.7 0.7 1.0 N A:GLN320 4.7 0.5 1.0 CA A:ALA291 4.7 0.8 1.0 O A:ALA291 4.7 0.2 1.0 CA A:ASP292 4.8 0.2 1.0 CB A:ASN286 4.8 0.2 1.0 CA A:ASN286 5.0 0.6 1.0

Calcium binding site 2 out of 8 in the Integrin Alpha V Beta 6 in Complex with Pro-Tgf-Beta


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Integrin Alpha V Beta 6 in Complex with Pro-Tgf-Beta within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2002 b:0.5 occ:1.00 OD1 A:ASP353 2.3 1.0 1.0 OD1 A:ASP357 2.4 0.4 1.0 OD2 A:ASP357 2.4 0.3 1.0 OD2 A:ASP353 2.5 0.5 1.0 OD1 A:ASP351 2.5 0.2 1.0 O A:PHE355 2.5 0.0 1.0 OD1 A:ASP349 2.6 0.8 1.0 CG A:ASP353 2.6 0.6 1.0 CG A:ASP357 2.7 0.8 1.0 CG A:ASP351 3.3 0.5 1.0 OD2 A:ASP351 3.5 0.9 1.0 C A:PHE355 3.7 0.6 1.0 CG A:ASP349 3.7 0.0 1.0 ND2 A:ASN377 3.9 0.5 1.0 CB A:ASP353 4.0 0.9 1.0 CB A:ASP357 4.2 0.7 1.0 N A:ASP353 4.3 1.0 1.0 OD2 A:ASP349 4.3 0.8 1.0 N A:PHE355 4.4 0.3 1.0 N A:ASP351 4.4 0.2 1.0 CA A:PHE355 4.4 0.8 1.0 C A:ASN356 4.5 0.8 1.0 CA A:ASP349 4.6 0.9 1.0 O A:ASN356 4.6 0.5 1.0 CB A:PHE355 4.6 0.6 1.0 N A:ASP357 4.6 0.3 1.0 N A:LEU350 4.7 0.3 1.0 CB A:ASP351 4.7 0.4 1.0 N A:GLY378 4.7 0.3 1.0 CA A:ASP353 4.7 0.3 1.0 N A:ASN356 4.7 0.8 1.0 N A:GLN352 4.7 0.3 1.0 CB A:ASP349 4.7 0.3 1.0 CB A:ASN377 4.8 0.8 1.0 C A:ASP349 4.8 0.8 1.0 CA A:ASN356 4.8 0.5 1.0 CG A:ASN377 4.9 0.8 1.0 CA A:ASP351 4.9 0.8 1.0 O A:GLY378 4.9 0.2 1.0 CA A:ASP357 4.9 0.8 1.0 C A:ASP351 5.0 1.0 1.0

Calcium binding site 3 out of 8 in the Integrin Alpha V Beta 6 in Complex with Pro-Tgf-Beta


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Integrin Alpha V Beta 6 in Complex with Pro-Tgf-Beta within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2003 b:0.9 occ:1.00 OD1 A:ASN418 2.2 0.2 1.0 ND2 A:ASN418 2.3 0.8 1.0 OD2 A:ASP422 2.4 0.6 1.0 O A:TYR420 2.4 0.4 1.0 OD1 A:ASP422 2.4 0.1 1.0 CG A:ASN418 2.4 0.8 1.0 OD1 A:ASP416 2.6 0.5 1.0 OD1 A:ASP414 2.6 0.2 1.0 CG A:ASP422 2.7 0.3 1.0 C A:TYR420 3.4 0.3 1.0 CG A:ASP416 3.5 0.8 1.0 CB A:ASN418 3.7 0.4 1.0 OD2 A:ASP416 3.7 0.3 1.0 CG A:ASP414 3.8 0.7 1.0 CB A:TYR420 4.0 0.7 1.0 CA A:TYR420 4.1 0.5 1.0 N A:TYR420 4.1 0.5 1.0 N A:ALA438 4.1 0.9 1.0 CB A:ASP422 4.2 0.4 1.0 O A:ALA438 4.2 0.6 1.0 CB A:ALA438 4.3 0.5 1.0 C A:PRO421 4.4 0.5 1.0 N A:ASP422 4.4 0.6 1.0 N A:PRO421 4.5 0.7 1.0 OD2 A:ASP414 4.5 0.9 1.0 O A:PRO421 4.6 0.5 1.0 CA A:ASN418 4.7 0.4 1.0 N A:ASN418 4.7 0.6 1.0 CA A:ASP422 4.7 0.1 1.0 CA A:ALA438 4.7 0.2 1.0 CA A:PRO421 4.7 0.1 1.0 CA A:ASP414 4.7 1.0 1.0 CB A:ASP414 4.8 0.4 1.0 CB A:ASP416 4.9 0.6 1.0 N A:ASP416 4.9 0.2 1.0 C A:ALA438 4.9 0.2 1.0 N A:ILE415 5.0 0.4 1.0 C A:ASN418 5.0 0.8 1.0

Calcium binding site 4 out of 8 in the Integrin Alpha V Beta 6 in Complex with Pro-Tgf-Beta


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Integrin Alpha V Beta 6 in Complex with Pro-Tgf-Beta within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2004 b:0.9 occ:1.00 O A:ILE236 2.2 0.4 1.0 OD1 A:ASN232 2.3 0.7 1.0 OD1 A:ASP234 2.3 0.3 1.0 OD1 A:ASP238 2.3 0.4 1.0 OD2 A:ASP238 2.4 0.8 1.0 OD1 A:ASP230 2.6 0.2 1.0 CG A:ASP238 2.6 0.1 1.0 CG A:ASN232 3.2 0.2 1.0 CG A:ASP234 3.2 0.2 1.0 C A:ILE236 3.3 0.8 1.0 ND2 A:ASN232 3.5 0.5 1.0 OD2 A:ASP234 3.5 0.1 1.0 CG A:ASP230 3.7 0.4 1.0 N A:ILE236 3.8 1.0 1.0 CA A:ILE236 3.9 0.3 1.0 CB A:ILE236 4.0 0.1 1.0 CB A:ASP238 4.1 0.3 1.0 OD1 A:ASP257 4.2 0.9 1.0 N A:ASP238 4.3 0.0 1.0 N A:PHE231 4.4 0.5 1.0 CA A:ASP230 4.4 0.2 1.0 N A:ASP237 4.4 0.4 1.0 N A:ASN232 4.5 0.8 1.0 C A:ASP237 4.5 0.8 1.0 CB A:ASP234 4.5 0.4 1.0 N A:GLY235 4.5 0.4 1.0 OD2 A:ASP230 4.5 0.2 1.0 CB A:ASP230 4.5 0.0 1.0 CB A:ASN232 4.6 0.6 1.0 CA A:ASP238 4.6 0.4 1.0 N A:ASP234 4.7 0.5 1.0 CG2 A:ILE236 4.8 0.5 1.0 CA A:ASP237 4.8 0.7 1.0 C A:GLY235 4.9 0.2 1.0 C A:ASP230 4.9 0.3 1.0 O A:ASP237 5.0 0.8 1.0 CA A:ASN232 5.0 0.6 1.0

Calcium binding site 5 out of 8 in the Integrin Alpha V Beta 6 in Complex with Pro-Tgf-Beta


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Integrin Alpha V Beta 6 in Complex with Pro-Tgf-Beta within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca2001 b:0.8 occ:1.00 O E:TYR290 2.3 0.8 1.0 OD1 E:ASP292 2.3 0.5 1.0 OD1 E:ASN286 2.4 0.8 1.0 OD2 E:ASP292 2.4 0.1 1.0 OD1 E:ASP284 2.4 0.5 1.0 OD1 E:ASP288 2.4 0.4 1.0 CG E:ASP292 2.6 0.9 1.0 CG E:ASP288 3.1 0.6 1.0 OD2 E:ASP288 3.2 0.7 1.0 CG E:ASN286 3.5 0.7 1.0 C E:TYR290 3.5 0.7 1.0 CG E:ASP284 3.5 0.2 1.0 ND2 E:ASN286 3.9 0.7 1.0 CA E:ASP284 4.0 0.5 1.0 N E:ILE285 4.0 0.9 1.0 CB E:TYR290 4.1 0.2 1.0 CB E:ASP292 4.1 0.0 1.0 CB E:ASP284 4.1 0.1 1.0 CA E:TYR290 4.2 0.3 1.0 N E:TYR290 4.3 0.0 1.0 N E:ASN286 4.3 0.7 1.0 C E:ASP284 4.4 0.7 1.0 N E:ASP292 4.5 0.3 1.0 C E:ALA291 4.5 0.5 1.0 OD2 E:ASP284 4.5 0.7 1.0 O E:GLN320 4.5 0.6 1.0 N E:ALA291 4.6 0.9 1.0 CB E:ASP288 4.6 0.2 1.0 N E:GLN320 4.7 0.4 1.0 CB E:ASN286 4.7 0.9 1.0 N E:ASP288 4.7 0.9 1.0 CA E:ASP292 4.7 0.7 1.0 O E:ALA291 4.8 0.5 1.0 CA E:ALA291 4.8 0.4 1.0 CA E:ASN286 4.9 0.2 1.0

Calcium binding site 6 out of 8 in the Integrin Alpha V Beta 6 in Complex with Pro-Tgf-Beta


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Integrin Alpha V Beta 6 in Complex with Pro-Tgf-Beta within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca2002 b:0.4 occ:1.00 OD1 E:ASP353 2.4 0.2 1.0 OD2 E:ASP357 2.4 0.4 1.0 OD1 E:ASP357 2.4 0.9 1.0 OD1 E:ASP349 2.4 0.1 1.0 OD1 E:ASP351 2.4 0.2 1.0 OD2 E:ASP353 2.5 0.2 1.0 O E:PHE355 2.5 0.6 1.0 CG E:ASP353 2.7 0.7 1.0 CG E:ASP357 2.7 0.8 1.0 CG E:ASP351 3.3 0.5 1.0 OD2 E:ASP351 3.5 0.9 1.0 CG E:ASP349 3.6 0.9 1.0 C E:PHE355 3.7 1.0 1.0 ND2 E:ASN377 3.9 0.1 1.0 CB E:ASP353 4.0 0.2 1.0 OD2 E:ASP349 4.2 0.0 1.0 CB E:ASP357 4.2 0.6 1.0 N E:ASP353 4.2 0.5 1.0 N E:ASP351 4.3 0.0 1.0 N E:PHE355 4.4 0.3 1.0 CA E:ASP349 4.4 0.5 1.0 CA E:PHE355 4.5 0.5 1.0 C E:ASN356 4.5 0.2 1.0 N E:LEU350 4.5 0.1 1.0 O E:ASN356 4.6 0.3 1.0 CB E:ASP349 4.6 0.8 1.0 C E:ASP349 4.6 0.8 1.0 N E:ASP357 4.6 0.9 1.0 CB E:ASP351 4.6 0.3 1.0 CB E:PHE355 4.6 0.5 1.0 CA E:ASP353 4.7 0.2 1.0 N E:GLN352 4.7 0.9 1.0 N E:ASN356 4.7 0.3 1.0 N E:GLY378 4.7 0.4 1.0 CB E:ASN377 4.8 0.0 1.0 CA E:ASN356 4.8 0.8 1.0 CA E:ASP351 4.8 0.1 1.0 CG E:ASN377 4.9 1.0 1.0 CA E:ASP357 4.9 0.9 1.0 C E:ASP351 4.9 0.7 1.0 O E:GLY378 5.0 0.6 1.0

Calcium binding site 7 out of 8 in the Integrin Alpha V Beta 6 in Complex with Pro-Tgf-Beta


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Integrin Alpha V Beta 6 in Complex with Pro-Tgf-Beta within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca2003 b:0.9 occ:1.00 OD1 E:ASP422 2.3 0.4 1.0 OD1 E:ASP416 2.3 0.9 1.0 O E:TYR420 2.3 0.7 1.0 OD1 E:ASN418 2.4 1.0 1.0 OD2 E:ASP422 2.5 0.7 1.0 OD1 E:ASP414 2.5 0.5 1.0 CG E:ASP422 2.7 0.4 1.0 CG E:ASN418 3.2 0.4 1.0 CG E:ASP416 3.4 0.3 1.0 C E:TYR420 3.5 0.8 1.0 CG E:ASP414 3.7 0.6 1.0 ND2 E:ASN418 3.7 0.1 1.0 OD2 E:ASP416 3.7 0.5 1.0 CB E:ASP422 4.2 0.4 1.0 N E:TYR420 4.2 0.9 1.0 CA E:TYR420 4.2 0.9 1.0 CB E:ASN418 4.3 0.9 1.0 CB E:TYR420 4.3 0.6 1.0 N E:ASP422 4.4 0.7 1.0 CA E:ASP414 4.4 0.8 1.0 C E:PRO421 4.4 0.6 1.0 N E:ASP416 4.4 0.3 1.0 N E:PRO421 4.5 0.4 1.0 N E:ILE415 4.5 0.6 1.0 N E:ASN418 4.5 0.3 1.0 OD2 E:ASP414 4.5 0.6 1.0 CB E:ASP414 4.5 0.1 1.0 CB E:ASP416 4.6 0.3 1.0 CA E:PRO421 4.6 0.4 1.0 N E:ALA438 4.6 0.9 1.0 CA E:ASP422 4.7 0.9 1.0 C E:ASP414 4.7 1.0 1.0 O E:PRO421 4.7 0.4 1.0 O E:ALA438 4.8 0.9 1.0 CA E:ASN418 4.9 0.1 1.0 CB E:ALA438 4.9 0.5 1.0 CA E:ASP416 4.9 0.1 1.0

Calcium binding site 8 out of 8 in the Integrin Alpha V Beta 6 in Complex with Pro-Tgf-Beta


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Integrin Alpha V Beta 6 in Complex with Pro-Tgf-Beta within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca2004 b:0.6 occ:1.00 OD1 E:ASN232 2.3 0.2 1.0 OD1 E:ASP238 2.3 0.8 1.0 OD1 E:ASP234 2.4 0.1 1.0 O E:ILE236 2.4 0.1 1.0 OD2 E:ASP238 2.4 0.0 1.0 CG E:ASP238 2.7 0.9 1.0 CG E:ASN232 3.1 0.6 1.0 CG E:ASP234 3.1 0.0 1.0 ND2 E:ASN232 3.1 0.7 1.0 OD2 E:ASP234 3.3 0.2 1.0 OD1 E:ASP230 3.4 0.3 1.0 C E:ILE236 3.5 0.6 1.0 OD1 E:ASP257 3.7 0.2 1.0 CB E:ILE236 3.9 0.8 1.0 N E:ILE236 3.9 0.4 1.0 CA E:ILE236 3.9 0.3 1.0 CB E:ASP238 4.1 0.1 1.0 CB E:ASP234 4.4 0.9 1.0 N E:ASP238 4.5 0.3 1.0 CG E:ASP230 4.5 0.2 1.0 CB E:ASN232 4.5 0.3 1.0 N E:ASP237 4.6 0.2 1.0 CG2 E:ILE236 4.6 0.6 1.0 C E:ASP237 4.6 0.1 1.0 N E:ASN232 4.7 0.7 1.0 CA E:ASP238 4.7 0.3 1.0 N E:GLY235 4.7 0.3 1.0 N E:GLY258 4.8 0.4 1.0 N E:PHE231 4.9 0.0 1.0 CG E:ASP257 4.9 0.9 1.0 N E:ASP234 4.9 0.7 1.0 CG1 E:ILE236 5.0 0.2 1.0 CA E:ASP237 5.0 0.2 1.0 O E:ASP237 5.0 0.2 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