Calcium in PDB 9dia: Cryo-Em Structure of ALPHA5BETA1 Integrin in Complex with Neonectin Candidate 2

The structure of Cryo-Em Structure of ALPHA5BETA1 Integrin in Complex with Neonectin Candidate 2 also contains other interesting chemical elements:

Manganese

(Mn)

2 atoms

The binding sites of Calcium atom in the Cryo-Em Structure of ALPHA5BETA1 Integrin in Complex with Neonectin Candidate 2 (pdb code 9dia). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Cryo-Em Structure of ALPHA5BETA1 Integrin in Complex with Neonectin Candidate 2, PDB code: 9dia:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Cryo-Em Structure of ALPHA5BETA1 Integrin in Complex with Neonectin Candidate 2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Cryo-Em Structure of ALPHA5BETA1 Integrin in Complex with Neonectin Candidate 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1001 b:75.3 occ:1.00 OD1 A:ASP426 2.3 74.8 1.0 OD1 A:ASP424 2.4 74.5 1.0 O A:TYR430 2.5 74.1 1.0 OD1 A:ASN428 2.6 75.3 1.0 OD1 A:ASP432 2.9 72.0 1.0 CG A:ASP426 3.0 74.8 1.0 OD2 A:ASP426 3.1 74.8 1.0 HB2 A:TYR430 3.1 74.1 1.0 HB3 A:ARG447 3.4 71.9 1.0 CG A:ASN428 3.5 75.3 1.0 H A:TYR430 3.5 74.1 1.0 CG A:ASP424 3.5 74.5 1.0 HD22 A:ASN428 3.6 75.3 1.0 C A:TYR430 3.6 74.1 1.0 H A:GLY448 3.6 70.4 1.0 CG A:ASP432 3.7 72.0 1.0 OD2 A:ASP432 3.7 72.0 1.0 H A:ASN428 3.8 75.3 1.0 ND2 A:ASN428 3.9 75.3 1.0 CB A:TYR430 3.9 74.1 1.0 H A:ASP426 3.9 74.8 1.0 CA A:TYR430 4.1 74.1 1.0 OD2 A:ASP424 4.1 74.5 1.0 HB3 A:TYR430 4.1 74.1 1.0 O A:PRO431 4.1 71.0 1.0 N A:TYR430 4.1 74.1 1.0 HA A:ASP424 4.2 74.5 1.0 H A:LEU425 4.2 73.5 1.0 N A:GLY448 4.2 70.4 1.0 HA A:ARG447 4.3 71.9 1.0 CB A:ARG447 4.3 71.9 1.0 H A:GLY427 4.4 76.4 1.0 CB A:ASP426 4.4 74.8 1.0 C A:PRO431 4.5 71.0 1.0 N A:ASP426 4.5 74.8 1.0 HB2 A:ARG447 4.6 71.9 1.0 N A:ASN428 4.6 75.3 1.0 HD21 A:ASN428 4.6 75.3 1.0 CB A:ASN428 4.7 75.3 1.0 HA3 A:GLY448 4.7 70.4 1.0 CB A:ASP424 4.7 74.5 1.0 N A:PRO431 4.7 71.0 1.0 HD2 A:ARG447 4.7 71.9 1.0 CA A:ARG447 4.7 71.9 1.0 HB3 A:ASN428 4.7 75.3 1.0 HB3 A:ASP426 4.8 74.8 1.0 N A:LEU425 4.8 73.5 1.0 HD2 A:TYR430 4.8 74.1 1.0 CA A:ASP424 4.8 74.5 1.0 O A:GLY448 4.8 70.4 1.0 N A:GLY427 4.9 76.4 1.0 C A:ARG447 4.9 71.9 1.0 CA A:GLY448 4.9 70.4 1.0 H A:GLY429 4.9 75.5 1.0 CA A:ASP426 5.0 74.8 1.0 HB2 A:ASP424 5.0 74.5 1.0 HA A:PRO431 5.0 71.0 1.0

Calcium binding site 2 out of 3 in the Cryo-Em Structure of ALPHA5BETA1 Integrin in Complex with Neonectin Candidate 2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Cryo-Em Structure of ALPHA5BETA1 Integrin in Complex with Neonectin Candidate 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1003 b:61.0 occ:1.00 OD2 A:ASP297 2.3 65.5 1.0 OD1 A:ASN295 2.3 65.5 1.0 O A:LEU299 2.3 64.8 1.0 OD1 A:ASP301 2.3 66.0 1.0 OD2 A:ASP301 2.4 66.0 1.0 OD1 A:ASP297 2.4 65.5 1.0 OD1 A:ASP293 2.5 66.6 1.0 CG A:ASP297 2.7 65.5 1.0 CG A:ASP301 2.7 66.0 1.0 HD22 A:ASN295 3.2 65.5 1.0 CG A:ASN295 3.3 65.5 1.0 HB2 A:LEU299 3.5 64.8 1.0 C A:LEU299 3.5 64.8 1.0 H A:LEU299 3.5 64.8 1.0 HA A:ASP293 3.5 66.6 1.0 CG A:ASP293 3.7 66.6 1.0 ND2 A:ASN295 3.7 65.5 1.0 H A:GLN329 3.7 64.7 1.0 H A:ASN295 3.8 65.5 1.0 H A:ASP297 3.9 65.5 1.0 H A:VAL294 3.9 66.5 1.0 HB3 A:GLN329 4.0 64.7 1.0 CB A:ASP297 4.1 65.5 1.0 N A:LEU299 4.1 64.8 1.0 CB A:ASP301 4.2 66.0 1.0 CA A:LEU299 4.2 64.8 1.0 CB A:LEU299 4.2 64.8 1.0 O A:GLN329 4.3 64.7 1.0 CA A:ASP293 4.3 66.6 1.0 C A:ASP300 4.4 67.1 1.0 HB3 A:ASP297 4.5 65.5 1.0 N A:ASP301 4.5 66.0 1.0 OD2 A:ASP293 4.5 66.6 1.0 N A:ASP300 4.5 67.1 1.0 CB A:ASP293 4.5 66.6 1.0 N A:GLN329 4.5 64.7 1.0 N A:VAL294 4.5 66.5 1.0 HD21 A:ASN295 4.5 65.5 1.0 N A:ASN295 4.5 65.5 1.0 O A:ASP300 4.5 67.1 1.0 HB2 A:ASP301 4.5 66.0 1.0 HA A:ASP300 4.6 67.1 1.0 HD23 A:LEU328 4.6 66.2 1.0 N A:ASP297 4.6 65.5 1.0 HB3 A:ASP301 4.7 66.0 1.0 HB2 A:ASP297 4.7 65.5 1.0 H A:ASP301 4.7 66.0 1.0 CB A:ASN295 4.7 65.5 1.0 HB2 A:ASP293 4.7 66.6 1.0 CA A:ASP300 4.7 67.1 1.0 HB3 A:LEU328 4.8 66.2 1.0 HA A:LEU328 4.8 66.2 1.0 CA A:ASP301 4.8 66.0 1.0 CB A:GLN329 4.8 64.7 1.0 C A:ASP293 4.8 66.6 1.0 HB3 A:LEU299 4.8 64.8 1.0 H A:GLY298 4.9 66.2 1.0 CA A:ASP297 4.9 65.5 1.0 HA A:ASP301 4.9 66.0 1.0 HG22 A:VAL294 4.9 66.5 1.0

Calcium binding site 3 out of 3 in the Cryo-Em Structure of ALPHA5BETA1 Integrin in Complex with Neonectin Candidate 2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Cryo-Em Structure of ALPHA5BETA1 Integrin in Complex with Neonectin Candidate 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1004 b:68.8 occ:1.00 OD1 A:ASP364 2.4 72.6 1.0 O A:TYR366 2.5 68.6 1.0 OD1 A:ASP368 2.6 68.6 1.0 HB3 A:ASP362 2.8 75.0 1.0 OD2 A:ASP368 2.9 68.6 1.0 CG A:ASP368 3.0 68.6 1.0 H A:ASP362 3.0 75.0 1.0 CG A:ASP364 3.2 72.6 1.0 HB2 A:ASP362 3.3 75.0 1.0 OD2 A:ASP364 3.4 72.6 1.0 CB A:ASP362 3.4 75.0 1.0 OD1 A:ASP360 3.6 71.8 1.0 C A:TYR366 3.7 68.6 1.0 H A:ASP364 3.8 72.6 1.0 H A:GLY389 3.8 67.9 1.0 H A:TYR366 3.8 68.6 1.0 N A:ASP362 3.8 75.0 1.0 HB2 A:TYR366 3.9 68.6 1.0 HA A:ASP360 4.0 71.8 1.0 CA A:ASP362 4.2 75.0 1.0 H A:LEU361 4.3 70.8 1.0 HA A:ASN367 4.4 68.2 1.0 H A:GLN363 4.4 73.8 1.0 C A:ASN367 4.4 68.2 1.0 CB A:ASP368 4.4 68.6 1.0 CA A:TYR366 4.5 68.6 1.0 N A:TYR366 4.5 68.6 1.0 HA A:PRO388 4.5 66.6 1.0 CB A:ASP364 4.5 72.6 1.0 N A:LEU361 4.6 70.8 1.0 N A:ASP368 4.6 68.6 1.0 O A:ASN367 4.6 68.2 1.0 CB A:TYR366 4.6 68.6 1.0 N A:GLY389 4.6 67.9 1.0 N A:ASP364 4.6 72.6 1.0 N A:ASN367 4.6 68.2 1.0 CG A:ASP362 4.7 75.0 1.0 C A:ASP362 4.7 75.0 1.0 HB3 A:LEU361 4.7 70.8 1.0 N A:GLN363 4.7 73.8 1.0 HB3 A:ASP364 4.7 72.6 1.0 CA A:ASN367 4.7 68.2 1.0 HB2 A:ASP368 4.7 68.6 1.0 CG A:ASP360 4.8 71.8 1.0 CA A:ASP360 4.8 71.8 1.0 C A:ASP360 4.8 71.8 1.0 H A:ASP368 4.8 68.6 1.0 HB3 A:PRO388 4.8 66.6 1.0 OD2 A:ASP362 4.9 75.0 1.0 HA A:ASP368 4.9 68.6 1.0 HB2 A:PRO388 4.9 66.6 1.0 CA A:ASP368 4.9 68.6 1.0 HB3 A:TYR366 5.0 68.6 1.0 C A:LEU361 5.0 70.8 1.0

X.Wang, J.Guillem-Marti, S.Kumar, D.S.Lee, D.Cabrerizo-Aguado, R.Werther, K.A.E.Alamo, Y.T.Zhao, A.Nguyen, I.Kopyeva, B.Huang, J.Li, Y.Hao, X.Li, A.Brizuela-Velasco, A.Murray, S.Gerben, A.Roy, C.A.Deforest, T.Springer, H.Ruohola-Baker, J.A.Cooper, M.G.Campbell, J.M.Manero, M.P.Ginebra, D.Baker. De Novo Design of Integrin Alpha 5 Beta 1 Modulating Proteins to Enhance Biomaterial Properties. Adv Mater 00872 2025.
ISSN: ESSN 1521-4095
PubMed: 40489013
DOI: 10.1002/ADMA.202500872