Calcium in PDB 6ujc: Integrin Alpha-V Beta-8 in Complex with the Fabs C6-RGD3 and 11D12V2

The structure of Integrin Alpha-V Beta-8 in Complex with the Fabs C6-RGD3 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 C6-RGD3 and 11D12V2 (pdb code 6ujc). 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 C6-RGD3 and 11D12V2, PDB code: 6ujc:
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 C6-RGD3 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 C6-RGD3 and 11D12V2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2001 b:73.5 occ:1.00 OD1 A:ASP288 2.2 70.6 1.0 OD2 A:ASP292 2.2 69.5 1.0 O A:TYR290 2.3 70.5 1.0 OD2 A:ASP288 2.3 70.3 1.0 OD1 A:ASP292 2.3 69.5 1.0 OD1 A:ASN286 2.5 72.8 1.0 CG A:ASP288 2.5 73.8 1.0 CG A:ASP292 2.6 69.2 1.0 OD1 A:ASP284 3.4 72.3 1.0 C A:TYR290 3.4 71.4 1.0 CG A:ASN286 3.5 72.1 1.0 ND2 A:ASN286 3.9 72.2 1.0 CG A:ASP284 3.9 72.0 1.0 CB A:ASP288 4.0 72.4 1.0 N A:TYR290 4.0 71.7 1.0 CA A:TYR290 4.0 70.8 1.0 CB A:ASP292 4.0 67.7 1.0 CB A:TYR290 4.1 71.2 1.0 CA A:ASP284 4.1 71.4 1.0 N A:ILE285 4.3 70.9 1.0 N A:ASP292 4.3 69.0 1.0 C A:ALA291 4.3 68.8 1.0 O A:GLN320 4.4 70.7 1.0 CB A:ASP284 4.4 71.0 1.0 N A:ALA291 4.4 69.7 1.0 N A:ASP288 4.5 72.2 1.0 OD2 A:ASP284 4.5 72.4 1.0 N A:ASN286 4.5 71.6 1.0 O A:ALA291 4.6 68.5 1.0 CA A:ASP292 4.6 66.3 1.0 N A:GLN320 4.6 67.4 1.0 C A:ASP284 4.7 70.7 1.0 CA A:ASP288 4.7 73.1 1.0 CA A:ALA291 4.7 68.8 1.0 CB A:ASN286 4.8 71.7 1.0 CD2 A:LEU319 4.8 69.6 1.0 O A:THR283 4.9 69.5 1.0 C A:ASP288 4.9 72.5 1.0 N A:ASP289 5.0 72.7 1.0

Calcium binding site 2 out of 5 in the Integrin Alpha-V Beta-8 in Complex with the Fabs C6-RGD3 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 C6-RGD3 and 11D12V2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2002 b:52.5 occ:1.00 OD1 A:ASP351 2.1 78.9 1.0 OD1 A:ASP353 2.1 76.3 1.0 OD1 A:ASP349 2.2 84.1 1.0 O A:PHE355 2.2 65.8 1.0 OD1 A:ASP357 2.2 74.2 1.0 OD2 A:ASP357 2.5 74.8 1.0 CG A:ASP357 2.7 80.5 1.0 CG A:ASP353 3.0 79.3 1.0 CG A:ASP351 3.2 80.7 1.0 CG A:ASP349 3.3 77.5 1.0 C A:PHE355 3.4 80.4 1.0 OD2 A:ASP353 3.6 77.0 1.0 OD2 A:ASP351 3.7 81.1 1.0 N A:ASP353 3.9 81.7 1.0 CA A:ASP349 3.9 75.3 1.0 N A:ASP351 4.0 77.8 1.0 N A:PHE355 4.0 75.9 1.0 OD2 A:ASP349 4.1 80.6 1.0 CB A:ASP353 4.1 76.5 1.0 C A:ASP349 4.2 80.0 1.0 CB A:ASP349 4.2 80.2 1.0 CA A:PHE355 4.2 77.4 1.0 CB A:ASP357 4.2 75.1 1.0 C A:ASN356 4.3 75.7 1.0 N A:GLN352 4.3 79.0 1.0 N A:LEU350 4.3 73.9 1.0 N A:ASP357 4.3 74.4 1.0 CB A:ASP351 4.4 80.2 1.0 N A:ASN356 4.4 75.6 1.0 ND2 A:ASN377 4.4 76.2 1.0 CA A:ASN356 4.5 76.0 1.0 CA A:ASP351 4.5 78.8 1.0 CA A:ASP353 4.5 79.5 1.0 CB A:PHE355 4.5 74.2 1.0 C A:ASP351 4.5 79.5 1.0 O A:ASN356 4.6 77.0 1.0 O A:ASP349 4.7 78.0 1.0 N A:GLY354 4.8 78.2 1.0 CA A:ASP357 4.8 72.4 1.0 O A:GLY348 4.9 72.7 1.0 N A:GLY378 4.9 73.0 1.0 C A:ASP353 4.9 79.4 1.0 C A:GLN352 4.9 79.5 1.0 CA A:GLN352 5.0 78.3 1.0

Calcium binding site 3 out of 5 in the Integrin Alpha-V Beta-8 in Complex with the Fabs C6-RGD3 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 C6-RGD3 and 11D12V2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2003 b:58.1 occ:1.00 OD1 A:ASP415 2.1 82.0 1.0 OD1 A:ASP413 2.1 0.9 1.0 O A:TYR419 2.2 75.6 1.0 OD1 A:ASP421 2.2 76.0 1.0 OD2 A:ASP421 2.6 79.7 1.0 CG A:ASP421 2.7 80.6 1.0 OD1 A:ASN417 2.7 81.1 1.0 CG A:ASP415 3.1 83.0 1.0 CG A:ASP413 3.3 74.9 1.0 C A:TYR419 3.4 82.4 1.0 CG A:ASN417 3.5 81.5 1.0 OD2 A:ASP415 3.6 83.3 1.0 ND2 A:ASN417 3.9 84.1 1.0 OD2 A:ASP413 4.0 80.8 1.0 N A:ASP415 4.1 80.4 1.0 CB A:ASP421 4.2 78.0 1.0 C A:PRO420 4.2 77.1 1.0 N A:ASP421 4.2 76.4 1.0 CA A:ASP413 4.2 77.6 1.0 N A:PRO420 4.2 78.6 1.0 CA A:TYR419 4.3 79.2 1.0 O A:ALA437 4.3 83.4 1.0 N A:ALA437 4.3 79.7 1.0 CB A:ASP413 4.3 79.3 1.0 N A:TYR419 4.3 79.7 1.0 N A:ILE414 4.3 78.2 1.0 CB A:ASP415 4.4 82.0 1.0 CA A:PRO420 4.4 77.7 1.0 O A:PRO420 4.5 78.2 1.0 N A:ASN417 4.5 79.7 1.0 CB A:TYR419 4.5 80.4 1.0 CA A:ASP415 4.6 80.2 1.0 CA A:ASP421 4.6 76.9 1.0 C A:ASP413 4.7 77.2 1.0 N A:LYS416 4.7 80.0 1.0 CB A:ALA437 4.7 81.0 1.0 CB A:ASN417 4.7 81.1 1.0 C A:ASP415 4.8 80.7 1.0 CA A:ALA437 4.9 81.0 1.0 CB A:ARG436 4.9 79.9 1.0

Calcium binding site 4 out of 5 in the Integrin Alpha-V Beta-8 in Complex with the Fabs C6-RGD3 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 C6-RGD3 and 11D12V2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2004 b:63.5 occ:1.00 OD1 A:ASP234 2.2 68.8 1.0 OD2 A:ASP238 2.2 66.5 1.0 O A:ILE236 2.2 68.1 1.0 OD1 A:ASP238 2.3 68.2 1.0 OD2 A:ASP234 2.3 67.8 1.0 OD1 A:ASN232 2.4 69.1 1.0 CG A:ASP238 2.5 67.2 1.0 CG A:ASP234 2.6 68.7 1.0 CG A:ASN232 3.3 68.5 1.0 C A:ILE236 3.4 67.9 1.0 ND2 A:ASN232 3.5 67.5 1.0 OD1 A:ASP230 3.8 68.3 1.0 CB A:ILE236 3.9 67.4 1.0 CA A:ILE236 4.0 67.6 1.0 CB A:ASP238 4.0 65.5 1.0 CB A:ASP234 4.0 68.5 1.0 N A:ILE236 4.0 68.8 1.0 CG A:ASP230 4.2 68.6 1.0 N A:ASP238 4.2 65.9 1.0 C A:ASP237 4.3 66.7 1.0 N A:ASP237 4.5 67.3 1.0 N A:ASP234 4.5 68.2 1.0 CA A:ASP238 4.5 65.5 1.0 N A:ASN232 4.5 68.1 1.0 CG2 A:ILE236 4.6 67.0 1.0 N A:PHE231 4.6 67.7 1.0 OD2 A:ASP230 4.6 68.3 1.0 O A:ASP237 4.6 66.6 1.0 CB A:ASN232 4.6 68.2 1.0 CA A:ASP230 4.6 66.7 1.0 CA A:ASP234 4.7 68.6 1.0 CA A:ASP237 4.7 67.4 1.0 N A:GLY258 4.8 66.8 1.0 CB A:ASP230 4.9 67.6 1.0 N A:GLY235 5.0 68.4 1.0 C A:ASP234 5.0 68.9 1.0

Calcium binding site 5 out of 5 in the Integrin Alpha-V Beta-8 in Complex with the Fabs C6-RGD3 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 C6-RGD3 and 11D12V2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2001 b:56.0 occ:1.00 OD2 B:ASP151 2.1 51.7 1.0 OD1 B:ASP209 2.2 53.8 1.0 O B:PRO211 2.2 53.5 1.0 O B:ASP209 2.2 53.0 1.0 OD1 B:ASN207 2.3 51.4 1.0 CG B:ASP209 2.9 52.7 1.0 OE1 B:GLU212 3.0 51.3 1.0 CG B:ASN207 3.3 51.7 1.0 C B:ASP209 3.3 52.5 1.0 OD2 B:ASP209 3.3 52.7 1.0 CG B:ASP151 3.3 51.6 1.0 C B:PRO211 3.4 52.4 1.0 CD B:GLU212 3.7 51.8 1.0 CB B:ASP209 3.9 53.2 1.0 CB B:ASP151 4.0 50.2 1.0 C B:THR210 4.0 52.5 1.0 CA B:ASP209 4.0 52.7 1.0 ND2 B:ASN207 4.0 52.4 1.0 O B:THR210 4.1 53.4 1.0 N B:PRO211 4.1 52.3 1.0 OE2 B:GLU212 4.1 51.7 1.0 CB B:ASN207 4.1 52.1 1.0 NE2 B:HIS247 4.2 53.2 1.0 CA B:GLU212 4.2 50.8 1.0 N B:ASP209 4.2 53.6 1.0 OD1 B:ASP151 4.2 52.1 1.0 N B:THR210 4.2 52.7 1.0 N B:GLU212 4.2 51.5 1.0 CA B:PRO211 4.4 51.3 1.0 CA B:THR210 4.5 52.6 1.0 CD B:PRO211 4.7 53.6 1.0 CD2 B:HIS247 4.8 52.1 1.0 CG B:GLU212 4.8 51.4 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