Calcium in PDB 9axl: Structure of the Semi-Extended ALPHAIIBBETA3 in Complex with R21D10 Fab

The structure of Structure of the Semi-Extended ALPHAIIBBETA3 in Complex with R21D10 Fab also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Calcium atom in the Structure of the Semi-Extended ALPHAIIBBETA3 in Complex with R21D10 Fab (pdb code 9axl). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Structure of the Semi-Extended ALPHAIIBBETA3 in Complex with R21D10 Fab, PDB code: 9axl:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Structure of the Semi-Extended ALPHAIIBBETA3 in Complex with R21D10 Fab


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of the Semi-Extended ALPHAIIBBETA3 in Complex with R21D10 Fab within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1101 b:28.5 occ:1.00 OE2 A:GLU243 2.3 22.1 1.0 OE1 A:GLU252 2.3 27.6 1.0 OE1 A:GLU243 2.4 20.7 1.0 O A:ASP247 2.5 44.0 1.0 OE2 A:GLU252 2.7 25.1 1.0 CD A:GLU243 2.7 17.0 1.0 O A:THR250 2.7 42.2 1.0 OG1 A:THR250 2.7 34.5 1.0 CD A:GLU252 2.8 21.6 1.0 C A:THR250 3.2 39.6 1.0 OD1 A:ASP245 3.4 25.8 1.0 CB A:THR250 3.7 41.1 1.0 C A:ASP247 3.7 44.2 1.0 CG A:ASP245 3.8 26.3 1.0 CA A:THR250 3.8 40.1 1.0 OD2 A:ASP245 3.8 25.9 1.0 N A:THR251 3.9 29.1 1.0 N A:THR250 3.9 41.8 1.0 CG A:GLU243 4.1 14.6 1.0 CA A:THR251 4.3 27.6 1.0 CG A:GLU252 4.3 12.4 1.0 N A:ASP247 4.4 40.1 1.0 CA A:ASP247 4.5 41.8 1.0 CB A:ASP247 4.6 44.4 1.0 C A:THR251 4.7 23.0 1.0 CA A:GLU243 4.7 18.7 1.0 N A:ASP245 4.7 18.1 1.0 N A:LEU248 4.7 38.3 1.0 N A:PHE244 4.8 16.0 1.0 CB A:GLU243 4.8 16.3 1.0 N A:GLU252 4.8 14.1 1.0 CB A:ASP245 4.8 25.6 1.0 CA A:LEU248 4.9 37.0 1.0 CG2 A:THR250 5.0 42.2 1.0

Calcium binding site 2 out of 6 in the Structure of the Semi-Extended ALPHAIIBBETA3 in Complex with R21D10 Fab


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of the Semi-Extended ALPHAIIBBETA3 in Complex with R21D10 Fab within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1102 b:0.0 occ:1.00 O A:ARG303 2.2 17.2 1.0 ND2 A:ASN299 2.2 16.2 1.0 OD1 A:ASP301 2.3 27.3 1.0 OD1 A:ASP305 2.3 18.1 1.0 OD2 A:ASP305 3.0 13.9 1.0 OD1 A:ASP297 3.0 14.7 1.0 CG A:ASP305 3.0 7.7 1.0 CG A:ASP301 3.2 30.0 1.0 CG A:ASN299 3.3 15.1 1.0 OD2 A:ASP301 3.3 25.9 1.0 C A:ARG303 3.3 14.9 1.0 OD1 A:ASN299 3.6 21.9 1.0 CA A:ARG303 4.0 18.6 1.0 N A:ARG303 4.0 26.6 1.0 CB A:ARG303 4.1 24.9 1.0 CG A:ASP297 4.1 11.0 1.0 N A:HIS304 4.4 5.5 1.0 CB A:ASP305 4.4 0.4 1.0 C A:HIS304 4.4 5.8 1.0 N A:ASP305 4.5 0.4 1.0 CB A:ASP301 4.6 23.7 1.0 CB A:ASN299 4.6 9.6 1.0 O A:HIS304 4.7 13.9 1.0 N A:ASP301 4.7 23.0 1.0 CA A:HIS304 4.7 10.0 1.0 N A:ASN299 4.8 11.3 1.0 CA A:ASP297 4.8 1.7 1.0 O A:GLN333 4.9 22.4 1.0 OD2 A:ASP297 4.9 13.0 1.0 N A:GLN333 4.9 0.3 1.0 CA A:ASP305 5.0 1.3 1.0

Calcium binding site 3 out of 6 in the Structure of the Semi-Extended ALPHAIIBBETA3 in Complex with R21D10 Fab


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of the Semi-Extended ALPHAIIBBETA3 in Complex with R21D10 Fab within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1103 b:19.0 occ:1.00 OD1 A:ASP369 2.2 24.1 1.0 OD1 A:ASP373 2.3 29.9 1.0 O A:TYR371 2.3 22.3 1.0 OD2 A:ASP373 3.0 27.5 1.0 CG A:ASP373 3.0 24.8 1.0 CG A:ASP369 3.0 20.4 1.0 OD1 A:ASP367 3.1 17.8 1.0 OD2 A:ASP369 3.2 24.6 1.0 C A:TYR371 3.6 20.1 1.0 OD1 A:ASP365 3.6 18.3 1.0 CG A:ASP367 4.1 18.7 1.0 CD2 A:LEU393 4.1 11.4 1.0 N A:TYR371 4.3 20.1 1.0 CB A:ASP369 4.3 17.2 1.0 CA A:TYR371 4.4 16.4 1.0 CB A:ASP373 4.4 12.0 1.0 OD2 A:ASP367 4.4 25.7 1.0 C A:ASN372 4.5 7.5 1.0 N A:ASN372 4.5 11.7 1.0 N A:LEU366 4.6 12.2 1.0 N A:GLY394 4.6 10.1 1.0 CA A:ASN372 4.6 8.8 1.0 CB A:TYR371 4.6 21.9 1.0 N A:ASP373 4.6 1.9 1.0 N A:ASP367 4.6 16.9 1.0 O A:GLY394 4.7 29.2 1.0 O A:ASN372 4.7 18.3 1.0 N A:ASP369 4.7 17.8 1.0 CG A:ASP365 4.8 23.2 1.0 CA A:ASP365 4.9 21.0 1.0 CB A:LEU393 5.0 22.0 1.0

Calcium binding site 4 out of 6 in the Structure of the Semi-Extended ALPHAIIBBETA3 in Complex with R21D10 Fab


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of the Semi-Extended ALPHAIIBBETA3 in Complex with R21D10 Fab within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1104 b:0.0 occ:1.00 OD1 A:ASP434 2.2 10.7 1.0 OD1 A:ASN430 2.2 18.0 1.0 OD1 A:ASP426 2.4 16.1 1.0 OD2 A:ASP434 2.6 13.5 1.0 O A:TYR432 2.6 14.2 1.0 CG A:ASP434 2.7 5.7 1.0 OD1 A:ASP428 2.9 24.1 1.0 CG A:ASN430 3.3 19.9 1.0 CG A:ASP426 3.5 18.0 1.0 CG A:ASP428 3.6 21.3 1.0 OD2 A:ASP428 3.7 26.4 1.0 C A:TYR432 3.7 7.4 1.0 ND2 A:ASN430 4.0 13.0 1.0 CB A:ASP434 4.2 0.3 1.0 OD2 A:ASP426 4.2 20.5 1.0 N A:TYR432 4.3 6.6 1.0 N A:ILE427 4.4 14.9 1.0 O A:ALA450 4.4 22.0 1.0 CB A:ASN430 4.5 21.0 1.0 N A:ASP434 4.5 12.4 1.0 CA A:TYR432 4.5 6.0 1.0 CA A:ASP426 4.5 9.4 1.0 N A:ASP428 4.5 17.1 1.0 N A:ASN430 4.5 17.2 1.0 CB A:ASP426 4.5 15.3 1.0 N A:ALA450 4.6 15.0 1.0 CB A:TYR432 4.6 8.2 1.0 C A:PRO433 4.7 8.8 1.0 N A:PRO433 4.7 0.4 1.0 CA A:ASP434 4.8 3.8 1.0 CA A:PRO433 4.8 4.3 1.0 C A:ASP426 4.8 11.5 1.0 CB A:ASP428 4.9 16.3 1.0 CA A:ASN430 4.9 18.8 1.0 N A:ASP429 4.9 32.9 1.0

Calcium binding site 5 out of 6 in the Structure of the Semi-Extended ALPHAIIBBETA3 in Complex with R21D10 Fab


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of the Semi-Extended ALPHAIIBBETA3 in Complex with R21D10 Fab within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1000 b:34.7 occ:1.00 O B:HOH1103 2.2 25.3 1.0 OD1 B:ASP126 2.2 35.6 1.0 OD2 B:ASP126 2.5 40.8 1.0 CG B:ASP126 2.7 38.0 1.0 O B:SER123 3.1 22.7 1.0 O B:MET335 3.6 23.4 1.0 OD1 B:ASP127 3.8 22.9 1.0 CB B:ASP126 4.2 32.0 1.0 C B:SER123 4.2 22.1 1.0 C B:MET335 4.5 24.2 1.0 N B:ASP126 4.6 29.8 1.0 CG B:ASP127 4.8 20.2 1.0 CA B:ASP126 4.9 27.8 1.0 CA B:MET124 4.9 15.5 1.0 N B:MET124 4.9 17.9 1.0 N B:LYS125 5.0 17.6 1.0 N B:ASP127 5.0 21.0 1.0

Calcium binding site 6 out of 6 in the Structure of the Semi-Extended ALPHAIIBBETA3 in Complex with R21D10 Fab


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of the Semi-Extended ALPHAIIBBETA3 in Complex with R21D10 Fab within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1001 b:12.5 occ:1.00 OD1 B:ASP217 2.1 4.9 1.0 OD2 B:ASP158 2.2 14.0 1.0 ND2 B:ASN215 2.2 1.8 1.0 O B:PRO219 2.2 21.7 1.0 OE1 B:GLU220 2.8 20.8 1.0 CG B:ASP217 2.9 5.1 1.0 OD2 B:ASP217 3.1 11.2 1.0 CG B:ASP158 3.2 12.6 1.0 C B:PRO219 3.4 8.8 1.0 CG B:ASN215 3.5 6.4 1.0 CB B:ASP158 3.5 0.3 1.0 CD B:GLU220 3.7 20.0 1.0 O B:ASP217 3.8 10.7 1.0 CA B:GLU220 3.8 2.5 1.0 N B:GLU220 4.0 1.8 1.0 C B:ASP217 4.2 4.8 1.0 CB B:ASP217 4.2 3.7 1.0 NE2 B:HIS255 4.3 11.7 1.0 OD1 B:ASP158 4.3 17.0 1.0 CB B:ASN215 4.3 1.6 1.0 OD1 B:ASN215 4.3 10.6 1.0 OE2 B:GLU220 4.4 22.0 1.0 CB B:GLU220 4.5 7.6 1.0 CD2 B:HIS255 4.5 16.1 1.0 CA B:ASP217 4.5 3.2 1.0 CG B:GLU220 4.6 11.5 1.0 N B:ASP217 4.6 6.2 1.0 CA B:PRO219 4.6 4.0 1.0 N B:PRO219 4.7 2.0 1.0 C B:ALA218 4.7 8.1 1.0 O B:VAL157 4.8 10.7 1.0 N B:GLY221 4.8 1.9 1.0 C B:GLU220 4.8 7.3 1.0 O B:ALA218 4.8 13.3 1.0 N B:ALA218 4.9 10.4 1.0 CA B:ASP158 4.9 0.0 1.0

L.Wang, J.Wang, J.Li, T.Walz, B.S.Coller. An Alpha Iib Beta 3 Monoclonal Antibody Traps A Semiextended Conformation and Allosterically Inhibits Large Ligand Binding. Blood Adv V. 8 4398 2024.
ISSN: ESSN 2473-9537
PubMed: 38968144
DOI: 10.1182/BLOODADVANCES.2024013177