Calcium in PDB 8t2v: Cryo-Em Structures of Full-Length Integrin ALPHAIIBBETA3 in Native Lipids

The structure of Cryo-Em Structures of Full-Length Integrin ALPHAIIBBETA3 in Native Lipids also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Calcium atom in the Cryo-Em Structures of Full-Length Integrin ALPHAIIBBETA3 in Native Lipids (pdb code 8t2v). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the Cryo-Em Structures of Full-Length Integrin ALPHAIIBBETA3 in Native Lipids, PDB code: 8t2v:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in the Cryo-Em Structures of Full-Length Integrin ALPHAIIBBETA3 in Native Lipids


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Cryo-Em Structures of Full-Length Integrin ALPHAIIBBETA3 in Native Lipids within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1101 b:148.8 occ:1.00 OD1 A:ASN299 2.0 205.3 1.0 OD1 A:ASP301 2.2 174.9 1.0 OD2 A:ASP305 2.3 95.5 1.0 OD1 A:ASP297 2.3 165.9 1.0 OD2 A:ASP301 2.3 181.6 1.0 O A:ARG303 2.4 94.1 1.0 ND2 A:ASN299 2.5 176.0 1.0 CG A:ASN299 2.5 178.2 1.0 OD1 A:ASP305 2.6 96.7 1.0 CG A:ASP301 2.6 151.9 1.0 CG A:ASP305 2.7 90.7 1.0 CG A:ASP297 3.5 131.6 1.0 C A:ARG303 3.6 86.9 1.0 CB A:ASN299 3.9 125.7 1.0 CB A:ASP301 4.1 139.5 1.0 CB A:ASP305 4.1 86.0 1.0 OD2 A:ASP297 4.2 144.1 1.0 N A:ASN299 4.2 100.2 1.0 N A:ASP305 4.2 70.5 1.0 CA A:ASP297 4.3 89.7 1.0 N A:ARG303 4.3 115.5 1.0 CA A:ARG303 4.3 116.4 1.0 CB A:ARG303 4.4 134.2 1.0 CD2 A:LEU332 4.4 119.5 1.0 CB A:ASP297 4.5 90.7 1.0 C A:HIS304 4.5 61.0 1.0 CA A:ASN299 4.5 102.4 1.0 N A:ASP301 4.6 130.9 1.0 N A:HIS304 4.6 73.1 1.0 N A:VAL298 4.6 64.3 1.0 CA A:ASP305 4.6 84.7 1.0 C A:ASP297 4.7 84.9 1.0 N A:GLY300 4.7 94.2 1.0 CA A:HIS304 4.8 74.6 1.0 CA A:ASP301 4.9 140.0 1.0 C A:ASN299 4.9 96.2 1.0 N A:GLN333 4.9 92.2 1.0

Calcium binding site 2 out of 7 in the Cryo-Em Structures of Full-Length Integrin ALPHAIIBBETA3 in Native Lipids


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Cryo-Em Structures of Full-Length Integrin ALPHAIIBBETA3 in Native Lipids within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1102 b:206.3 occ:1.00 OE1 A:GLU243 1.8 212.2 1.0 OE1 A:GLU252 1.8 162.2 1.0 OD1 A:ASP245 2.1 188.7 1.0 CD A:GLU243 2.4 198.4 1.0 CD A:GLU252 2.4 142.1 1.0 O A:ASP247 2.4 186.8 1.0 OE2 A:GLU252 2.5 165.4 1.0 OE2 A:GLU243 2.5 231.5 1.0 OG1 A:THR250 2.5 191.6 1.0 O A:THR250 2.6 152.9 1.0 CG A:ASP245 3.0 164.6 1.0 CB A:THR250 3.2 197.8 1.0 C A:THR250 3.3 142.4 1.0 C A:ASP247 3.6 202.9 1.0 CB A:ASP245 3.7 162.3 1.0 CA A:THR250 3.7 149.7 1.0 CG A:GLU243 3.8 158.2 1.0 OD2 A:ASP245 3.9 164.1 1.0 CG A:GLU252 3.9 148.8 1.0 N A:ASP245 4.0 133.2 1.0 N A:ASP247 4.0 171.0 1.0 CA A:GLU243 4.2 133.8 1.0 N A:THR251 4.2 143.4 1.0 N A:THR250 4.2 152.1 1.0 CA A:ASP245 4.3 150.1 1.0 N A:GLY246 4.3 123.2 1.0 CA A:ASP247 4.3 207.4 1.0 N A:PHE244 4.4 144.8 1.0 N A:GLU252 4.4 103.3 1.0 CB A:GLU243 4.5 145.4 1.0 CG2 A:THR250 4.6 217.0 1.0 C A:GLU243 4.6 118.9 1.0 CA A:THR251 4.6 145.8 1.0 N A:LEU248 4.6 214.0 1.0 C A:ASP245 4.7 158.0 1.0 CB A:ASP247 4.8 241.9 1.0 O A:GLY242 4.8 147.4 1.0 CA A:LEU248 4.9 230.1 1.0 CB A:GLU252 4.9 97.6 1.0 C A:LEU248 5.0 218.7 1.0

Calcium binding site 3 out of 7 in the Cryo-Em Structures of Full-Length Integrin ALPHAIIBBETA3 in Native Lipids


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Cryo-Em Structures of Full-Length Integrin ALPHAIIBBETA3 in Native Lipids within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1103 b:158.1 occ:1.00 OD1 A:ASP373 2.0 143.0 1.0 OD2 A:ASP369 2.1 172.9 1.0 OD1 A:ASP367 2.2 203.3 1.0 OD2 A:ASP373 2.3 128.7 1.0 CG A:ASP373 2.4 118.4 1.0 OD1 A:ASP369 2.5 154.6 1.0 O A:TYR371 2.5 121.4 1.0 CG A:ASP369 2.5 195.3 1.0 OD1 A:ASP365 3.2 140.2 1.0 CG A:ASP367 3.3 167.1 1.0 OD2 A:ASP367 3.7 173.6 1.0 C A:TYR371 3.7 98.4 1.0 CB A:ASP373 3.9 81.5 1.0 CB A:ASP369 4.0 179.1 1.0 N A:ASP367 4.2 116.7 1.0 CD2 A:LEU393 4.3 105.6 1.0 CG A:ASP365 4.3 159.2 1.0 N A:LEU366 4.3 71.2 1.0 N A:ASP369 4.4 159.2 1.0 CA A:ASP365 4.4 113.2 1.0 N A:GLY394 4.5 91.3 1.0 C A:ASN372 4.5 99.8 1.0 N A:ASP373 4.5 92.9 1.0 N A:TYR371 4.6 82.7 1.0 CA A:TYR371 4.6 96.5 1.0 CB A:ASP367 4.6 116.8 1.0 C A:ASP365 4.6 94.2 1.0 O A:ASN372 4.7 101.3 1.0 N A:ASN372 4.7 85.8 1.0 CB A:LEU393 4.7 121.5 1.0 CA A:ASP369 4.7 165.0 1.0 CA A:ASN372 4.8 94.8 1.0 CA A:ASP367 4.8 110.9 1.0 N A:ARG368 4.8 97.7 1.0 O A:GLY394 4.8 120.3 1.0 CA A:ASP373 4.8 73.5 1.0 CB A:TYR371 4.8 115.8 1.0 O A:GLY364 5.0 76.4 1.0 CB A:ASP365 5.0 136.9 1.0

Calcium binding site 4 out of 7 in the Cryo-Em Structures of Full-Length Integrin ALPHAIIBBETA3 in Native Lipids


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Cryo-Em Structures of Full-Length Integrin ALPHAIIBBETA3 in Native Lipids within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1104 b:154.5 occ:1.00 OD1 A:ASN430 1.9 130.8 1.0 OD1 A:ASP434 2.0 111.9 1.0 OD1 A:ASP428 2.0 190.4 1.0 OD2 A:ASP434 2.0 100.0 1.0 CG A:ASP434 2.3 97.8 1.0 OD2 A:ASP428 2.3 135.4 1.0 O A:TYR432 2.3 99.6 1.0 CG A:ASP428 2.4 187.1 1.0 CG A:ASN430 2.8 134.1 1.0 OD1 A:ASP426 3.2 156.3 1.0 ND2 A:ASN430 3.2 181.1 1.0 C A:TYR432 3.5 86.7 1.0 CB A:ASP434 3.8 74.2 1.0 CB A:ASP428 3.9 158.3 1.0 CB A:ASN430 4.0 109.8 1.0 N A:TYR432 4.2 85.5 1.0 CA A:TYR432 4.2 87.3 1.0 N A:ASP434 4.3 78.5 1.0 CB A:TYR432 4.3 101.4 1.0 C A:PRO433 4.4 75.9 1.0 N A:ASP428 4.4 148.3 1.0 N A:ALA450 4.4 122.9 1.0 CG A:ASP426 4.4 198.7 1.0 N A:ASN430 4.4 121.3 1.0 O A:ALA450 4.4 172.0 1.0 CA A:ASP434 4.5 70.2 1.0 N A:PRO433 4.5 86.9 1.0 CB A:ALA450 4.5 106.1 1.0 CA A:ASP428 4.6 139.9 1.0 CA A:PRO433 4.6 92.6 1.0 CA A:ASN430 4.7 114.7 1.0 O A:PRO433 4.7 73.8 1.0 N A:ILE427 4.8 97.7 1.0 CA A:ASP426 4.8 136.3 1.0 CA A:ALA450 4.9 103.3 1.0

Calcium binding site 5 out of 7 in the Cryo-Em Structures of Full-Length Integrin ALPHAIIBBETA3 in Native Lipids


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Cryo-Em Structures of Full-Length Integrin ALPHAIIBBETA3 in Native Lipids within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1109 b:297.0 occ:1.00 OE1 A:GLU642 1.8 305.3 1.0 OD2 A:ASP605 2.0 295.2 1.0 OD1 A:ASP605 2.1 292.5 1.0 CG A:ASP605 2.2 311.1 1.0 O A:CYS602 2.4 275.8 1.0 CD A:GLU642 2.5 301.6 1.0 O A:VAL607 2.5 268.5 1.0 OE2 A:GLU642 2.5 285.5 1.0 C A:CYS602 3.5 266.7 1.0 C A:VAL607 3.5 258.1 1.0 CB A:ASP605 3.6 306.3 1.0 CG A:GLU642 3.9 299.6 1.0 N A:VAL607 4.1 272.5 1.0 N A:GLY603 4.3 242.0 1.0 CA A:CYS602 4.3 274.6 1.0 N A:VAL609 4.4 266.1 1.0 N A:CYS608 4.4 251.7 1.0 CA A:VAL607 4.4 274.9 1.0 CA A:GLY603 4.4 247.1 1.0 CA A:CYS608 4.4 271.2 1.0 CA A:ASP605 4.5 297.3 1.0 N A:ASP605 4.5 279.7 1.0 CG2 A:VAL609 4.6 261.5 1.0 N A:ASP606 4.6 283.9 1.0 CB A:CYS602 4.8 276.7 1.0 C A:ASP605 4.8 291.2 1.0 C A:GLY603 4.8 286.6 1.0 C A:CYS608 4.9 257.1 1.0 CB A:VAL607 4.9 277.8 1.0 CB A:VAL609 5.0 281.2 1.0

Calcium binding site 6 out of 7 in the Cryo-Em Structures of Full-Length Integrin ALPHAIIBBETA3 in Native Lipids


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Cryo-Em Structures of Full-Length Integrin ALPHAIIBBETA3 in Native Lipids within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca805 b:111.7 occ:1.00 OE1 B:GLU220 1.8 138.5 1.0 OD2 B:ASP158 2.0 130.8 1.0 OD1 B:ASN215 2.0 86.8 1.0 OD1 B:ASP217 2.1 77.4 1.0 O B:PRO219 2.1 98.7 1.0 CG B:ASP217 2.5 109.1 1.0 O B:ASP217 2.5 95.1 1.0 CG B:ASN215 2.7 100.7 1.0 OD2 B:ASP217 2.8 76.1 1.0 CD B:GLU220 2.9 103.3 1.0 ND2 B:ASN215 3.2 112.5 1.0 CG B:ASP158 3.2 150.1 1.0 C B:PRO219 3.3 71.1 1.0 C B:ASP217 3.4 98.8 1.0 CB B:ASP217 3.6 109.4 1.0 OE2 B:GLU220 3.6 135.5 1.0 CA B:ASP217 3.8 103.7 1.0 N B:ASP217 3.8 117.8 1.0 CB B:ASN215 3.9 87.8 1.0 CA B:GLU220 4.0 78.7 1.0 N B:GLU220 4.0 69.6 1.0 OD1 B:ASP158 4.0 147.5 1.0 CG B:GLU220 4.1 80.5 1.0 CB B:ASP158 4.2 113.3 1.0 CB B:GLU220 4.4 64.1 1.0 C B:ALA218 4.4 121.4 1.0 O B:ALA218 4.4 97.0 1.0 CA B:PRO219 4.4 74.9 1.0 N B:PRO219 4.5 86.2 1.0 N B:ALA218 4.5 93.6 1.0 C B:ARG216 4.6 96.9 1.0 C B:ASN215 4.7 69.0 1.0 N B:ARG216 4.7 64.4 1.0 O B:HOH904 4.7 72.8 1.0 O B:ASN215 4.9 76.5 1.0 CA B:ALA218 5.0 141.1 1.0 CA B:ASN215 5.0 66.5 1.0

Calcium binding site 7 out of 7 in the Cryo-Em Structures of Full-Length Integrin ALPHAIIBBETA3 in Native Lipids


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Cryo-Em Structures of Full-Length Integrin ALPHAIIBBETA3 in Native Lipids within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca806 b:221.0 occ:1.00 O B:HOH903 1.9 108.7 1.0 OD1 B:ASP126 1.9 246.0 1.0 OD2 B:ASP126 2.0 222.7 1.0 O B:HOH901 2.1 126.1 1.0 OD1 B:ASP127 2.1 199.7 1.0 CG B:ASP126 2.2 221.7 1.0 O B:SER123 2.4 201.2 1.0 O B:MET335 2.6 179.9 1.0 CG B:ASP127 2.8 156.8 1.0 OD2 B:ASP127 3.2 133.5 1.0 C B:SER123 3.6 147.1 1.0 CB B:ASP126 3.7 198.1 1.0 C B:MET335 3.8 148.0 1.0 N B:ASP127 3.8 149.7 1.0 CB B:ASP127 4.0 141.3 1.0 CA B:MET124 4.0 156.1 1.0 CE B:MET335 4.2 252.6 1.0 N B:MET124 4.3 123.7 1.0 CA B:ASP126 4.4 176.5 1.0 N B:ASP126 4.4 177.2 1.0 CA B:ASP127 4.5 136.9 1.0 C B:MET124 4.5 109.7 1.0 C B:ASP126 4.5 145.4 1.0 CA B:ASP336 4.6 142.9 1.0 N B:ASP336 4.6 144.2 1.0 CA B:SER123 4.7 155.0 1.0 CA B:MET335 4.8 153.5 1.0 O B:MET124 4.9 103.0 1.0 N B:LYS125 5.0 119.4 1.0

B.D.Adair, J.P.Xiong, M.Yeager, M.A.Arnaout. Cryo-Em Structures of Full-Length Integrin Alpha Iib Beta 3 in Native Lipids. Nat Commun V. 14 4168 2023.
ISSN: ESSN 2041-1723
PubMed: 37443315
DOI: 10.1038/S41467-023-39763-0