Calcium in PDB 9ef2: Cryo-Em Structure of ALPHA5BETA1 Integrin in Complex with Neonectin Candidate 2, Open Conformation

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

Manganese

(Mn)

3 atoms

The binding sites of Calcium atom in the Cryo-Em Structure of ALPHA5BETA1 Integrin in Complex with Neonectin Candidate 2, Open Conformation (pdb code 9ef2). 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, Open Conformation, PDB code: 9ef2:
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, Open Conformation


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, Open Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1001 b:97.9 occ:1.00 OD1 A:ASP297 2.3 96.4 1.0 OD1 A:ASN295 2.3 95.5 1.0 OD1 A:ASP301 2.3 91.9 1.0 OD2 A:ASP301 2.3 92.0 1.0 OD2 A:ASP297 2.4 96.8 1.0 CG A:ASP301 2.6 88.0 1.0 O A:LEU299 2.6 95.6 1.0 CG A:ASP297 2.6 98.1 1.0 OD1 A:ASP293 3.1 90.9 1.0 CG A:ASN295 3.3 95.3 1.0 C A:LEU299 3.7 95.2 1.0 ND2 A:ASN295 3.8 95.1 1.0 CB A:ASP297 4.0 100.4 1.0 CB A:ASP301 4.1 80.7 1.0 CG A:ASP293 4.2 90.7 1.0 N A:LEU299 4.3 96.7 1.0 O A:GLN329 4.4 95.2 1.0 N A:ASP297 4.4 96.6 1.0 CA A:LEU299 4.4 93.8 1.0 C A:ASP300 4.5 88.2 1.0 CB A:LEU299 4.5 94.0 1.0 N A:ASP301 4.5 85.2 1.0 N A:ASN295 4.6 86.8 1.0 O A:ASP300 4.6 89.3 1.0 CB A:ASN295 4.6 93.7 1.0 N A:GLN329 4.6 94.1 1.0 CA A:ASP293 4.6 87.4 1.0 N A:ASP300 4.7 91.6 1.0 CA A:ASP297 4.7 97.3 1.0 CA A:ASP301 4.8 81.8 1.0 N A:VAL294 4.9 89.2 1.0 CB A:ASP293 4.9 88.2 1.0 CA A:ASP300 4.9 92.2 1.0 N A:GLY296 5.0 94.2 1.0 CA A:ASN295 5.0 89.6 1.0 OD2 A:ASP293 5.0 90.2 1.0

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


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, Open Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1002 b:122.9 occ:1.00 OD1 A:ASP247 2.3 113.2 1.0 OD1 A:ASP243 2.3 125.6 1.0 O A:THR245 2.3 111.5 1.0 OG A:SER241 2.3 108.1 1.0 OD2 A:ASP247 2.3 108.0 1.0 CG A:ASP247 2.6 107.8 1.0 CG A:ASP243 3.4 126.9 1.0 C A:THR245 3.5 114.8 1.0 CB A:SER241 3.5 106.4 1.0 N A:SER241 3.9 105.7 1.0 OD2 A:ASP243 3.9 127.9 1.0 CB A:ASP247 4.0 98.9 1.0 N A:ASP247 4.2 107.0 1.0 O A:ASP243 4.2 124.4 1.0 CA A:SER241 4.2 107.0 1.0 N A:ASP243 4.3 123.5 1.0 N A:THR245 4.3 125.9 1.0 N A:GLY242 4.3 111.3 1.0 N A:PHE240 4.3 99.0 1.0 CA A:THR245 4.3 120.3 1.0 C A:GLU246 4.4 111.0 1.0 CA A:GLU239 4.4 102.8 1.0 N A:GLU246 4.5 113.7 1.0 C A:ASP243 4.5 125.4 1.0 CA A:GLU246 4.6 111.7 1.0 CB A:THR245 4.6 121.4 1.0 O A:ASN266 4.6 101.7 1.0 CA A:ASP247 4.6 101.5 1.0 CB A:ASP243 4.6 125.2 1.0 CA A:ASP243 4.7 124.8 1.0 C A:SER241 4.8 110.2 1.0 C A:GLU239 4.8 102.6 1.0 CB A:GLU239 4.8 96.8 1.0 O A:GLU246 4.9 111.8 1.0 C A:PHE240 4.9 102.7 1.0

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


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, Open Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1003 b:109.9 occ:1.00 OD1 A:ASP362 2.3 110.8 1.0 OD1 A:ASP368 2.3 94.7 1.0 OD2 A:ASP362 2.3 101.2 1.0 O A:TYR366 2.3 99.5 1.0 CG A:ASP362 2.6 107.0 1.0 OD1 A:ASP364 2.7 108.9 1.0 CG A:ASP368 3.1 92.8 1.0 OD2 A:ASP368 3.2 97.4 1.0 C A:TYR366 3.3 96.9 1.0 OD2 A:ASP364 3.4 107.0 1.0 CG A:ASP364 3.4 106.7 1.0 CB A:TYR366 3.9 95.4 1.0 CA A:TYR366 4.0 96.3 1.0 N A:GLY389 4.1 86.8 1.0 CB A:ASP362 4.1 102.8 1.0 N A:TYR366 4.1 104.4 1.0 O A:ASN367 4.2 98.7 1.0 C A:ASN367 4.2 94.9 1.0 N A:ASN367 4.3 91.9 1.0 CB A:ASP368 4.5 88.2 1.0 N A:ASP368 4.6 93.2 1.0 CA A:ASN367 4.6 91.2 1.0 N A:ASP362 4.6 99.8 1.0 O A:GLY389 4.7 93.9 1.0 CA A:GLY389 4.7 87.3 1.0 CB A:ASP364 4.8 101.8 1.0 CA A:ASP362 4.9 101.5 1.0 C A:GLY389 4.9 90.2 1.0 CA A:ASP368 4.9 89.3 1.0 N A:ASP364 4.9 104.6 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