Calcium in PDB 7la4: Integrin ALPHAIIBBETA3-PT25-2 Complex

The structure of Integrin ALPHAIIBBETA3-PT25-2 Complex also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Calcium atom in the Integrin ALPHAIIBBETA3-PT25-2 Complex (pdb code 7la4). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Integrin ALPHAIIBBETA3-PT25-2 Complex, PDB code: 7la4:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Integrin ALPHAIIBBETA3-PT25-2 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Integrin ALPHAIIBBETA3-PT25-2 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1101 b:43.0 occ:1.00 OD1 A:ASP245 2.4 41.2 1.0 OE2 A:GLU243 2.4 38.4 1.0 O A:ASP247 2.4 43.9 1.0 OE1 A:GLU243 2.4 38.4 1.0 OE1 A:GLU252 2.4 37.6 1.0 OE2 A:GLU252 2.4 37.6 1.0 O A:THR250 2.4 42.1 1.0 CD A:GLU243 2.7 38.4 1.0 CD A:GLU252 2.8 37.6 1.0 OG1 A:THR250 2.8 42.1 1.0 C A:THR250 3.1 42.1 1.0 CG A:ASP245 3.5 41.2 1.0 C A:ASP247 3.5 43.9 1.0 N A:THR251 3.8 38.7 1.0 CB A:THR250 3.8 42.1 1.0 CA A:THR250 3.9 42.1 1.0 CA A:THR251 4.0 38.7 1.0 OD2 A:ASP245 4.0 41.2 1.0 N A:ASP247 4.2 43.9 1.0 CA A:ASP247 4.2 43.9 1.0 N A:THR250 4.2 42.1 1.0 CG A:GLU243 4.3 38.4 1.0 CG A:GLU252 4.3 37.6 1.0 CB A:ASP247 4.3 43.9 1.0 C A:THR251 4.3 38.7 1.0 N A:ASP245 4.5 41.2 1.0 N A:LEU248 4.6 42.1 1.0 N A:GLU252 4.6 37.6 1.0 CB A:ASP245 4.7 41.2 1.0 N A:GLY246 4.7 42.9 1.0 CA A:LEU248 4.8 42.1 1.0 CA A:GLU243 4.8 38.4 1.0 C A:GLY246 4.8 42.9 1.0 C A:ASP245 4.8 41.2 1.0 N A:PHE244 4.9 36.9 1.0 O A:THR251 4.9 38.7 1.0 CA A:ASP245 4.9 41.2 1.0 CB A:GLU243 5.0 38.4 1.0 C A:LEU248 5.0 42.1 1.0

Calcium binding site 2 out of 6 in the Integrin ALPHAIIBBETA3-PT25-2 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Integrin ALPHAIIBBETA3-PT25-2 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1102 b:37.9 occ:1.00 OD1 A:ASP301 2.3 39.4 1.0 OD2 A:ASP305 2.3 34.3 1.0 O A:HOH1203 2.4 37.9 1.0 OD1 A:ASN299 2.4 37.5 1.0 O A:ARG303 2.4 39.1 1.0 OD1 A:ASP297 2.5 38.7 1.0 OD1 A:ASP305 2.6 34.3 1.0 CG A:ASP305 2.7 34.3 1.0 CG A:ASP301 3.0 39.4 1.0 OD2 A:ASP301 3.1 39.4 1.0 C A:ARG303 3.2 39.1 1.0 CB A:ARG303 3.4 39.1 1.0 CG A:ASN299 3.4 37.5 1.0 CA A:ARG303 3.6 39.1 1.0 CG A:ASP297 3.6 38.7 1.0 N A:ARG303 3.7 39.1 1.0 ND2 A:ASN299 3.7 37.5 1.0 CB A:ASP305 3.9 34.3 1.0 N A:ASP305 4.0 34.3 1.0 N A:HIS304 4.2 35.7 1.0 CA A:ASP297 4.3 38.7 1.0 CG A:ARG303 4.4 39.1 1.0 CB A:ASP297 4.4 38.7 1.0 OD2 A:ASP297 4.4 38.7 1.0 O A:GLN333 4.4 35.4 1.0 CB A:ASP301 4.4 39.4 1.0 CA A:ASP305 4.5 34.3 1.0 N A:ASN299 4.5 37.5 1.0 N A:VAL298 4.5 35.6 1.0 N A:ASP301 4.6 39.4 1.0 C A:HIS304 4.7 35.7 1.0 C A:ASP297 4.7 38.7 1.0 N A:GLN333 4.8 35.4 1.0 CB A:ASN299 4.8 37.5 1.0 CA A:HIS304 4.8 35.7 1.0 C A:GLY302 4.8 39.9 1.0 N A:GLY302 4.9 39.9 1.0 CA A:ASP301 4.9 39.4 1.0 C A:ASP301 5.0 39.4 1.0

Calcium binding site 3 out of 6 in the Integrin ALPHAIIBBETA3-PT25-2 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Integrin ALPHAIIBBETA3-PT25-2 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1103 b:40.1 occ:1.00 O A:HOH1202 2.4 37.6 1.0 O A:TYR371 2.4 39.4 1.0 OD2 A:ASP373 2.4 34.9 1.0 OD1 A:ASP365 2.4 39.9 1.0 OD1 A:ASP367 2.4 42.1 1.0 OD1 A:ASP369 2.7 42.6 1.0 CG A:ASP373 3.0 34.9 1.0 OD1 A:ASP373 3.2 34.9 1.0 N A:LEU366 3.3 38.8 1.0 CA A:ASP365 3.4 39.9 1.0 CG A:ASP365 3.4 39.9 1.0 C A:TYR371 3.6 39.4 1.0 C A:ASP365 3.6 39.9 1.0 N A:ASP367 3.6 42.1 1.0 CG A:ASP367 3.7 42.1 1.0 CG A:ASP369 3.9 42.6 1.0 CB A:ASP365 4.0 39.9 1.0 N A:ARG368 4.2 44.0 1.0 N A:ASP369 4.2 42.6 1.0 O A:GLY364 4.3 34.5 1.0 CB A:ASP373 4.3 34.9 1.0 CA A:LEU366 4.3 38.8 1.0 OD2 A:ASP367 4.4 42.1 1.0 CA A:ASN372 4.4 37.4 1.0 OD2 A:ASP365 4.4 39.9 1.0 N A:TYR371 4.4 39.4 1.0 C A:ASN372 4.4 37.4 1.0 N A:ASN372 4.4 37.4 1.0 C A:LEU366 4.4 38.8 1.0 CA A:ASP367 4.5 42.1 1.0 N A:ASP373 4.5 34.9 1.0 N A:ASP365 4.5 39.9 1.0 CA A:TYR371 4.6 39.4 1.0 O A:ASP365 4.6 39.9 1.0 C A:ASP367 4.6 42.1 1.0 OD2 A:ASP369 4.6 42.6 1.0 CB A:ASP367 4.7 42.1 1.0 CB A:LEU366 4.7 38.8 1.0 C A:GLY364 4.8 34.5 1.0 CB A:ASP369 4.9 42.6 1.0 O A:ASN372 4.9 37.4 1.0 CA A:ASP369 4.9 42.6 1.0 CA A:ARG368 4.9 44.0 1.0 N A:GLY370 4.9 41.1 1.0

Calcium binding site 4 out of 6 in the Integrin ALPHAIIBBETA3-PT25-2 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Integrin ALPHAIIBBETA3-PT25-2 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1104 b:40.2 occ:1.00 O A:HOH1201 2.4 40.5 1.0 OD1 A:ASP434 2.4 36.4 1.0 OD1 A:ASP426 2.4 40.0 1.0 O A:TYR432 2.5 42.2 1.0 OD2 A:ASP434 2.5 36.4 1.0 CG A:ASP434 2.8 36.4 1.0 OD1 A:ASN430 3.0 43.5 1.0 CB A:ASN430 3.1 43.5 1.0 OD1 A:ASP428 3.2 42.1 1.0 CG A:ASP426 3.5 40.0 1.0 CG A:ASN430 3.5 43.5 1.0 N A:ASN430 3.5 43.5 1.0 C A:TYR432 3.6 42.2 1.0 N A:TYR432 3.8 42.2 1.0 CA A:ASN430 3.8 43.5 1.0 OD2 A:ASP426 3.9 40.0 1.0 CA A:TYR432 4.1 42.2 1.0 CB A:TYR432 4.2 42.2 1.0 CB A:ASP434 4.3 36.4 1.0 O A:ALA450 4.3 40.9 1.0 CG A:ASP428 4.4 42.1 1.0 C A:ASN430 4.4 43.5 1.0 N A:GLY431 4.5 44.8 1.0 N A:ALA450 4.5 40.9 1.0 CB A:ASP426 4.6 40.0 1.0 N A:ASP429 4.7 43.8 1.0 C A:PRO433 4.7 37.4 1.0 N A:PRO433 4.7 37.4 1.0 CA A:ASP426 4.7 40.0 1.0 C A:ASP429 4.7 43.8 1.0 N A:ILE427 4.8 39.8 1.0 N A:ASP434 4.8 36.4 1.0 O A:PRO433 4.8 37.4 1.0 ND2 A:ASN430 4.8 43.5 1.0 N A:ASP428 4.9 42.1 1.0 OD2 A:ASP428 4.9 42.1 1.0 C A:GLY431 5.0 44.8 1.0 C A:ALA450 5.0 40.9 1.0 CA A:ASP434 5.0 36.4 1.0 CA A:PRO433 5.0 37.4 1.0

Calcium binding site 5 out of 6 in the Integrin ALPHAIIBBETA3-PT25-2 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Integrin ALPHAIIBBETA3-PT25-2 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2002 b:50.1 occ:1.00 OD2 B:ASP126 2.4 47.6 1.0 O B:SER123 2.5 45.5 1.0 OD1 B:ASP126 2.5 47.6 1.0 CG B:ASP126 2.8 47.6 1.0 O B:MET335 3.2 49.4 1.0 OD2 B:ASP127 3.4 49.4 1.0 C B:SER123 3.7 45.5 1.0 OD2 B:ASP251 3.8 37.0 1.0 CG B:ASP127 4.1 49.4 1.0 C B:MET335 4.2 49.4 1.0 OD1 B:ASP127 4.3 49.4 1.0 CB B:ASP126 4.3 47.6 1.0 CA B:MET124 4.3 44.0 1.0 N B:MET124 4.4 44.0 1.0 CA B:MET335 4.7 49.4 1.0 CA B:SER123 4.7 45.5 1.0 CB B:SER123 4.8 45.5 1.0 CG B:ASP251 4.8 37.0 1.0 C B:MET124 4.9 44.0 1.0

Calcium binding site 6 out of 6 in the Integrin ALPHAIIBBETA3-PT25-2 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Integrin ALPHAIIBBETA3-PT25-2 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2003 b:39.8 occ:1.00 OD2 B:ASP158 2.4 34.6 1.0 OD1 B:ASP217 2.4 35.3 1.0 ND2 B:ASN215 2.4 39.5 1.0 O B:PRO219 2.5 31.1 1.0 CG B:ASN215 3.2 39.5 1.0 O B:ASP217 3.2 35.3 1.0 CB B:ASN215 3.2 39.5 1.0 CG B:ASP158 3.3 34.6 1.0 CB B:ASP158 3.5 34.6 1.0 CG B:ASP217 3.6 35.3 1.0 C B:PRO219 3.7 31.1 1.0 OE1 B:GLU220 3.8 33.7 1.0 C B:ASP217 4.1 35.3 1.0 N B:ASP217 4.2 35.3 1.0 CA B:GLU220 4.2 33.7 1.0 OD1 B:ASN215 4.3 39.5 1.0 OD2 B:ASP217 4.3 35.3 1.0 N B:GLU220 4.4 33.7 1.0 NE2 B:HIS255 4.4 30.4 1.0 OD1 B:ASP158 4.5 34.6 1.0 N B:ARG216 4.5 38.3 1.0 CA B:ASP217 4.5 35.3 1.0 O B:TYR164 4.5 35.3 1.0 CB B:TYR164 4.5 35.3 1.0 CD B:GLU220 4.6 33.7 1.0 CB B:ASP217 4.6 35.3 1.0 O B:VAL157 4.6 35.4 1.0 CA B:ASN215 4.6 39.5 1.0 CA B:PRO219 4.8 31.1 1.0 N B:PRO219 4.8 31.1 1.0 CA B:ASP158 4.9 34.6 1.0 C B:ALA218 4.9 33.5 1.0 C B:ASN215 5.0 39.5 1.0

D.Nesic, M.Bush, A.Spasic, J.Li, T.Kamata, M.Handa, M.Filizola, T.Walz, B.S.Coller. Electron Microscopy Shows That Binding of Monoclonal Antibody PT25-2 Primes Integrin Alpha Iib Beta 3 For Ligand Binding. Blood Adv V. 5 1781 2021.
ISSN: ESSN 2473-9537
PubMed: 33760023
DOI: 10.1182/BLOODADVANCES.2020004166