Calcium in PDB 9dax: The Structure of ALPHAIIBBETA3 in Apo State

The structure of The Structure of ALPHAIIBBETA3 in Apo State also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Calcium atom in the The Structure of ALPHAIIBBETA3 in Apo State (pdb code 9dax). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the The Structure of ALPHAIIBBETA3 in Apo State, PDB code: 9dax:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the The Structure of ALPHAIIBBETA3 in Apo State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The Structure of ALPHAIIBBETA3 in Apo State within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1101 b:46.5 occ:1.00 O A:ARG303 2.3 63.3 1.0 OD1 A:ASN299 2.3 50.7 1.0 OD1 A:ASP301 2.4 62.7 1.0 ND2 A:ASN299 2.5 52.2 1.0 CG A:ASN299 2.7 48.9 1.0 OD2 A:ASP305 2.8 34.9 1.0 OD1 A:ASP305 2.8 37.3 1.0 OD2 A:ASP301 2.9 67.5 1.0 CG A:ASP301 3.0 64.8 1.0 CG A:ASP305 3.1 33.1 1.0 C A:ARG303 3.2 62.2 1.0 CB A:ARG303 3.3 63.6 1.0 CA A:ARG303 3.5 64.8 1.0 N A:ARG303 3.6 64.7 1.0 OD1 A:ASP297 4.0 49.6 1.0 CB A:ASN299 4.2 45.2 1.0 N A:HIS304 4.4 46.0 1.0 CB A:ASP301 4.5 63.1 1.0 CG A:ARG303 4.6 64.4 1.0 CB A:ASP305 4.6 32.5 1.0 N A:ASP305 4.6 42.7 1.0 CG A:ASP297 4.7 49.7 1.0 N A:GLY302 4.7 64.6 1.0 O A:GLN333 4.7 59.8 1.0 NE A:ARG303 4.7 65.7 1.0 N A:GLN333 4.8 52.2 1.0 C A:GLY302 4.8 63.6 1.0 N A:ASN299 4.8 50.5 1.0 N A:ASP301 4.9 64.5 1.0 C A:HIS304 4.9 46.8 1.0

Calcium binding site 2 out of 6 in the The Structure of ALPHAIIBBETA3 in Apo State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The Structure of ALPHAIIBBETA3 in Apo State within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1102 b:93.2 occ:1.00 OG1 A:THR250 2.5 79.7 1.0 O A:THR250 2.6 73.9 1.0 CG A:GLU252 2.8 36.7 1.0 OE2 A:GLU252 2.8 42.8 1.0 CB A:ASP245 2.9 60.4 1.0 CB A:THR250 3.0 78.6 1.0 C A:THR250 3.2 76.2 1.0 OD2 A:ASP245 3.2 63.4 1.0 CD A:GLU252 3.2 40.1 1.0 CG A:ASP245 3.5 63.0 1.0 CA A:THR250 3.6 78.8 1.0 O A:ASP247 3.9 79.1 1.0 N A:GLU252 4.0 46.3 1.0 CB A:GLU252 4.1 37.6 1.0 N A:THR251 4.1 66.7 1.0 CA A:ASP245 4.1 62.7 1.0 N A:ASP245 4.2 65.0 1.0 N A:THR250 4.3 79.4 1.0 CG2 A:THR250 4.4 78.0 1.0 C A:THR251 4.4 64.0 1.0 CA A:GLU252 4.4 43.5 1.0 OE1 A:GLU252 4.5 38.9 1.0 CA A:THR251 4.5 66.8 1.0 OD1 A:ASP245 4.7 65.9 1.0 C A:ASP247 5.0 78.5 1.0 C A:ASP245 5.0 64.9 1.0

Calcium binding site 3 out of 6 in the The Structure of ALPHAIIBBETA3 in Apo State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of The Structure of ALPHAIIBBETA3 in Apo State within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1103 b:98.9 occ:1.00 OD1 A:ASP369 2.3 80.2 1.0 OD2 A:ASP373 2.3 50.4 1.0 OD1 A:ASP373 2.3 44.9 1.0 OD2 A:ASP369 2.4 77.2 1.0 O A:TYR371 2.5 68.8 1.0 CG A:ASP373 2.6 47.6 1.0 CG A:ASP369 2.6 79.9 1.0 C A:TYR371 3.6 64.1 1.0 OD1 A:ASP365 3.7 78.6 1.0 CB A:ASP373 4.1 45.0 1.0 CB A:ASP369 4.1 81.2 1.0 N A:TYR371 4.1 66.8 1.0 CA A:TYR371 4.2 64.4 1.0 O A:GLY394 4.3 58.5 1.0 N A:GLY394 4.4 52.1 1.0 N A:ASP373 4.4 40.5 1.0 C A:ASN372 4.4 51.1 1.0 CB A:TYR371 4.4 64.8 1.0 N A:ASP367 4.5 70.9 1.0 N A:ASP369 4.6 80.3 1.0 N A:ASN372 4.6 51.4 1.0 N A:LEU366 4.6 67.0 1.0 O A:ASN372 4.7 51.9 1.0 OD1 A:ASP367 4.7 71.2 1.0 CB A:ASP367 4.7 71.3 1.0 O A:GLY364 4.7 57.8 1.0 CA A:ASP373 4.7 39.7 1.0 CG A:ASP367 4.7 69.3 1.0 CA A:ASP365 4.8 80.8 1.0 CA A:ASN372 4.8 51.5 1.0 CA A:ASP369 4.8 82.1 1.0 CG A:ASP365 4.9 79.9 1.0 N A:GLY370 4.9 81.4 1.0 CD2 A:LEU393 4.9 38.8 1.0 CB A:LEU393 5.0 39.4 1.0 CA A:GLY394 5.0 50.8 1.0

Calcium binding site 4 out of 6 in the The Structure of ALPHAIIBBETA3 in Apo State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of The Structure of ALPHAIIBBETA3 in Apo State within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1104 b:80.4 occ:1.00 OD1 A:ASP434 2.3 34.2 1.0 OD1 A:ASN430 2.3 62.5 1.0 OD2 A:ASP428 2.4 54.5 1.0 ND2 A:ASN430 2.4 59.0 1.0 CG A:ASN430 2.6 64.4 1.0 O A:ALA450 3.0 33.5 1.0 OD1 A:ASP428 3.0 46.3 1.0 CG A:ASP428 3.0 51.5 1.0 O A:TYR432 3.3 50.4 1.0 N A:ALA450 3.3 20.3 1.0 CG A:ASP434 3.3 28.7 1.0 OD2 A:ASP434 3.7 33.3 1.0 C A:ALA450 3.8 29.4 1.0 CA A:ALA450 3.9 24.6 1.0 CB A:ASN430 3.9 66.8 1.0 CB A:ALA450 4.0 25.2 1.0 C A:ARG449 4.0 22.0 1.0 C A:TYR432 4.2 49.9 1.0 CA A:ARG449 4.3 19.8 1.0 CB A:TYR432 4.4 48.1 1.0 CB A:ARG449 4.4 17.2 1.0 CB A:ASP428 4.5 54.7 1.0 N A:TYR432 4.6 52.0 1.0 CB A:ASP434 4.6 23.0 1.0 CA A:TYR432 4.6 53.0 1.0 O A:PRO433 4.7 45.4 1.0 CD2 A:TYR432 4.8 52.0 1.0 O A:ARG449 4.8 27.1 1.0 C A:PRO433 4.8 40.2 1.0 OD1 A:ASP426 4.9 54.3 1.0 CA A:ASN430 4.9 62.9 1.0 CG A:ARG449 4.9 18.9 1.0 N A:ASP434 5.0 30.4 1.0

Calcium binding site 5 out of 6 in the The Structure of ALPHAIIBBETA3 in Apo State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of The Structure of ALPHAIIBBETA3 in Apo State within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca802 b:0.0 occ:1.00 OD2 B:ASP158 2.2 5.8 1.0 OD1 B:ASN215 2.2 3.4 1.0 OD1 B:ASP217 2.3 0.2 1.0 O B:PRO219 2.4 20.0 1.0 CG B:ASN215 3.1 8.7 1.0 CG B:ASP158 3.2 5.2 1.0 CG B:ASP217 3.4 4.7 1.0 NE2 B:HIS255 3.5 7.5 1.0 CB B:ASP158 3.6 1.9 1.0 C B:PRO219 3.6 8.8 1.0 ND2 B:ASN215 3.9 6.8 1.0 CB B:ASN215 4.0 7.7 1.0 OD2 B:ASP217 4.0 0.7 1.0 CD2 B:HIS255 4.0 0.0 1.0 O B:ASP217 4.0 16.9 1.0 CA B:GLU220 4.2 2.4 1.0 OE1 B:GLU220 4.3 13.7 1.0 N B:GLU220 4.3 3.0 1.0 OD1 B:ASP158 4.4 0.4 1.0 C B:ASP217 4.4 20.9 1.0 CD1 B:TYR164 4.4 5.8 1.0 CB B:ASP217 4.6 10.5 1.0 N B:ASP217 4.6 7.7 1.0 CB B:TYR164 4.7 4.1 1.0 CA B:PRO219 4.7 4.9 1.0 N B:PRO219 4.7 0.0 1.0 CG B:TYR164 4.7 9.5 1.0 CE1 B:HIS255 4.7 8.1 1.0 CA B:ASP217 4.8 14.8 1.0 O B:VAL157 4.8 5.3 1.0 C B:ALA218 5.0 2.5 1.0 CD B:GLU220 5.0 14.5 1.0

Calcium binding site 6 out of 6 in the The Structure of ALPHAIIBBETA3 in Apo State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of The Structure of ALPHAIIBBETA3 in Apo State within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca803 b:95.0 occ:1.00 OD1 B:ASP126 2.3 55.4 1.0 O B:HOH901 2.3 39.9 1.0 O B:MET335 2.4 61.3 1.0 OD2 B:ASP126 2.4 59.0 1.0 O B:HOH904 2.5 27.6 1.0 CG B:ASP126 2.6 58.1 1.0 OD2 B:ASP127 2.8 62.2 1.0 CG B:ASP127 3.3 64.3 1.0 C B:MET335 3.5 65.4 1.0 OD1 B:ASP127 3.7 63.9 1.0 N B:ASP127 3.8 60.8 1.0 O B:SER123 3.8 26.1 1.0 CA B:MET335 4.0 65.6 1.0 CB B:ASP126 4.0 56.0 1.0 CB B:MET335 4.0 66.5 1.0 CB B:ASP127 4.2 58.7 1.0 OD1 B:ASP251 4.3 27.3 1.0 C B:ASP126 4.4 55.3 1.0 CA B:ASP127 4.5 62.0 1.0 N B:ASP126 4.5 53.2 1.0 CA B:ASP126 4.5 53.7 1.0 N B:ASP336 4.6 74.0 1.0 CG B:MET335 4.6 65.5 1.0 C B:SER123 5.0 26.1 1.0 CA B:ASP336 5.0 73.7 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