Calcium in PDB 6ujb: Integrin Alpha-V Beta-8 in Complex with the Fabs C6D4 and 11D12V2

The structure of Integrin Alpha-V Beta-8 in Complex with the Fabs C6D4 and 11D12V2 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 the Fabs C6D4 and 11D12V2 (pdb code 6ujb). 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 the Fabs C6D4 and 11D12V2, PDB code: 6ujb:
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 the Fabs C6D4 and 11D12V2


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 the Fabs C6D4 and 11D12V2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2001 b:30.5 occ:1.00 OD2 A:ASP292 2.2 40.4 1.0 OD1 A:ASP288 2.2 41.1 1.0 O A:TYR290 2.3 42.2 1.0 OD2 A:ASP288 2.3 40.4 1.0 OD1 A:ASP292 2.3 40.2 1.0 OD1 A:ASN286 2.5 42.1 1.0 CG A:ASP292 2.5 41.5 1.0 CG A:ASP288 2.6 43.1 1.0 OD1 A:ASP284 3.4 40.0 1.0 C A:TYR290 3.4 40.1 1.0 CG A:ASN286 3.5 40.2 1.0 ND2 A:ASN286 3.9 39.6 1.0 CG A:ASP284 3.9 42.0 1.0 CB A:ASP288 4.0 41.4 1.0 CB A:ASP292 4.0 36.1 1.0 N A:TYR290 4.1 42.2 1.0 CA A:TYR290 4.1 41.7 1.0 CB A:TYR290 4.1 41.7 1.0 CA A:ASP284 4.2 38.6 1.0 N A:ASP292 4.2 37.1 1.0 C A:ALA291 4.3 37.9 1.0 N A:ILE285 4.3 39.9 1.0 N A:ALA291 4.5 39.3 1.0 CB A:ASP284 4.5 38.1 1.0 N A:ASN286 4.5 40.5 1.0 N A:ASP288 4.5 40.8 1.0 OD2 A:ASP284 4.5 43.0 1.0 O A:ALA291 4.5 38.4 1.0 O A:GLN320 4.5 42.4 1.0 CA A:ASP292 4.6 36.1 1.0 C A:ASP284 4.6 40.3 1.0 N A:GLN320 4.6 39.4 1.0 CA A:ALA291 4.7 37.2 1.0 CA A:ASP288 4.7 41.3 1.0 CB A:ASN286 4.8 39.6 1.0 CD2 A:LEU319 4.9 38.1 1.0 O A:THR283 4.9 38.1 1.0 C A:ASP288 5.0 43.0 1.0

Calcium binding site 2 out of 5 in the Integrin Alpha-V Beta-8 in Complex with the Fabs C6D4 and 11D12V2


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 the Fabs C6D4 and 11D12V2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2002 b:19.9 occ:1.00 OD1 A:ASP351 2.1 50.0 1.0 OD1 A:ASP353 2.1 52.6 1.0 OD1 A:ASP349 2.2 39.0 1.0 OD1 A:ASP357 2.2 47.0 1.0 O A:PHE355 2.2 51.4 1.0 OD2 A:ASP357 2.6 43.4 1.0 CG A:ASP357 2.7 43.4 1.0 CG A:ASP353 3.0 45.2 1.0 CG A:ASP351 3.2 45.0 1.0 CG A:ASP349 3.4 48.8 1.0 C A:PHE355 3.4 42.7 1.0 OD2 A:ASP353 3.6 45.2 1.0 OD2 A:ASP351 3.7 45.4 1.0 N A:ASP353 3.9 47.1 1.0 N A:ASP351 4.0 45.2 1.0 CA A:ASP349 4.0 44.6 1.0 N A:PHE355 4.0 45.5 1.0 CB A:ASP353 4.1 47.4 1.0 OD2 A:ASP349 4.1 45.6 1.0 C A:ASP349 4.1 44.6 1.0 N A:LEU350 4.2 44.4 1.0 CA A:PHE355 4.2 43.7 1.0 CB A:ASP357 4.2 40.0 1.0 CB A:ASP349 4.2 44.0 1.0 C A:ASN356 4.3 40.9 1.0 N A:ASP357 4.3 40.3 1.0 N A:GLN352 4.3 46.2 1.0 ND2 A:ASN377 4.4 43.1 1.0 N A:ASN356 4.4 41.8 1.0 CB A:ASP351 4.4 47.4 1.0 CA A:ASN356 4.5 42.0 1.0 CB A:PHE355 4.5 45.0 1.0 CA A:ASP353 4.5 46.3 1.0 CA A:ASP351 4.5 46.5 1.0 C A:ASP351 4.5 48.0 1.0 O A:ASN356 4.7 41.8 1.0 N A:GLY354 4.7 46.5 1.0 O A:ASP349 4.8 45.4 1.0 CA A:ASP357 4.8 39.5 1.0 C A:ASP353 4.9 47.0 1.0 O A:GLY348 4.9 43.1 1.0 C A:GLN352 4.9 48.1 1.0 C A:LEU350 5.0 46.6 1.0 N A:GLY378 5.0 40.9 1.0

Calcium binding site 3 out of 5 in the Integrin Alpha-V Beta-8 in Complex with the Fabs C6D4 and 11D12V2


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 the Fabs C6D4 and 11D12V2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2003 b:38.1 occ:1.00 OD1 A:ASP415 2.1 48.3 1.0 OD1 A:ASP413 2.1 47.5 1.0 O A:TYR419 2.2 47.1 1.0 OD1 A:ASP421 2.2 45.8 1.0 OD2 A:ASP421 2.8 46.8 1.0 CG A:ASP421 2.8 46.7 1.0 OD1 A:ASN417 2.8 47.5 1.0 CG A:ASP415 3.1 46.7 1.0 CG A:ASP413 3.3 47.7 1.0 C A:TYR419 3.4 45.2 1.0 OD2 A:ASP415 3.5 47.0 1.0 CG A:ASN417 3.6 47.3 1.0 OD2 A:ASP413 3.9 49.0 1.0 ND2 A:ASN417 4.0 46.5 1.0 O A:ALA437 4.1 47.8 1.0 C A:PRO420 4.2 42.9 1.0 N A:ASP415 4.2 49.3 1.0 N A:ASP421 4.2 42.7 1.0 N A:PRO420 4.3 43.8 1.0 CB A:ASP421 4.3 42.4 1.0 CA A:TYR419 4.3 46.1 1.0 N A:ALA437 4.3 44.5 1.0 CB A:ASP413 4.3 45.6 1.0 N A:TYR419 4.3 46.1 1.0 CA A:ASP413 4.3 45.5 1.0 CA A:PRO420 4.4 43.9 1.0 CB A:ASP415 4.4 48.0 1.0 N A:ILE414 4.5 47.5 1.0 CB A:TYR419 4.5 46.4 1.0 N A:ASN417 4.5 48.2 1.0 O A:PRO420 4.5 44.0 1.0 CB A:ALA437 4.6 44.5 1.0 N A:LYS416 4.6 48.7 1.0 CA A:ASP421 4.6 41.5 1.0 CA A:ASP415 4.7 48.4 1.0 C A:ASP413 4.7 47.1 1.0 C A:ASP415 4.8 48.8 1.0 CB A:ASN417 4.8 48.3 1.0 CA A:ALA437 4.9 45.0 1.0 C A:ALA437 4.9 47.8 1.0

Calcium binding site 4 out of 5 in the Integrin Alpha-V Beta-8 in Complex with the Fabs C6D4 and 11D12V2


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 the Fabs C6D4 and 11D12V2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2004 b:35.0 occ:1.00 OD1 A:ASP234 2.2 43.1 1.0 OD1 A:ASP238 2.2 41.1 1.0 O A:ILE236 2.2 41.1 1.0 OD2 A:ASP238 2.3 37.4 1.0 OD2 A:ASP234 2.3 39.6 1.0 OD1 A:ASN232 2.4 41.2 1.0 CG A:ASP238 2.5 40.1 1.0 CG A:ASP234 2.5 41.9 1.0 CG A:ASN232 3.3 40.0 1.0 C A:ILE236 3.4 40.1 1.0 ND2 A:ASN232 3.5 39.6 1.0 OD1 A:ASP230 3.8 40.6 1.0 CB A:ASP238 4.0 37.5 1.0 CB A:ILE236 4.0 40.7 1.0 CB A:ASP234 4.0 40.9 1.0 CA A:ILE236 4.0 40.4 1.0 N A:ILE236 4.1 41.5 1.0 N A:ASP238 4.1 38.6 1.0 CG A:ASP230 4.2 40.5 1.0 C A:ASP237 4.3 39.3 1.0 CA A:ASP238 4.4 37.6 1.0 N A:ASP237 4.5 39.6 1.0 N A:ASP234 4.5 41.5 1.0 O A:ASP237 4.6 38.7 1.0 N A:ASN232 4.6 40.1 1.0 OD2 A:ASP230 4.6 39.8 1.0 CG2 A:ILE236 4.6 40.5 1.0 CB A:ASN232 4.6 40.4 1.0 N A:PHE231 4.6 39.8 1.0 CA A:ASP230 4.7 38.0 1.0 N A:GLY258 4.7 39.3 1.0 CA A:ASP237 4.7 39.1 1.0 CA A:ASP234 4.7 40.7 1.0 CB A:ASP230 4.9 38.4 1.0 N A:GLY235 5.0 40.6 1.0

Calcium binding site 5 out of 5 in the Integrin Alpha-V Beta-8 in Complex with the Fabs C6D4 and 11D12V2


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 the Fabs C6D4 and 11D12V2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2001 b:25.3 occ:1.00 OD2 B:ASP151 2.1 25.7 1.0 OD1 B:ASP209 2.1 27.3 1.0 O B:PRO211 2.2 26.3 1.0 O B:ASP209 2.3 27.5 1.0 OD1 B:ASN207 2.4 27.3 1.0 CG B:ASP209 3.0 26.5 1.0 CG B:ASN207 3.1 26.2 1.0 OE1 B:GLU212 3.3 25.4 1.0 C B:ASP209 3.3 27.4 1.0 CG B:ASP151 3.3 25.4 1.0 C B:PRO211 3.4 26.9 1.0 OD2 B:ASP209 3.5 26.4 1.0 ND2 B:ASN207 3.6 26.1 1.0 CA B:ASP209 3.9 27.3 1.0 N B:ASP209 4.0 27.5 1.0 CD B:GLU212 4.0 26.2 1.0 C B:THR210 4.0 27.3 1.0 CB B:ASP209 4.0 26.7 1.0 O B:THR210 4.1 28.1 1.0 N B:PRO211 4.1 27.2 1.0 CB B:ASP151 4.1 24.7 1.0 OD1 B:ASP151 4.1 25.7 1.0 CB B:ASN207 4.2 26.3 1.0 CA B:GLU212 4.3 25.4 1.0 N B:GLU212 4.3 25.9 1.0 N B:THR210 4.3 27.5 1.0 CA B:PRO211 4.4 26.5 1.0 NE2 B:HIS247 4.4 26.0 1.0 OE2 B:GLU212 4.5 25.6 1.0 CD B:PRO211 4.6 28.2 1.0 CA B:THR210 4.6 27.3 1.0 O B:TYR157 4.8 27.3 1.0 CG B:GLU212 4.9 25.9 1.0 C B:ILE208 4.9 27.5 1.0 CD2 B:HIS247 4.9 25.8 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