Calcium in PDB 8tcg: Integrin Alpha-V Beta-6 in Complex with Minibinder B6_BP_DSLF

The structure of Integrin Alpha-V Beta-6 in Complex with Minibinder B6_BP_DSLF also contains other interesting chemical elements:

Manganese

(Mn)

3 atoms

The binding sites of Calcium atom in the Integrin Alpha-V Beta-6 in Complex with Minibinder B6_BP_DSLF (pdb code 8tcg). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Integrin Alpha-V Beta-6 in Complex with Minibinder B6_BP_DSLF, PDB code: 8tcg:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Integrin Alpha-V Beta-6 in Complex with Minibinder B6_BP_DSLF


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 Minibinder B6_BP_DSLF within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2001 b:72.2 occ:1.00 OD1 A:ASP288 2.1 71.8 1.0 OD2 A:ASP292 2.2 72.0 1.0 O A:TYR290 2.2 72.0 1.0 OD1 A:ASP284 2.2 71.8 1.0 OD1 A:ASP292 2.6 72.3 1.0 OD1 A:ASN286 2.6 71.2 1.0 OD2 A:ASP288 2.6 71.9 1.0 CG A:ASP288 2.7 71.9 1.0 CG A:ASP292 2.7 71.9 1.0 HA A:ASP284 3.0 85.4 1.0 CG A:ASP284 3.3 71.7 1.0 H A:ASP288 3.3 86.0 1.0 H A:TYR290 3.3 86.4 1.0 H A:ASN286 3.3 85.0 1.0 C A:TYR290 3.4 72.0 1.0 H A:ILE285 3.4 85.1 1.0 HB2 A:TYR290 3.5 87.5 1.0 CG A:ASN286 3.7 71.4 1.0 HD21 A:ASN286 3.7 86.2 1.0 CA A:ASP284 3.8 71.2 1.0 N A:TYR290 4.0 72.0 1.0 H A:GLN320 4.0 87.4 1.0 CB A:ASP284 4.0 71.3 1.0 N A:ILE285 4.0 70.9 1.0 CB A:ASP288 4.1 71.9 1.0 CA A:TYR290 4.1 72.3 1.0 OD2 A:ASP284 4.1 71.7 1.0 CB A:ASP292 4.1 72.0 1.0 ND2 A:ASN286 4.2 71.8 1.0 N A:ASP288 4.2 71.7 1.0 C A:ASP284 4.2 70.9 1.0 HB2 A:ASP284 4.3 85.6 1.0 CB A:TYR290 4.3 72.9 1.0 N A:ASP292 4.3 72.1 1.0 N A:ASN286 4.3 70.8 1.0 C A:ALA291 4.3 72.1 1.0 HB3 A:GLN320 4.4 87.6 1.0 HG22 A:ILE285 4.4 85.2 1.0 HA A:ALA291 4.4 86.9 1.0 H A:ASP292 4.4 86.5 1.0 N A:ALA291 4.4 72.5 1.0 HB3 A:ASP288 4.5 86.2 1.0 HG A:LEU319 4.5 86.5 1.0 HB2 A:ASP292 4.5 86.3 1.0 H A:GLY287 4.5 85.6 1.0 CA A:ASP288 4.5 71.9 1.0 O A:GLN320 4.6 72.9 1.0 H A:ASP289 4.6 86.3 1.0 O A:ALA291 4.7 73.0 1.0 CA A:ALA291 4.7 72.4 1.0 CA A:ASP292 4.7 72.0 1.0 HB3 A:TYR290 4.7 87.5 1.0 HA A:ASP292 4.8 86.4 1.0 HB2 A:ASP288 4.8 86.2 1.0 C A:ASP288 4.8 72.0 1.0 N A:ASP289 4.8 71.9 1.0 HA A:LEU319 4.8 87.0 1.0 O A:THR283 4.8 71.8 1.0 N A:GLY287 4.8 71.3 1.0 N A:GLN320 4.8 72.8 1.0 HB3 A:ASP292 4.8 86.3 1.0 CB A:ASN286 4.9 70.8 1.0 HD2 A:TYR290 4.9 87.0 1.0 HB3 A:ASP284 5.0 85.6 1.0

Calcium binding site 2 out of 4 in the Integrin Alpha-V Beta-6 in Complex with Minibinder B6_BP_DSLF


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 Minibinder B6_BP_DSLF within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2002 b:82.2 occ:1.00 OD2 A:ASP357 2.1 70.0 1.0 OD1 A:ASP353 2.1 69.9 1.0 OD1 A:ASP351 2.1 70.3 1.0 OD1 A:ASP349 2.2 69.4 1.0 O A:PHE355 2.2 69.8 1.0 CG A:ASP357 2.9 70.0 1.0 H A:ASP353 2.9 84.9 1.0 CG A:ASP353 3.0 70.6 1.0 OD1 A:ASP357 3.0 69.8 1.0 H A:ASP351 3.0 84.4 1.0 HA A:ASP349 3.2 84.1 1.0 CG A:ASP351 3.2 71.1 1.0 H A:PHE355 3.3 84.5 1.0 CG A:ASP349 3.3 71.1 1.0 OD2 A:ASP353 3.4 70.6 1.0 C A:PHE355 3.4 69.7 1.0 OD2 A:ASP351 3.6 71.0 1.0 HB2 A:PHE355 3.8 84.4 1.0 H A:LEU350 3.8 83.7 1.0 N A:ASP353 3.9 70.8 1.0 CA A:ASP349 3.9 70.1 1.0 HD22 A:ASN377 4.0 84.5 1.0 N A:ASP351 4.0 70.4 1.0 N A:PHE355 4.0 70.4 1.0 N A:LEU350 4.1 69.8 1.0 C A:ASP349 4.1 70.2 1.0 CB A:ASP353 4.1 70.9 1.0 OD2 A:ASP349 4.1 70.6 1.0 HA A:ASN356 4.2 83.5 1.0 CA A:PHE355 4.2 70.2 1.0 H A:GLN352 4.2 85.0 1.0 CB A:ASP349 4.2 70.2 1.0 CB A:ASP357 4.3 69.7 1.0 HB3 A:ASP353 4.3 85.1 1.0 H A:GLY378 4.4 84.1 1.0 H A:GLY354 4.4 84.8 1.0 N A:GLN352 4.4 70.8 1.0 N A:ASP357 4.4 69.4 1.0 C A:ASN356 4.4 69.4 1.0 N A:ASN356 4.5 69.9 1.0 CB A:ASP351 4.5 71.2 1.0 CA A:ASP353 4.5 70.8 1.0 CB A:PHE355 4.5 70.3 1.0 H A:ASP357 4.5 83.3 1.0 HB2 A:ASP357 4.5 83.7 1.0 HB3 A:LEU350 4.6 84.8 1.0 CA A:ASP351 4.6 71.1 1.0 CA A:ASN356 4.6 69.5 1.0 C A:ASP351 4.6 71.1 1.0 HB2 A:ASP349 4.7 84.3 1.0 N A:GLY354 4.7 70.6 1.0 O A:ASP349 4.7 70.6 1.0 O A:ASN356 4.8 70.1 1.0 ND2 A:ASN377 4.8 70.4 1.0 C A:ASP353 4.8 70.7 1.0 O A:GLY348 4.8 70.3 1.0 CA A:ASP357 4.9 69.3 1.0 C A:GLN352 4.9 71.0 1.0 CA A:LEU350 5.0 70.2 1.0 C A:LEU350 5.0 70.6 1.0 HB3 A:PHE355 5.0 84.4 1.0

Calcium binding site 3 out of 4 in the Integrin Alpha-V Beta-6 in Complex with Minibinder B6_BP_DSLF


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 Minibinder B6_BP_DSLF within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2003 b:71.4 occ:1.00 OD1 A:ASP416 2.1 70.8 1.0 OD1 A:ASP414 2.1 70.5 1.0 OD2 A:ASP422 2.1 70.8 1.0 O A:TYR420 2.2 70.6 1.0 OD1 A:ASP422 2.6 70.8 1.0 OD1 A:ASN418 2.7 70.8 1.0 CG A:ASP422 2.7 70.5 1.0 HA A:ASP414 2.9 84.8 1.0 H A:ASP416 3.0 85.4 1.0 CG A:ASP416 3.2 70.9 1.0 CG A:ASP414 3.2 70.6 1.0 H A:ASN418 3.3 85.0 1.0 H A:ILE415 3.3 85.1 1.0 C A:TYR420 3.4 70.2 1.0 H A:TYR420 3.6 85.3 1.0 CG A:ASN418 3.6 71.0 1.0 OD2 A:ASP416 3.7 70.8 1.0 CA A:ASP414 3.7 70.7 1.0 H A:ALA438 3.8 85.3 1.0 N A:ILE415 3.8 70.9 1.0 CB A:ASP414 4.0 70.5 1.0 HB2 A:TYR420 4.0 85.7 1.0 HD21 A:ASN418 4.0 85.7 1.0 N A:ASP416 4.0 71.2 1.0 HG22 A:ILE415 4.0 86.3 1.0 HB3 A:ALA438 4.0 86.0 1.0 C A:ASP414 4.0 70.8 1.0 H A:LYS417 4.1 85.1 1.0 OD2 A:ASP414 4.1 70.7 1.0 HA A:PRO421 4.1 84.0 1.0 ND2 A:ASN418 4.2 71.4 1.0 CB A:ASP422 4.2 70.5 1.0 N A:TYR420 4.2 71.1 1.0 N A:ASN418 4.3 70.8 1.0 CA A:TYR420 4.3 70.4 1.0 N A:ASP422 4.3 70.2 1.0 C A:PRO421 4.3 70.1 1.0 N A:PRO421 4.3 70.2 1.0 HB2 A:ASP414 4.3 84.6 1.0 H A:ASP422 4.4 84.3 1.0 CB A:ASP416 4.5 71.3 1.0 N A:LYS417 4.5 70.9 1.0 CA A:PRO421 4.5 70.0 1.0 O A:ALA438 4.5 71.7 1.0 HB2 A:ASP422 4.6 84.6 1.0 CA A:ASP416 4.6 71.3 1.0 H A:GLY419 4.6 85.0 1.0 CB A:TYR420 4.6 71.4 1.0 CB A:ASN418 4.7 70.7 1.0 O A:PRO421 4.7 70.4 1.0 CA A:ASP422 4.7 70.3 1.0 C A:ASP416 4.7 71.0 1.0 N A:ALA438 4.8 71.1 1.0 HA A:ASP422 4.8 84.4 1.0 HB3 A:ASN418 4.8 84.8 1.0 O A:THR413 4.8 70.8 1.0 HA A:ARG437 4.9 85.4 1.0 HB3 A:ASP422 4.9 84.6 1.0 HB3 A:ARG437 4.9 85.4 1.0 CA A:ILE415 4.9 71.2 1.0 HB3 A:ASP414 4.9 84.6 1.0 C A:ILE415 4.9 71.4 1.0 HB3 A:ASP416 4.9 85.6 1.0 CA A:ASN418 5.0 70.6 1.0 HG2 A:ARG437 5.0 85.5 1.0 N A:ASP414 5.0 70.3 1.0 O A:ASP414 5.0 71.3 1.0 CG2 A:ILE415 5.0 71.9 1.0

Calcium binding site 4 out of 4 in the Integrin Alpha-V Beta-6 in Complex with Minibinder B6_BP_DSLF


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 Minibinder B6_BP_DSLF within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2004 b:78.3 occ:1.00 OD1 A:ASP234 2.2 78.2 1.0 O A:ILE236 2.2 77.8 1.0 OD1 A:ASP238 2.2 77.1 1.0 OD2 A:ASP238 2.2 77.5 1.0 OD2 A:ASP234 2.3 77.7 1.0 OD1 A:ASN232 2.4 77.1 1.0 CG A:ASP238 2.5 77.3 1.0 CG A:ASP234 2.6 77.6 1.0 HD21 A:ASN232 3.0 92.6 1.0 HB A:ILE236 3.1 93.6 1.0 CG A:ASN232 3.3 77.1 1.0 H A:ILE236 3.3 93.5 1.0 C A:ILE236 3.4 77.8 1.0 ND2 A:ASN232 3.5 77.2 1.0 H A:ASP234 3.6 93.2 1.0 HA A:ASP230 3.6 91.8 1.0 H A:GLY258 3.7 93.0 1.0 H A:PHE231 3.8 91.4 1.0 OD1 A:ASP230 3.8 76.9 1.0 H A:ASN232 3.9 91.7 1.0 CA A:ILE236 4.0 78.0 1.0 CB A:ILE236 4.0 78.0 1.0 CB A:ASP238 4.0 76.9 1.0 N A:ILE236 4.0 77.9 1.0 CB A:ASP234 4.0 77.8 1.0 N A:ASP238 4.2 77.3 1.0 CG A:ASP230 4.2 77.2 1.0 HG22 A:ILE236 4.3 93.6 1.0 H A:ASP238 4.3 92.7 1.0 C A:ASP237 4.3 77.6 1.0 HB3 A:ASP234 4.4 93.3 1.0 HA A:ASP238 4.4 92.4 1.0 HA3 A:GLY258 4.4 93.2 1.0 HB2 A:ASP238 4.4 92.3 1.0 N A:ASP234 4.4 77.7 1.0 HD22 A:ASN232 4.5 92.6 1.0 N A:ASP237 4.5 78.1 1.0 CA A:ASP238 4.5 77.0 1.0 N A:ASN232 4.6 76.4 1.0 OD2 A:ASP230 4.6 77.4 1.0 N A:PHE231 4.6 76.2 1.0 CA A:ASP230 4.6 76.5 1.0 H A:GLY235 4.6 93.5 1.0 CB A:ASN232 4.6 77.1 1.0 HA A:ASP237 4.6 93.2 1.0 N A:GLY258 4.6 77.5 1.0 HB3 A:ASP238 4.6 92.3 1.0 HB2 A:ASP234 4.7 93.3 1.0 H A:GLY233 4.7 92.7 1.0 CG2 A:ILE236 4.7 78.0 1.0 CA A:ASP234 4.7 77.7 1.0 O A:ASP237 4.7 77.5 1.0 CA A:ASP237 4.8 77.6 1.0 HA A:ASP257 4.8 92.6 1.0 CB A:ASP230 4.8 77.0 1.0 HB2 A:ASP230 4.9 92.4 1.0 N A:GLY235 4.9 77.9 1.0 HB3 A:ASN232 5.0 92.5 1.0 C A:ASP234 5.0 77.9 1.0 OD1 A:ASP257 5.0 77.9 1.0 HD11 A:LEU264 5.0 91.9 1.0

A.Roy, L.Shi, A.Chang, X.Dong, A.Fernandez, J.C.Kraft, J.Li, V.Q.Le, R.V.Winegar, G.M.Cherf, D.Slocum, P.D.Poulson, G.E.Casper, M.L.Vallecillo-Zuniga, J.C.Valdoz, M.C.Miranda, H.Bai, Y.Kipnis, A.Olshefsky, T.Priya, L.Carter, R.Ravichandran, C.M.Chow, M.R.Johnson, S.Cheng, M.Smith, C.Overed-Sayer, D.K.Finch, D.Lowe, A.K.Bera, G.Matute-Bello, T.P.Birkland, F.Dimaio, G.Raghu, J.R.Cochran, L.J.Stewart, M.G.Campbell, P.M.Van Ry, T.Springer, D.Baker. De Novo Design of Highly Selective Miniprotein Inhibitors of Integrins Alpha V Beta 6 and Alpha V Beta 8. Nat Commun V. 14 5660 2023.
ISSN: ESSN 2041-1723
PubMed: 37704610
DOI: 10.1038/S41467-023-41272-Z