Calcium in PDB 6uja: Integrin Alpha-V Beta-8 in Complex with Pro-Tgf-BETA1

The structure of Integrin Alpha-V Beta-8 in Complex with Pro-Tgf-BETA1 also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Calcium atom in the Integrin Alpha-V Beta-8 in Complex with Pro-Tgf-BETA1 (pdb code 6uja). 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 Alpha-V Beta-8 in Complex with Pro-Tgf-BETA1, PDB code: 6uja:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in the Integrin Alpha-V Beta-8 in Complex with Pro-Tgf-BETA1


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-8 in Complex with Pro-Tgf-BETA1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2001 b:28.5 occ:1.00 OD1 A:ASP288 2.2 13.9 1.0 OD2 A:ASP292 2.2 14.8 1.0 OD2 A:ASP288 2.3 16.7 1.0 OD1 A:ASP292 2.3 16.4 1.0 O A:TYR290 2.3 15.1 1.0 OD1 A:ASN286 2.4 16.2 1.0 CG A:ASP288 2.5 17.4 1.0 CG A:ASP292 2.6 16.9 1.0 C A:TYR290 3.4 17.5 1.0 CG A:ASN286 3.4 17.1 1.0 OD1 A:ASP284 3.5 14.8 1.0 ND2 A:ASN286 3.8 16.7 1.0 CB A:ASP288 4.0 16.6 1.0 CG A:ASP284 4.0 17.5 1.0 CB A:TYR290 4.1 15.9 1.0 CA A:TYR290 4.1 15.2 1.0 N A:TYR290 4.1 16.3 1.0 CB A:ASP292 4.1 15.5 1.0 CA A:ASP284 4.3 16.1 1.0 N A:ASP292 4.4 15.7 1.0 O A:GLN320 4.4 18.8 1.0 C A:ALA291 4.4 16.4 1.0 N A:ILE285 4.4 15.2 1.0 N A:ALA291 4.5 16.9 1.0 N A:ASN286 4.5 15.9 1.0 N A:GLN320 4.5 16.9 1.0 N A:ASP288 4.5 16.0 1.0 O A:ALA291 4.6 16.7 1.0 OD2 A:ASP284 4.6 17.0 1.0 CB A:ASP284 4.6 16.1 1.0 CA A:ASP292 4.7 15.4 1.0 CA A:ASP288 4.7 16.2 1.0 CB A:ASN286 4.7 14.9 1.0 CD2 A:LEU319 4.8 15.8 1.0 CA A:ALA291 4.8 15.9 1.0 C A:ASP284 4.8 16.3 1.0 C A:ASP288 5.0 15.7 1.0

Calcium binding site 2 out of 5 in the Integrin Alpha-V Beta-8 in Complex with Pro-Tgf-BETA1


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-8 in Complex with Pro-Tgf-BETA1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2002 b:21.5 occ:1.00 OD1 A:ASP353 2.1 20.8 1.0 OD1 A:ASP351 2.1 23.0 1.0 OD1 A:ASP357 2.2 20.5 1.0 O A:PHE355 2.2 19.5 1.0 OD1 A:ASP349 2.3 17.0 1.0 OD2 A:ASP357 2.6 19.4 1.0 CG A:ASP357 2.7 21.6 1.0 CG A:ASP353 3.0 22.0 1.0 CG A:ASP351 3.2 24.4 1.0 C A:PHE355 3.4 20.1 1.0 OD2 A:ASP353 3.5 20.1 1.0 CG A:ASP349 3.5 22.7 1.0 OD2 A:ASP351 3.7 24.1 1.0 N A:ASP353 3.9 23.0 1.0 N A:ASP351 4.0 23.5 1.0 N A:PHE355 4.1 20.0 1.0 CB A:ASP353 4.1 21.4 1.0 CB A:ASP357 4.2 19.1 1.0 CA A:PHE355 4.2 19.1 1.0 CA A:ASP349 4.2 21.9 1.0 OD2 A:ASP349 4.2 23.6 1.0 N A:LEU350 4.3 21.8 1.0 C A:ASP349 4.3 23.3 1.0 C A:ASN356 4.3 18.6 1.0 ND2 A:ASN377 4.3 22.0 1.0 N A:ASP357 4.3 18.8 1.0 CB A:ASP349 4.4 21.8 1.0 N A:ASN356 4.4 18.9 1.0 N A:GLN352 4.4 23.8 1.0 CB A:ASP351 4.4 25.4 1.0 CB A:PHE355 4.5 18.0 1.0 CA A:ASP353 4.5 22.0 1.0 CA A:ASN356 4.5 19.4 1.0 CA A:ASP351 4.5 25.1 1.0 C A:ASP351 4.6 26.5 1.0 O A:ASN356 4.6 18.9 1.0 CA A:ASP357 4.8 18.0 1.0 N A:GLY354 4.8 20.9 1.0 N A:GLY378 4.9 18.1 1.0 C A:ASP353 4.9 20.4 1.0 O A:ASP349 4.9 23.9 1.0 C A:GLN352 5.0 25.4 1.0

Calcium binding site 3 out of 5 in the Integrin Alpha-V Beta-8 in Complex with Pro-Tgf-BETA1


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-8 in Complex with Pro-Tgf-BETA1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2003 b:35.6 occ:1.00 OD1 A:ASP415 2.1 27.9 1.0 OD1 A:ASP413 2.1 25.8 1.0 OD1 A:ASP421 2.2 25.1 1.0 O A:TYR419 2.2 25.2 1.0 OD2 A:ASP421 2.7 24.7 1.0 CG A:ASP421 2.8 26.4 1.0 OD1 A:ASN417 2.8 29.7 1.0 CG A:ASP415 3.1 28.4 1.0 CG A:ASP413 3.3 27.2 1.0 C A:TYR419 3.4 27.6 1.0 OD2 A:ASP415 3.5 29.6 1.0 CG A:ASN417 3.6 30.5 1.0 OD2 A:ASP413 3.9 29.1 1.0 ND2 A:ASN417 3.9 31.6 1.0 N A:ASP415 4.2 26.9 1.0 O A:ALA437 4.2 31.2 1.0 C A:PRO420 4.2 25.2 1.0 N A:ASP421 4.2 24.5 1.0 CB A:ASP421 4.3 24.3 1.0 N A:PRO420 4.3 25.2 1.0 CB A:ASP413 4.3 24.9 1.0 CA A:ASP413 4.3 24.4 1.0 CA A:TYR419 4.3 28.8 1.0 N A:TYR419 4.3 28.5 1.0 N A:ALA437 4.3 26.4 1.0 CA A:PRO420 4.4 25.0 1.0 CB A:ASP415 4.4 27.3 1.0 N A:ILE414 4.4 25.7 1.0 N A:ASN417 4.4 29.4 1.0 O A:PRO420 4.5 25.7 1.0 CB A:TYR419 4.6 29.1 1.0 CA A:ASP415 4.6 26.4 1.0 N A:LYS416 4.6 27.3 1.0 CA A:ASP421 4.7 23.0 1.0 C A:ASP413 4.7 24.8 1.0 CB A:ASN417 4.7 30.8 1.0 CB A:ALA437 4.8 28.0 1.0 C A:ASP415 4.8 27.4 1.0 CA A:ALA437 4.9 27.1 1.0 C A:ALA437 5.0 30.9 1.0

Calcium binding site 4 out of 5 in the Integrin Alpha-V Beta-8 in Complex with Pro-Tgf-BETA1


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-8 in Complex with Pro-Tgf-BETA1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2004 b:23.6 occ:1.00 OD1 A:ASP234 2.2 16.6 1.0 OD1 A:ASP238 2.2 17.1 1.0 OD2 A:ASP238 2.3 15.0 1.0 O A:ILE236 2.3 15.9 1.0 OD2 A:ASP234 2.3 18.2 1.0 OD1 A:ASN232 2.4 17.3 1.0 CG A:ASP238 2.5 17.9 1.0 CG A:ASP234 2.6 17.6 1.0 CG A:ASN232 3.3 17.4 1.0 C A:ILE236 3.4 17.7 1.0 ND2 A:ASN232 3.5 17.2 1.0 OD1 A:ASP230 3.8 17.8 1.0 CB A:ASP238 4.0 16.5 1.0 CB A:ASP234 4.0 16.6 1.0 CA A:ILE236 4.1 16.7 1.0 CB A:ILE236 4.1 17.0 1.0 N A:ILE236 4.1 16.9 1.0 N A:ASP238 4.2 16.6 1.0 CG A:ASP230 4.2 17.3 1.0 C A:ASP237 4.3 17.2 1.0 CA A:ASP238 4.4 16.3 1.0 N A:ASP234 4.5 16.6 1.0 N A:ASP237 4.5 16.2 1.0 N A:ASN232 4.5 16.2 1.0 N A:PHE231 4.6 15.2 1.0 CB A:ASN232 4.6 17.3 1.0 OD2 A:ASP230 4.6 17.1 1.0 O A:ASP237 4.6 17.5 1.0 CA A:ASP230 4.6 15.7 1.0 N A:GLY258 4.7 16.3 1.0 CA A:ASP237 4.7 16.8 1.0 CG2 A:ILE236 4.7 17.7 1.0 CA A:ASP234 4.7 15.7 1.0 CB A:ASP230 4.8 16.5 1.0 CA A:ASN232 5.0 16.8 1.0 N A:GLY235 5.0 16.8 1.0

Calcium binding site 5 out of 5 in the Integrin Alpha-V Beta-8 in Complex with Pro-Tgf-BETA1


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-8 in Complex with Pro-Tgf-BETA1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2001 b:25.5 occ:1.00 OD1 B:ASP209 2.1 23.1 1.0 OD2 B:ASP151 2.1 22.4 1.0 O B:PRO211 2.2 20.4 1.0 O B:ASP209 2.3 22.8 1.0 OD1 B:ASN207 2.4 23.5 1.0 OE1 B:GLU212 2.9 23.1 1.0 CG B:ASP209 3.0 23.0 1.0 CG B:ASN207 3.1 24.9 1.0 C B:ASP209 3.3 23.2 1.0 CG B:ASP151 3.3 22.2 1.0 C B:PRO211 3.4 21.2 1.0 ND2 B:ASN207 3.4 23.7 1.0 OD2 B:ASP209 3.5 22.1 1.0 CD B:GLU212 3.7 22.9 1.0 CA B:ASP209 3.9 23.4 1.0 N B:ASP209 4.0 22.9 1.0 CB B:ASP209 4.0 22.2 1.0 CB B:ASP151 4.1 22.1 1.0 N B:PRO211 4.1 22.1 1.0 C B:THR210 4.1 22.4 1.0 OE2 B:GLU212 4.1 23.7 1.0 CA B:GLU212 4.2 21.6 1.0 OD1 B:ASP151 4.2 21.5 1.0 N B:GLU212 4.2 21.9 1.0 O B:THR210 4.3 23.2 1.0 CB B:ASN207 4.3 23.7 1.0 NE2 B:HIS247 4.3 21.3 1.0 N B:THR210 4.3 22.9 1.0 CA B:PRO211 4.4 23.5 1.0 CD B:PRO211 4.6 22.3 1.0 CG B:GLU212 4.7 22.8 1.0 CA B:THR210 4.7 21.8 1.0 CD2 B:HIS247 4.8 21.2 1.0 C B:ILE208 4.9 23.8 1.0 CB B:GLU212 4.9 22.4 1.0

M.G.Campbell, A.Cormier, S.Ito, R.I.Seed, A.J.Bondesson, J.Lou, J.D.Marks, J.L.Baron, Y.Cheng, S.L.Nishimura. Cryo-Em Reveals Integrin-Mediated Tgf-Beta Activation Without Release From Latent Tgf-Beta. Cell 2020.
ISSN: ISSN 1097-4172
PubMed: 31955848
DOI: 10.1016/J.CELL.2019.12.030