Calcium in PDB 9dao: ALPHAIIBBETA3 in Fully-Extended Conformation in Complex with R6H8 Fab

The structure of ALPHAIIBBETA3 in Fully-Extended Conformation in Complex with R6H8 Fab also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Calcium atom in the ALPHAIIBBETA3 in Fully-Extended Conformation in Complex with R6H8 Fab (pdb code 9dao). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the ALPHAIIBBETA3 in Fully-Extended Conformation in Complex with R6H8 Fab, PDB code: 9dao:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in the ALPHAIIBBETA3 in Fully-Extended Conformation in Complex with R6H8 Fab


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of ALPHAIIBBETA3 in Fully-Extended Conformation in Complex with R6H8 Fab within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1101 b:18.0 occ:1.00 OD1 A:ASP305 2.3 30.6 1.0 O A:ARG303 2.4 30.6 1.0 OD2 A:ASP305 2.4 31.9 1.0 OD1 A:ASP297 2.5 25.6 1.0 CG A:ASP305 2.7 27.5 1.0 OD1 A:ASP301 3.0 33.1 1.0 CB A:ASN299 3.4 19.2 1.0 C A:ARG303 3.5 24.4 1.0 CG A:ASP297 3.7 28.1 1.0 CG A:ASP301 3.7 30.1 1.0 OD2 A:ASP301 3.8 30.1 1.0 N A:ASN299 4.1 26.6 1.0 CB A:ASP305 4.2 26.1 1.0 CA A:ARG303 4.2 22.1 1.0 CB A:ARG303 4.3 24.3 1.0 N A:ARG303 4.3 23.5 1.0 CA A:ASN299 4.3 19.0 1.0 CA A:ASP297 4.4 28.0 1.0 N A:ASP305 4.4 31.7 1.0 CB A:ASP297 4.5 30.7 1.0 C A:HIS304 4.5 31.3 1.0 CG A:ASN299 4.5 23.9 1.0 CD2 A:LEU332 4.6 30.3 1.0 OD2 A:ASP297 4.6 30.9 1.0 N A:HIS304 4.6 28.8 1.0 N A:VAL298 4.6 32.9 1.0 N A:GLN333 4.6 32.0 1.0 O A:GLN333 4.8 34.0 1.0 OD1 A:ASN299 4.8 25.9 1.0 CA A:ASP305 4.8 28.9 1.0 O A:HIS304 4.8 34.2 1.0 C A:ASP297 4.8 31.9 1.0 CA A:HIS304 4.8 28.1 1.0 N A:GLY300 4.9 26.0 1.0 C A:ASN299 4.9 19.8 1.0 N A:ASP301 4.9 29.3 1.0

Calcium binding site 2 out of 5 in the ALPHAIIBBETA3 in Fully-Extended Conformation in Complex with R6H8 Fab


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of ALPHAIIBBETA3 in Fully-Extended Conformation in Complex with R6H8 Fab within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1102 b:34.1 occ:1.00 O A:ASP247 2.5 76.6 1.0 OE1 A:GLU243 2.5 34.3 1.0 OE1 A:GLU252 2.6 23.8 1.0 O A:THR250 2.6 54.3 1.0 OG1 A:THR250 2.9 56.3 1.0 OE2 A:GLU252 3.1 29.5 1.0 CD A:GLU252 3.2 25.7 1.0 C A:THR250 3.5 55.1 1.0 CB A:ASP245 3.5 33.8 1.0 CD A:GLU243 3.5 34.7 1.0 C A:ASP247 3.6 76.0 1.0 CG A:GLU243 3.9 32.1 1.0 N A:ASP245 4.1 34.9 1.0 CB A:THR250 4.1 55.8 1.0 N A:ASP247 4.1 75.9 1.0 CA A:THR250 4.2 55.4 1.0 CA A:ASP247 4.3 76.1 1.0 CA A:ASP245 4.3 36.1 1.0 N A:THR251 4.3 43.4 1.0 N A:THR250 4.4 57.8 1.0 CB A:ASP247 4.4 77.6 1.0 N A:PHE244 4.4 23.0 1.0 N A:GLY246 4.5 58.3 1.0 CG A:ASP245 4.6 36.6 1.0 OE2 A:GLU243 4.6 36.5 1.0 CA A:THR251 4.6 43.0 1.0 CA A:GLU243 4.6 29.0 1.0 CG A:GLU252 4.7 17.6 1.0 N A:LEU248 4.7 58.8 1.0 C A:ASP245 4.8 38.8 1.0 OD2 A:ASP245 4.8 38.5 1.0 C A:THR251 4.9 42.0 1.0 CB A:GLU243 4.9 31.9 1.0 C A:GLU243 4.9 29.3 1.0 CG2 A:THR250 5.0 56.0 1.0 C A:PHE244 5.0 21.8 1.0 CA A:LEU248 5.0 58.2 1.0

Calcium binding site 3 out of 5 in the ALPHAIIBBETA3 in Fully-Extended Conformation in Complex with R6H8 Fab


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of ALPHAIIBBETA3 in Fully-Extended Conformation in Complex with R6H8 Fab within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1103 b:15.0 occ:1.00 OD1 A:ASP373 2.2 28.9 1.0 OD1 A:ASP369 2.3 31.6 1.0 O A:TYR371 2.5 29.2 1.0 OD1 A:ASP367 2.8 31.4 1.0 OD2 A:ASP373 2.9 33.2 1.0 CG A:ASP373 2.9 31.2 1.0 OD1 A:ASP365 3.0 27.1 1.0 CG A:ASP369 3.3 34.2 1.0 C A:TYR371 3.6 22.3 1.0 OD2 A:ASP369 3.7 37.0 1.0 CG A:ASP367 3.9 29.3 1.0 CG A:ASP365 4.2 29.8 1.0 N A:GLY394 4.3 29.9 1.0 OD2 A:ASP367 4.3 30.9 1.0 N A:TYR371 4.3 21.6 1.0 CD2 A:LEU393 4.3 28.2 1.0 CB A:ASP373 4.4 29.4 1.0 CA A:TYR371 4.4 19.8 1.0 C A:ASN372 4.4 30.7 1.0 N A:ASN372 4.6 27.7 1.0 O A:ASN372 4.6 35.6 1.0 CB A:ASP369 4.6 32.2 1.0 O A:GLY394 4.6 31.3 1.0 N A:LEU366 4.6 31.9 1.0 CB A:TYR371 4.6 20.9 1.0 CA A:ASP365 4.6 29.5 1.0 N A:ASP373 4.6 29.3 1.0 N A:ASP367 4.7 27.7 1.0 CA A:ASN372 4.7 28.3 1.0 N A:ASP369 4.8 31.9 1.0 C A:ASP365 4.9 34.1 1.0 CB A:LEU393 4.9 31.9 1.0 OD2 A:ASP365 5.0 34.9 1.0 CA A:GLY394 5.0 30.1 1.0 CA A:ASP373 5.0 27.8 1.0

Calcium binding site 4 out of 5 in the ALPHAIIBBETA3 in Fully-Extended Conformation in Complex with R6H8 Fab


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of ALPHAIIBBETA3 in Fully-Extended Conformation in Complex with R6H8 Fab within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1104 b:30.8 occ:1.00 OD1 A:ASP434 2.2 28.0 1.0 OD1 A:ASN430 2.2 35.1 1.0 OD1 A:ASP426 2.3 32.5 1.0 OD1 A:ASP428 2.4 45.4 1.0 O A:TYR432 2.5 29.0 1.0 OD2 A:ASP434 2.6 33.0 1.0 CG A:ASP434 2.7 28.4 1.0 CG A:ASN430 3.2 35.6 1.0 CG A:ASP428 3.5 45.5 1.0 CG A:ASP426 3.5 32.3 1.0 C A:TYR432 3.7 23.6 1.0 ND2 A:ASN430 3.8 32.0 1.0 OD2 A:ASP428 4.0 46.4 1.0 CB A:ASP434 4.2 28.8 1.0 OD2 A:ASP426 4.3 37.2 1.0 N A:ASP428 4.3 44.2 1.0 N A:ILE427 4.3 32.9 1.0 N A:TYR432 4.3 24.9 1.0 CB A:ASN430 4.4 35.5 1.0 O A:ALA450 4.4 34.2 1.0 CA A:ASP426 4.4 33.3 1.0 CB A:ASP426 4.5 31.6 1.0 N A:ASP434 4.5 33.3 1.0 CA A:TYR432 4.5 18.9 1.0 N A:ASN430 4.5 38.1 1.0 C A:PRO433 4.6 32.9 1.0 N A:ALA450 4.7 31.6 1.0 N A:PRO433 4.7 28.4 1.0 CB A:ASP428 4.7 42.2 1.0 CA A:PRO433 4.8 28.9 1.0 C A:ASP426 4.8 31.5 1.0 CA A:ASP434 4.8 30.2 1.0 CB A:TYR432 4.8 18.9 1.0 N A:GLY431 4.9 30.7 1.0 CA A:ASP428 4.9 44.1 1.0 CA A:ASN430 4.9 36.1 1.0 N A:ASP429 4.9 78.3 1.0 O A:PRO433 5.0 35.6 1.0

Calcium binding site 5 out of 5 in the ALPHAIIBBETA3 in Fully-Extended Conformation in Complex with R6H8 Fab


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of ALPHAIIBBETA3 in Fully-Extended Conformation in Complex with R6H8 Fab within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca802 b:26.9 occ:1.00 OD1 B:ASP217 2.2 34.6 1.0 OD2 B:ASP158 2.3 27.2 1.0 OD1 B:ASN215 2.3 24.2 1.0 O B:PRO219 2.3 36.4 1.0 OE2 B:GLU220 2.8 29.7 1.0 O B:ASP217 3.3 32.6 1.0 CG B:ASN215 3.4 22.7 1.0 CG B:ASP158 3.4 29.8 1.0 CG B:ASP217 3.5 33.4 1.0 C B:PRO219 3.5 33.0 1.0 CD B:GLU220 3.6 31.6 1.0 C B:ASP217 3.9 32.2 1.0 CB B:ASP158 4.0 29.7 1.0 ND2 B:ASN215 4.0 24.6 1.0 CA B:GLU220 4.0 30.8 1.0 OE1 B:GLU220 4.1 33.6 1.0 OD2 B:ASP217 4.2 32.1 1.0 N B:GLU220 4.2 30.4 1.0 N B:ASP217 4.3 29.5 1.0 NE2 B:HIS255 4.4 31.8 1.0 CA B:ASP217 4.4 30.1 1.0 CB B:ASP217 4.5 30.9 1.0 OD1 B:ASP158 4.5 32.2 1.0 CB B:ASN215 4.5 19.1 1.0 CG B:GLU220 4.5 30.6 1.0 N B:PRO219 4.6 31.5 1.0 CD2 B:HIS255 4.6 31.9 1.0 C B:ALA218 4.6 33.6 1.0 CA B:PRO219 4.7 30.9 1.0 N B:ALA218 4.7 32.2 1.0 O B:ALA218 4.8 36.1 1.0 CB B:GLU220 4.8 33.0 1.0 CD1 B:TYR164 5.0 32.6 1.0

J.Wang, L.Buitrago, L.Wang, J.Li, T.Walz, B.S.Coller. An Alpha Iib Beta 3 Ligand-Mimetic Murine Monoclonal Antibody That Produces Platelet Activation By Engaging the Fc Gamma Iia Receptor. Blood Adv 2025.
ISSN: ESSN 2473-9537
PubMed: 40101235
DOI: 10.1182/BLOODADVANCES.2024015368