Calcium in PDB 8tcf: Integrin Alpha-V Beta-8 in Complex with Minibinder B8_BP_DSULF

The structure of Integrin Alpha-V Beta-8 in Complex with Minibinder B8_BP_DSULF 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 Minibinder B8_BP_DSULF (pdb code 8tcf). 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 Minibinder B8_BP_DSULF, PDB code: 8tcf:
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 Minibinder B8_BP_DSULF


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 Minibinder B8_BP_DSULF within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:16.4 occ:1.00 OD1 A:ASP288 2.2 21.3 1.0 OD2 A:ASP292 2.2 18.9 1.0 OD1 A:ASP292 2.3 21.6 1.0 O A:TYR290 2.3 20.8 1.0 OD2 A:ASP288 2.3 20.3 1.0 OD1 A:ASN286 2.5 21.0 1.0 CG A:ASP292 2.6 21.4 1.0 CG A:ASP288 2.6 21.9 1.0 C A:TYR290 3.4 21.2 1.0 CG A:ASN286 3.5 20.6 1.0 OD1 A:ASP284 3.5 20.4 1.0 ND2 A:ASN286 3.8 20.6 1.0 CB A:ASP288 4.0 20.6 1.0 CB A:ASP292 4.1 19.4 1.0 CG A:ASP284 4.1 20.6 1.0 CA A:TYR290 4.1 21.9 1.0 N A:TYR290 4.1 20.5 1.0 CB A:TYR290 4.1 21.4 1.0 O A:GLN320 4.2 22.6 1.0 N A:ASP292 4.3 20.0 1.0 C A:ALA291 4.3 19.8 1.0 CA A:ASP284 4.4 19.5 1.0 N A:GLN320 4.4 21.5 1.0 N A:ILE285 4.5 20.3 1.0 N A:ALA291 4.5 20.1 1.0 N A:ASP288 4.5 21.2 1.0 N A:ASN286 4.6 20.7 1.0 O A:ALA291 4.6 20.2 1.0 OD2 A:ASP284 4.6 20.4 1.0 CA A:ASP292 4.6 19.0 1.0 CB A:ASP284 4.7 19.9 1.0 CA A:ALA291 4.7 19.4 1.0 CA A:ASP288 4.7 20.6 1.0 CB A:ASN286 4.8 20.5 1.0 CD2 A:LEU319 4.8 20.1 1.0 C A:ASP284 4.9 20.3 1.0 CB A:GLN320 5.0 21.5 1.0 C A:ASP288 5.0 21.7 1.0

Calcium binding site 2 out of 5 in the Integrin Alpha-V Beta-8 in Complex with Minibinder B8_BP_DSULF


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 Minibinder B8_BP_DSULF within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:18.1 occ:1.00 OD1 A:ASP353 2.1 21.7 1.0 OD1 A:ASP351 2.1 21.5 1.0 OD2 A:ASP357 2.1 19.8 1.0 O A:PHE355 2.2 20.2 1.0 OD1 A:ASP349 2.3 26.0 1.0 CG A:ASP357 2.8 20.6 1.0 OD1 A:ASP357 2.8 19.1 1.0 CG A:ASP353 3.0 18.8 1.0 CG A:ASP351 3.2 18.5 1.0 CG A:ASP349 3.4 18.9 1.0 OD2 A:ASP353 3.4 19.4 1.0 C A:PHE355 3.4 18.7 1.0 OD2 A:ASP351 3.7 19.2 1.0 N A:ASP353 3.9 19.5 1.0 N A:ASP351 4.1 19.1 1.0 N A:PHE355 4.1 19.8 1.0 CA A:ASP349 4.1 18.9 1.0 CB A:ASP353 4.1 19.4 1.0 OD2 A:ASP349 4.2 18.8 1.0 CA A:PHE355 4.2 18.8 1.0 CB A:ASP357 4.3 18.6 1.0 N A:LEU350 4.3 19.5 1.0 C A:ASP349 4.3 19.1 1.0 CB A:ASP349 4.3 19.2 1.0 C A:ASN356 4.4 19.1 1.0 N A:ASP357 4.4 19.1 1.0 N A:GLN352 4.4 19.6 1.0 N A:ASN356 4.4 18.9 1.0 ND2 A:ASN377 4.5 18.9 1.0 CB A:ASP351 4.5 19.5 1.0 CB A:PHE355 4.5 21.0 1.0 CA A:ASP353 4.5 19.2 1.0 CA A:ASN356 4.5 18.8 1.0 CA A:ASP351 4.6 19.6 1.0 C A:ASP351 4.6 19.6 1.0 O A:ASN356 4.7 19.9 1.0 N A:GLY354 4.8 19.4 1.0 C A:ASP353 4.9 19.6 1.0 CA A:ASP357 4.9 18.6 1.0 O A:ASP349 4.9 19.4 1.0 C A:GLN352 5.0 19.6 1.0

Calcium binding site 3 out of 5 in the Integrin Alpha-V Beta-8 in Complex with Minibinder B8_BP_DSULF


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 Minibinder B8_BP_DSULF within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:16.6 occ:1.00 OD1 A:ASP416 2.1 21.6 1.0 OD1 A:ASP414 2.1 17.3 1.0 OD1 A:ASP422 2.2 20.3 1.0 O A:TYR420 2.2 19.7 1.0 OD1 A:ASN418 2.7 20.4 1.0 CG A:ASP422 2.8 20.5 1.0 OD2 A:ASP422 2.9 20.6 1.0 CG A:ASP416 3.1 20.4 1.0 CG A:ASP414 3.3 21.4 1.0 C A:TYR420 3.4 20.2 1.0 CG A:ASN418 3.5 20.3 1.0 OD2 A:ASP416 3.5 20.5 1.0 ND2 A:ASN418 3.8 20.1 1.0 OD2 A:ASP414 3.9 20.1 1.0 O A:ALA438 4.0 19.8 1.0 N A:ASP416 4.2 20.7 1.0 N A:ASP422 4.2 19.9 1.0 C A:PRO421 4.2 19.5 1.0 CB A:ASP422 4.3 19.2 1.0 CB A:ASP414 4.3 19.9 1.0 N A:TYR420 4.3 20.3 1.0 CA A:TYR420 4.3 19.7 1.0 CA A:ASP414 4.3 20.3 1.0 N A:PRO421 4.3 19.4 1.0 N A:ALA438 4.4 19.6 1.0 CB A:ASP416 4.4 21.1 1.0 CA A:PRO421 4.4 19.2 1.0 N A:ILE415 4.5 20.9 1.0 N A:ASN418 4.5 20.5 1.0 CB A:TYR420 4.6 19.9 1.0 O A:PRO421 4.6 19.3 1.0 CA A:ASP422 4.7 19.2 1.0 CA A:ASP416 4.7 21.1 1.0 N A:LYS417 4.7 21.4 1.0 C A:ASP414 4.7 21.0 1.0 CB A:ASN418 4.7 20.2 1.0 CB A:ALA438 4.8 19.4 1.0 C A:ASP416 4.8 21.3 1.0 C A:ALA438 4.9 19.6 1.0 CA A:ALA438 4.9 19.3 1.0

Calcium binding site 4 out of 5 in the Integrin Alpha-V Beta-8 in Complex with Minibinder B8_BP_DSULF


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 Minibinder B8_BP_DSULF within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:18.5 occ:1.00 OD1 A:ASP234 2.2 22.2 1.0 OD1 A:ASP238 2.2 20.8 1.0 O A:ILE236 2.3 21.6 1.0 OD2 A:ASP238 2.3 19.4 1.0 OD2 A:ASP234 2.3 20.5 1.0 OD1 A:ASN232 2.4 21.6 1.0 CG A:ASP238 2.5 21.7 1.0 CG A:ASP234 2.6 21.4 1.0 CG A:ASN232 3.3 20.2 1.0 C A:ILE236 3.4 20.7 1.0 ND2 A:ASN232 3.5 20.6 1.0 OD1 A:ASP230 3.9 20.6 1.0 CB A:ASP238 4.0 20.0 1.0 CB A:ASP234 4.0 20.7 1.0 CA A:ILE236 4.1 20.9 1.0 N A:ILE236 4.1 21.1 1.0 CB A:ILE236 4.1 20.9 1.0 N A:ASP238 4.2 20.2 1.0 CG A:ASP230 4.3 20.3 1.0 C A:ASP237 4.3 21.0 1.0 N A:ASP234 4.4 21.3 1.0 CA A:ASP238 4.5 20.0 1.0 N A:ASP237 4.5 20.9 1.0 OD2 A:ASP230 4.6 20.6 1.0 N A:ASN232 4.6 20.8 1.0 CB A:ASN232 4.6 20.5 1.0 O A:ASP237 4.6 20.3 1.0 N A:GLY258 4.6 21.5 1.0 N A:PHE231 4.7 20.9 1.0 CG2 A:ILE236 4.7 21.2 1.0 CA A:ASP234 4.7 20.7 1.0 CA A:ASP237 4.8 20.2 1.0 CA A:ASP230 4.8 20.4 1.0 CB A:ASP230 5.0 20.6 1.0 N A:GLY235 5.0 20.9 1.0 C A:ASP234 5.0 20.9 1.0

Calcium binding site 5 out of 5 in the Integrin Alpha-V Beta-8 in Complex with Minibinder B8_BP_DSULF


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 Minibinder B8_BP_DSULF within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2001 b:20.9 occ:1.00 OD1 B:ASP209 2.1 23.1 1.0 OD2 B:ASP151 2.2 21.8 1.0 O B:PRO211 2.2 22.1 1.0 OD1 B:ASN207 2.5 23.7 1.0 O B:ASP209 2.5 22.9 1.0 CG B:ASP209 2.9 22.0 1.0 OE1 B:GLU212 3.1 22.8 1.0 CG B:ASN207 3.1 23.6 1.0 OD2 B:ASP209 3.2 21.6 1.0 CG B:ASP151 3.4 21.2 1.0 ND2 B:ASN207 3.4 23.3 1.0 C B:PRO211 3.4 21.4 1.0 C B:ASP209 3.5 22.8 1.0 CD B:GLU212 3.7 22.6 1.0 CB B:ASP209 4.0 21.9 1.0 CA B:ASP209 4.0 22.5 1.0 CB B:ASP151 4.1 21.6 1.0 NE2 B:HIS247 4.1 20.9 1.0 N B:ASP209 4.1 22.8 1.0 OE2 B:GLU212 4.1 23.0 1.0 N B:PRO211 4.2 21.8 1.0 CA B:GLU212 4.2 21.1 1.0 C B:THR210 4.3 22.1 1.0 CB B:ASN207 4.3 23.2 1.0 N B:GLU212 4.3 21.6 1.0 OD1 B:ASP151 4.3 21.1 1.0 CA B:PRO211 4.4 21.7 1.0 N B:THR210 4.5 22.8 1.0 O B:THR210 4.5 22.6 1.0 CD2 B:HIS247 4.6 20.9 1.0 CD B:PRO211 4.7 21.9 1.0 CG B:GLU212 4.8 22.2 1.0 CA B:THR210 4.9 22.8 1.0 CB B:GLU212 5.0 21.6 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