Calcium in PDB 8gcd: Full Length Integrin ALPHAIIBBETA3 in Inactive State

The structure of Full Length Integrin ALPHAIIBBETA3 in Inactive State also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Calcium atom in the Full Length Integrin ALPHAIIBBETA3 in Inactive State (pdb code 8gcd). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the Full Length Integrin ALPHAIIBBETA3 in Inactive State, PDB code: 8gcd:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in the Full Length Integrin ALPHAIIBBETA3 in Inactive State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Full Length Integrin ALPHAIIBBETA3 in Inactive State within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1101 b:55.0 occ:1.00 O A:THR250 2.3 49.9 1.0 OE2 A:GLU243 2.3 33.1 1.0 OD2 A:ASP245 2.3 43.2 1.0 O A:ASP247 2.4 57.2 1.0 OE2 A:GLU252 2.4 34.3 1.0 OG1 A:THR250 2.4 49.9 1.0 OE1 A:GLU252 2.4 34.3 1.0 OE1 A:GLU243 2.4 33.1 1.0 OD1 A:ASP245 2.4 43.2 1.0 CG A:ASP245 2.6 43.2 1.0 CD A:GLU243 2.7 33.1 1.0 CD A:GLU252 2.7 34.3 1.0 C A:THR250 3.0 49.9 1.0 C A:ASP247 3.5 57.2 1.0 CB A:THR250 3.5 49.9 1.0 CA A:THR250 3.7 49.9 1.0 N A:THR251 3.8 38.3 1.0 N A:THR250 4.1 49.9 1.0 N A:ASP247 4.1 57.2 1.0 CB A:ASP245 4.1 43.2 1.0 CA A:THR251 4.1 38.3 1.0 CG A:GLU243 4.2 33.1 1.0 CA A:ASP247 4.2 57.2 1.0 CG A:GLU252 4.2 34.3 1.0 N A:ASP245 4.4 43.2 1.0 N A:GLY246 4.4 49.4 1.0 CB A:ASP247 4.4 57.2 1.0 O A:LEU248 4.4 60.0 1.0 C A:THR251 4.5 38.3 1.0 N A:LEU248 4.6 60.0 1.0 C A:LEU248 4.7 60.0 1.0 CA A:ASP245 4.7 43.2 1.0 CG2 A:THR250 4.7 49.9 1.0 N A:PHE244 4.8 30.5 1.0 CA A:LEU248 4.8 60.0 1.0 N A:GLU252 4.8 34.3 1.0 C A:GLY246 4.8 49.4 1.0 CA A:GLU243 4.9 33.1 1.0 CB A:GLU243 5.0 33.1 1.0 O A:THR251 5.0 38.3 1.0

Calcium binding site 2 out of 7 in the Full Length Integrin ALPHAIIBBETA3 in Inactive State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Full Length Integrin ALPHAIIBBETA3 in Inactive State within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1102 b:19.7 occ:1.00 OD1 A:ASP305 2.3 18.8 1.0 OD1 A:ASP297 2.3 20.6 1.0 OD1 A:ASP301 2.3 23.1 1.0 OD1 A:ASN299 2.4 20.6 1.0 OD2 A:ASP305 2.4 18.8 1.0 O A:ARG303 2.4 26.4 1.0 CG A:ASP305 2.6 18.8 1.0 CG A:ASP301 3.4 23.1 1.0 CG A:ASN299 3.4 20.6 1.0 C A:ARG303 3.5 26.4 1.0 CG A:ASP297 3.6 20.6 1.0 ND2 A:ASN299 3.9 20.6 1.0 OD2 A:ASP301 4.0 23.1 1.0 CB A:ASP305 4.0 18.8 1.0 N A:ASP305 4.1 18.8 1.0 CA A:ARG303 4.3 26.4 1.0 N A:ARG303 4.3 26.4 1.0 CB A:ARG303 4.3 26.4 1.0 CA A:ASP297 4.3 20.6 1.0 OD2 A:ASP297 4.4 20.6 1.0 CB A:ASP297 4.4 20.6 1.0 CB A:ASP301 4.5 23.1 1.0 CA A:ASP305 4.5 18.8 1.0 N A:ASN299 4.5 20.6 1.0 N A:HIS304 4.6 20.4 1.0 C A:HIS304 4.6 20.4 1.0 CB A:ASN299 4.7 20.6 1.0 N A:ASP301 4.7 23.1 1.0 N A:GLN333 4.7 27.6 1.0 N A:VAL298 4.7 20.0 1.0 C A:ASP297 4.7 20.6 1.0 CB A:GLN333 4.8 27.6 1.0 CA A:HIS304 4.8 20.4 1.0 CD2 A:LEU332 4.8 22.2 1.0

Calcium binding site 3 out of 7 in the Full Length Integrin ALPHAIIBBETA3 in Inactive State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Full Length Integrin ALPHAIIBBETA3 in Inactive State within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1103 b:36.6 occ:1.00 OD1 A:ASP367 2.2 32.6 1.0 OD1 A:ASP369 2.3 36.2 1.0 O A:TYR371 2.3 31.9 1.0 OD1 A:ASP373 2.3 21.0 1.0 OD2 A:ASP373 2.4 21.0 1.0 OD2 A:ASP369 2.4 36.2 1.0 OD2 A:ASP367 2.5 32.6 1.0 OD1 A:ASP365 2.5 29.7 1.0 CG A:ASP369 2.6 36.2 1.0 CG A:ASP373 2.7 21.0 1.0 CG A:ASP367 2.7 32.6 1.0 C A:TYR371 3.5 31.9 1.0 CG A:ASP365 3.7 29.7 1.0 CB A:ASP369 4.0 36.2 1.0 CB A:ASP373 4.2 21.0 1.0 CB A:TYR371 4.2 31.9 1.0 CB A:ASP367 4.2 32.6 1.0 CA A:TYR371 4.2 31.9 1.0 N A:TYR371 4.3 31.9 1.0 OD2 A:ASP365 4.4 29.7 1.0 N A:ASP373 4.4 21.0 1.0 N A:ASP367 4.5 32.6 1.0 C A:ASN372 4.5 24.1 1.0 N A:ASN372 4.6 24.1 1.0 N A:ASP369 4.6 36.2 1.0 CA A:ASP365 4.6 29.7 1.0 O A:GLY394 4.7 26.0 1.0 CD2 A:LEU393 4.7 19.1 1.0 N A:LEU366 4.8 25.3 1.0 N A:GLY394 4.8 26.0 1.0 CA A:ASN372 4.8 24.1 1.0 CB A:ASP365 4.8 29.7 1.0 CA A:ASP373 4.8 21.0 1.0 CA A:ASP369 4.8 36.2 1.0 CA A:ASP367 4.9 32.6 1.0 CB A:LEU393 4.9 19.1 1.0 O A:ASN372 5.0 24.1 1.0 C A:ASP365 5.0 29.7 1.0

Calcium binding site 4 out of 7 in the Full Length Integrin ALPHAIIBBETA3 in Inactive State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Full Length Integrin ALPHAIIBBETA3 in Inactive State within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1104 b:29.4 occ:1.00 OD1 A:ASP434 2.2 20.5 1.0 ND2 A:ASN430 2.2 34.6 1.0 OD1 A:ASP426 2.3 25.7 1.0 OD1 A:ASN430 2.3 34.6 1.0 OD1 A:ASP428 2.4 33.0 1.0 O A:TYR432 2.4 31.3 1.0 OD2 A:ASP434 2.4 20.5 1.0 CG A:ASN430 2.6 34.6 1.0 CG A:ASP434 2.6 20.5 1.0 CG A:ASP426 3.4 25.7 1.0 CG A:ASP428 3.5 33.0 1.0 C A:TYR432 3.6 31.3 1.0 N A:ILE427 3.9 24.7 1.0 OD2 A:ASP428 4.0 33.0 1.0 CB A:ASP434 4.0 20.5 1.0 CB A:ASN430 4.1 34.6 1.0 OD2 A:ASP426 4.1 25.7 1.0 N A:ASP428 4.2 33.0 1.0 CA A:ASP426 4.3 25.7 1.0 N A:ASP434 4.3 20.5 1.0 N A:TYR432 4.3 31.3 1.0 CA A:TYR432 4.4 31.3 1.0 C A:PRO433 4.4 21.9 1.0 CB A:ASP426 4.4 25.7 1.0 N A:ASN430 4.5 34.6 1.0 N A:PRO433 4.6 21.9 1.0 CB A:TYR432 4.6 31.3 1.0 C A:ASP426 4.6 25.7 1.0 CA A:PRO433 4.7 21.9 1.0 CA A:ASP434 4.7 20.5 1.0 CB A:ASP428 4.8 33.0 1.0 O A:PRO433 4.8 21.9 1.0 CG2 A:ILE427 4.8 24.7 1.0 CA A:ASN430 4.8 34.6 1.0 O A:ALA450 4.9 24.2 1.0 CA A:ILE427 4.9 24.7 1.0 CA A:ASP428 4.9 33.0 1.0 N A:ALA450 5.0 24.2 1.0

Calcium binding site 5 out of 7 in the Full Length Integrin ALPHAIIBBETA3 in Inactive State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Full Length Integrin ALPHAIIBBETA3 in Inactive State within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1105 b:117.3 occ:1.00 O A:CYS602 2.2 109.7 1.0 N A:ASP605 2.3 109.7 1.0 N A:GLU604 2.3 112.5 1.0 OD2 A:ASP605 2.5 109.7 1.0 C A:GLY603 2.5 111.3 1.0 OE2 A:GLU642 2.7 101.4 1.0 CG A:ASP605 2.8 109.7 1.0 CA A:GLY603 2.9 111.3 1.0 C A:GLU604 3.1 112.5 1.0 CA A:GLU604 3.2 112.5 1.0 C A:CYS602 3.2 109.7 1.0 CB A:ASP605 3.2 109.7 1.0 CA A:ASP605 3.3 109.7 1.0 O A:GLY603 3.3 111.3 1.0 OD1 A:ASP605 3.4 109.7 1.0 N A:GLY603 3.5 111.3 1.0 CD A:GLU642 3.8 101.4 1.0 N A:ASP606 3.9 104.0 1.0 CB A:GLU604 4.0 112.5 1.0 C A:ASP605 4.1 109.7 1.0 OE1 A:GLU642 4.2 101.4 1.0 O A:GLU604 4.3 112.5 1.0 O A:VAL607 4.5 105.1 1.0 CA A:CYS602 4.6 109.7 1.0 CB A:CYS602 4.9 109.7 1.0

Calcium binding site 6 out of 7 in the Full Length Integrin ALPHAIIBBETA3 in Inactive State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Full Length Integrin ALPHAIIBBETA3 in Inactive State within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2002 b:51.1 occ:1.00 OD2 B:ASP126 2.4 48.5 1.0 OD1 B:ASP126 2.4 48.5 1.0 O B:SER123 2.5 43.1 1.0 CG B:ASP126 2.7 48.5 1.0 O B:MET335 3.0 54.7 1.0 C B:SER123 3.7 43.1 1.0 OD2 B:ASP251 3.7 46.4 1.0 CA B:MET124 3.9 47.0 1.0 CB B:ASP126 4.2 48.5 1.0 C B:MET335 4.2 54.7 1.0 N B:MET124 4.2 47.0 1.0 C B:MET124 4.7 47.0 1.0 N B:ASP126 4.8 48.5 1.0 N B:ASP127 4.8 50.4 1.0 CB B:MET124 4.8 47.0 1.0 CA B:SER123 4.8 43.1 1.0 CA B:MET335 4.9 54.7 1.0 CG B:MET124 4.9 47.0 1.0 CG B:ASP251 4.9 46.4 1.0 CA B:ASP126 5.0 48.5 1.0

Calcium binding site 7 out of 7 in the Full Length Integrin ALPHAIIBBETA3 in Inactive State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Full Length Integrin ALPHAIIBBETA3 in Inactive State within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2003 b:33.5 occ:1.00 O B:PRO219 2.2 30.7 1.0 ND2 B:ASN215 2.2 37.8 1.0 OD1 B:ASP217 2.3 34.2 1.0 OD2 B:ASP158 2.4 47.3 1.0 O B:ASP217 2.5 34.2 1.0 CG B:ASN215 3.2 37.8 1.0 CG B:ASP217 3.4 34.2 1.0 C B:PRO219 3.4 30.7 1.0 CG B:ASP158 3.5 47.3 1.0 C B:ASP217 3.5 34.2 1.0 CB B:ASN215 3.6 37.8 1.0 OE1 B:GLU220 4.0 40.4 1.0 N B:ASP217 4.1 34.2 1.0 CB B:ASP158 4.1 47.3 1.0 OD2 B:ASP217 4.1 34.2 1.0 CA B:GLU220 4.2 40.4 1.0 OD1 B:ASN215 4.2 37.8 1.0 CA B:ASP217 4.2 34.2 1.0 N B:GLU220 4.2 40.4 1.0 C B:ALA218 4.4 29.9 1.0 N B:PRO219 4.4 30.7 1.0 CB B:ASP217 4.4 34.2 1.0 O B:ALA218 4.4 29.9 1.0 CA B:PRO219 4.5 30.7 1.0 CD B:GLU220 4.6 40.4 1.0 NE2 B:HIS255 4.6 37.0 1.0 OD1 B:ASP158 4.6 47.3 1.0 N B:ALA218 4.6 29.9 1.0 N B:ARG216 4.7 38.1 1.0 CD2 B:HIS255 4.9 37.0 1.0 CA B:ALA218 4.9 29.9 1.0 CA B:ASN215 4.9 37.8 1.0 C B:ARG216 4.9 38.1 1.0 OE2 B:GLU220 5.0 40.4 1.0

T.Huo, H.Wu, Z.Moussa, M.Sen, V.Daltion, Z.Wang. Full-Length ALPHAIIBBETA3 Cryoem Structure Reveals Intact Integrin Initiate-Activation Intrinsic Architecture To Be Published.