Calcium in PDB 9der: Cryo-Em Structures of Full-Length Integrin ALPHAIIBBETA3 in Native Lipids Complexed with Tirofiban

The structure of Cryo-Em Structures of Full-Length Integrin ALPHAIIBBETA3 in Native Lipids Complexed with Tirofiban 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 Complexed with Tirofiban (pdb code 9der). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Cryo-Em Structures of Full-Length Integrin ALPHAIIBBETA3 in Native Lipids Complexed with Tirofiban, PDB code: 9der:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Cryo-Em Structures of Full-Length Integrin ALPHAIIBBETA3 in Native Lipids Complexed with Tirofiban


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 Complexed with Tirofiban within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1101 b:248.6 occ:1.00 HB2 A:ASP247 2.3 231.4 1.0 OG1 A:THR250 2.3 222.5 1.0 OD1 A:ASP245 2.4 237.9 1.0 OD2 A:ASP245 2.4 237.9 1.0 OE2 A:GLU252 2.6 226.9 1.0 CG A:ASP245 2.6 237.9 1.0 OD2 A:ASP247 3.0 231.4 1.0 CB A:ASP247 3.2 231.4 1.0 CG A:ASP247 3.5 231.4 1.0 CB A:THR250 3.5 222.5 1.0 CD A:GLU252 3.6 226.9 1.0 HB A:THR250 3.6 222.5 1.0 HB3 A:ASP247 3.6 231.4 1.0 HG3 A:GLU252 3.7 226.9 1.0 H A:ASP247 3.8 231.4 1.0 HG21 A:THR250 3.9 222.5 1.0 CG A:GLU252 4.0 226.9 1.0 CB A:ASP245 4.1 237.9 1.0 HG2 A:GLU252 4.1 226.9 1.0 CG2 A:THR250 4.2 222.5 1.0 O A:ASP247 4.3 231.4 1.0 CA A:ASP247 4.3 231.4 1.0 HB2 A:ASP245 4.3 237.9 1.0 HB2 A:ASP271 4.4 234.7 1.0 HG23 A:THR250 4.4 222.5 1.0 HD11 A:LEU277 4.4 223.3 1.0 N A:ASP247 4.5 231.4 1.0 HB3 A:ASP245 4.5 237.9 1.0 OE1 A:GLU252 4.6 226.9 1.0 H A:ASP245 4.7 237.9 1.0 HA A:ASP271 4.7 234.7 1.0 HB3 A:ASP271 4.7 234.7 1.0 CA A:THR250 4.7 222.5 1.0 H A:THR250 4.7 222.5 1.0 OD1 A:ASP247 4.7 231.4 1.0 O A:THR250 4.7 222.5 1.0 C A:ASP247 4.8 231.4 1.0 C A:THR250 4.8 222.5 1.0 H A:SER272 4.9 231.5 1.0 CB A:ASP271 4.9 234.7 1.0

Calcium binding site 2 out of 6 in the Cryo-Em Structures of Full-Length Integrin ALPHAIIBBETA3 in Native Lipids Complexed with Tirofiban


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 Complexed with Tirofiban within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1102 b:233.7 occ:1.00 HB2 A:ARG303 2.2 234.9 1.0 O A:ARG303 2.4 234.9 1.0 OD1 A:ASP305 2.4 230.1 1.0 HD21 A:ASN299 2.8 236.3 1.0 CB A:ARG303 3.0 234.9 1.0 OD1 A:ASN299 3.0 236.3 1.0 C A:ARG303 3.1 234.9 1.0 CG A:ASP305 3.2 230.1 1.0 HB3 A:ARG303 3.2 234.9 1.0 HB3 A:GLN333 3.2 220.8 1.0 H A:GLN333 3.3 220.8 1.0 OD1 A:ASP301 3.3 227.9 1.0 OD2 A:ASP305 3.4 230.1 1.0 ND2 A:ASN299 3.5 236.3 1.0 CA A:ARG303 3.5 234.9 1.0 HE A:ARG303 3.6 234.9 1.0 H A:ARG303 3.6 234.9 1.0 CG A:ASN299 3.7 236.3 1.0 OD1 A:ASP297 3.7 228.3 1.0 HH21 A:ARG303 3.8 234.9 1.0 NE A:ARG303 3.9 234.9 1.0 O A:GLN333 3.9 220.8 1.0 N A:GLN333 4.0 220.8 1.0 O A:HIS304 4.0 234.0 1.0 N A:ARG303 4.0 234.9 1.0 NH2 A:ARG303 4.1 234.9 1.0 CG A:ASP297 4.1 228.3 1.0 CB A:GLN333 4.1 220.8 1.0 CZ A:ARG303 4.1 234.9 1.0 N A:HIS304 4.2 234.0 1.0 CG A:ARG303 4.2 234.9 1.0 C A:HIS304 4.2 234.0 1.0 OD2 A:ASP297 4.2 228.3 1.0 CG A:ASP301 4.2 227.9 1.0 HD22 A:LEU332 4.3 218.4 1.0 HG3 A:ARG303 4.3 234.9 1.0 HD22 A:ASN299 4.3 236.3 1.0 HB2 A:GLN333 4.3 220.8 1.0 HA A:ASP297 4.3 228.3 1.0 HA A:ARG303 4.4 234.9 1.0 OD2 A:ASP301 4.4 227.9 1.0 CA A:GLN333 4.5 220.8 1.0 HB3 A:LEU332 4.5 218.4 1.0 HA A:LEU332 4.5 218.4 1.0 HH22 A:ARG303 4.6 234.9 1.0 CD A:ARG303 4.6 234.9 1.0 CB A:ASP305 4.6 230.1 1.0 N A:ASP305 4.6 230.1 1.0 CA A:HIS304 4.7 234.0 1.0 H A:ASP301 4.7 227.9 1.0 C A:GLN333 4.7 220.8 1.0 HA A:HIS304 4.7 234.0 1.0 HE21 A:GLN333 4.8 220.8 1.0 HA A:ASP305 4.8 230.1 1.0 H A:HIS304 4.8 234.0 1.0 HD2 A:ARG303 4.9 234.9 1.0 CA A:ASP305 4.9 230.1 1.0 C A:LEU332 5.0 218.4 1.0 NH1 A:ARG303 5.0 234.9 1.0 HG2 A:ARG303 5.0 234.9 1.0 H A:ASN299 5.0 236.3 1.0

Calcium binding site 3 out of 6 in the Cryo-Em Structures of Full-Length Integrin ALPHAIIBBETA3 in Native Lipids Complexed with Tirofiban


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 Complexed with Tirofiban within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1103 b:310.5 occ:1.00 O A:TYR371 2.4 259.7 1.0 OD1 A:ASP367 2.5 287.9 1.0 OD2 A:ASP373 2.6 261.2 1.0 HB2 A:TYR371 2.6 259.7 1.0 OD1 A:ASP365 2.8 262.3 1.0 HD11 A:LEU393 3.0 269.9 1.0 OD1 A:ASP373 3.1 261.2 1.0 CG A:ASP373 3.1 261.2 1.0 OD1 A:ASP369 3.2 269.5 1.0 CG A:ASP367 3.3 287.9 1.0 C A:TYR371 3.3 259.7 1.0 H A:ASP367 3.4 287.9 1.0 CB A:TYR371 3.4 259.7 1.0 H A:LEU366 3.5 280.2 1.0 OD2 A:ASP367 3.5 287.9 1.0 H A:TYR371 3.7 259.7 1.0 HB3 A:TYR371 3.7 259.7 1.0 CA A:TYR371 3.8 259.7 1.0 CG A:ASP365 3.9 262.3 1.0 CD1 A:LEU393 3.9 269.9 1.0 HG A:LEU393 4.0 269.9 1.0 CG A:ASP369 4.1 269.5 1.0 N A:TYR371 4.1 259.7 1.0 HD12 A:LEU393 4.1 269.9 1.0 HB3 A:LEU366 4.1 280.2 1.0 N A:ASP367 4.2 287.9 1.0 HA A:ASP365 4.3 262.3 1.0 N A:LEU366 4.3 280.2 1.0 HD2 A:TYR371 4.3 259.7 1.0 OD2 A:ASP369 4.3 269.5 1.0 OD2 A:ASP365 4.4 262.3 1.0 H A:ASP369 4.4 269.5 1.0 N A:ASN372 4.5 262.4 1.0 CG A:LEU393 4.5 269.9 1.0 CB A:ASP367 4.5 287.9 1.0 CB A:ASP373 4.5 261.2 1.0 HD13 A:LEU393 4.6 269.9 1.0 CG A:TYR371 4.6 259.7 1.0 C A:ASN372 4.6 262.4 1.0 H A:GLY370 4.7 253.3 1.0 O A:ASN372 4.7 262.4 1.0 H A:ARG368 4.7 275.9 1.0 HB3 A:ASP367 4.7 287.9 1.0 HB2 A:ASP373 4.7 261.2 1.0 HA A:TYR371 4.7 259.7 1.0 O A:GLY394 4.8 263.9 1.0 HA A:ASN372 4.8 262.4 1.0 CD2 A:TYR371 4.8 259.7 1.0 HD21 A:LEU393 4.8 269.9 1.0 N A:ASP373 4.8 261.2 1.0 CA A:ASN372 4.9 262.4 1.0 CA A:ASP367 4.9 287.9 1.0 CA A:ASP365 4.9 262.3 1.0 CB A:LEU366 4.9 280.2 1.0 CB A:ASP365 5.0 262.3 1.0 CA A:LEU366 5.0 280.2 1.0

Calcium binding site 4 out of 6 in the Cryo-Em Structures of Full-Length Integrin ALPHAIIBBETA3 in Native Lipids Complexed with Tirofiban


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 Complexed with Tirofiban within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1104 b:308.7 occ:1.00 OD1 A:ASP434 2.3 261.1 1.0 O A:TYR432 2.4 271.5 1.0 OD1 A:ASN430 2.4 279.6 1.0 OD1 A:ASP426 2.4 262.1 1.0 OD1 A:ASP428 2.5 272.4 1.0 HD21 A:ASN430 2.6 279.6 1.0 OD2 A:ASP434 2.7 261.1 1.0 CG A:ASP434 2.7 261.1 1.0 CG A:ASP426 2.8 262.1 1.0 CG A:ASN430 2.9 279.6 1.0 ND2 A:ASN430 3.0 279.6 1.0 OD2 A:ASP426 3.1 262.1 1.0 HA A:ASP426 3.1 262.1 1.0 H A:ILE427 3.3 260.0 1.0 H A:ASN430 3.4 279.6 1.0 H A:ASP428 3.5 272.4 1.0 C A:TYR432 3.6 271.5 1.0 H A:TYR432 3.6 271.5 1.0 CG A:ASP428 3.6 272.4 1.0 CB A:ASP426 3.7 262.1 1.0 HD22 A:ASN430 3.8 279.6 1.0 CA A:ASP426 3.8 262.1 1.0 N A:ILE427 3.9 260.0 1.0 HB2 A:ASP426 4.0 262.1 1.0 C A:PRO433 4.0 261.8 1.0 CB A:ASP434 4.0 261.1 1.0 N A:ASP434 4.1 261.1 1.0 H A:ASP429 4.1 280.7 1.0 OD2 A:ASP428 4.2 272.4 1.0 HB2 A:TYR432 4.2 271.5 1.0 N A:ASN430 4.2 279.6 1.0 O A:PRO433 4.2 261.8 1.0 H A:ASP434 4.2 261.1 1.0 HA A:PRO433 4.2 261.8 1.0 N A:ASP428 4.2 272.4 1.0 CB A:ASN430 4.3 279.6 1.0 N A:TYR432 4.3 271.5 1.0 C A:ASP426 4.3 262.1 1.0 HB2 A:ASP434 4.3 261.1 1.0 CA A:TYR432 4.4 271.5 1.0 CA A:PRO433 4.4 261.8 1.0 CA A:ASP434 4.5 261.1 1.0 N A:PRO433 4.5 261.8 1.0 HA A:ASP434 4.5 261.1 1.0 HB3 A:ASN430 4.5 279.6 1.0 HB3 A:ASP426 4.6 262.1 1.0 N A:ASP429 4.6 280.7 1.0 HD2 A:ARG449 4.6 266.7 1.0 H A:GLY431 4.7 269.9 1.0 HB3 A:ASP434 4.7 261.1 1.0 CA A:ASN430 4.7 279.6 1.0 HG2 A:ARG449 4.7 266.7 1.0 CB A:TYR432 4.8 271.5 1.0 CB A:ASP428 4.8 272.4 1.0 HB A:ILE427 4.8 260.0 1.0 HB3 A:ARG449 4.9 266.7 1.0 CA A:ASP428 4.9 272.4 1.0 HB2 A:ASN430 5.0 279.6 1.0 N A:GLY431 5.0 269.9 1.0 CA A:ILE427 5.0 260.0 1.0 O A:VAL425 5.0 251.2 1.0

Calcium binding site 5 out of 6 in the Cryo-Em Structures of Full-Length Integrin ALPHAIIBBETA3 in Native Lipids Complexed with Tirofiban


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 Complexed with Tirofiban within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2002 b:205.4 occ:1.00 OD2 B:ASP251 2.4 229.9 1.0 O B:SER123 2.7 197.3 1.0 OD1 B:ASP126 2.7 213.2 1.0 OD2 B:ASP126 2.8 213.2 1.0 CG B:ASP126 3.1 213.2 1.0 HB2 B:ASP251 3.2 229.9 1.0 CG B:ASP251 3.4 229.9 1.0 HB2 B:SER123 3.4 197.3 1.0 C B:SER123 3.5 197.3 1.0 HA B:MET124 3.7 229.3 1.0 CB B:ASP251 3.8 229.9 1.0 OD2 B:ASP127 4.0 220.6 1.0 H B:ASP127 4.1 220.6 1.0 CG B:ASP127 4.1 220.6 1.0 HB3 B:ASP251 4.2 229.9 1.0 CB B:SER123 4.2 197.3 1.0 N B:MET124 4.2 229.3 1.0 HB2 B:ASP127 4.3 220.6 1.0 CA B:SER123 4.3 197.3 1.0 OD1 B:ASP127 4.3 220.6 1.0 HA B:SER123 4.3 197.3 1.0 CA B:MET124 4.3 229.3 1.0 OD1 B:ASP251 4.5 229.9 1.0 CB B:ASP126 4.6 213.2 1.0 H B:ASP126 4.7 213.2 1.0 OG B:SER123 4.7 197.3 1.0 CB B:ASP127 4.7 220.6 1.0 N B:ASP127 4.8 220.6 1.0 C B:MET124 4.9 229.3 1.0 H B:MET124 4.9 229.3 1.0 HB3 B:ASP126 5.0 213.2 1.0 HB3 B:SER123 5.0 197.3 1.0

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


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 Complexed with Tirofiban within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2003 b:302.9 occ:1.00 OD1 B:ASP217 2.3 248.2 1.0 O B:PRO219 2.3 234.4 1.0 OD2 B:ASP158 2.4 245.2 1.0 OE1 B:GLU220 2.6 233.8 1.0 OD1 B:ASN215 2.6 218.6 1.0 O B:ASP217 2.7 248.2 1.0 HB2 B:ASP158 3.0 245.2 1.0 CD B:GLU220 3.2 233.8 1.0 HB2 B:ASN215 3.2 218.6 1.0 HA B:GLU220 3.2 233.8 1.0 CG B:ASN215 3.3 218.6 1.0 CG B:ASP158 3.4 245.2 1.0 CG B:ASP217 3.4 248.2 1.0 OE2 B:GLU220 3.4 233.8 1.0 HE2 B:HIS255 3.5 229.9 1.0 C B:PRO219 3.5 234.4 1.0 CB B:ASP158 3.6 245.2 1.0 C B:ASP217 3.7 248.2 1.0 CB B:ASN215 3.7 218.6 1.0 HD2 B:HIS255 3.8 229.9 1.0 H B:ASP217 3.8 248.2 1.0 HB3 B:ASP158 3.9 245.2 1.0 OD2 B:ASP217 4.0 248.2 1.0 HB3 B:ASN215 4.0 218.6 1.0 CA B:GLU220 4.0 233.8 1.0 NE2 B:HIS255 4.1 229.9 1.0 N B:GLU220 4.2 233.8 1.0 CD2 B:HIS255 4.3 229.9 1.0 N B:ASP217 4.3 248.2 1.0 CG B:GLU220 4.3 233.8 1.0 ND2 B:ASN215 4.4 218.6 1.0 CA B:ASP217 4.4 248.2 1.0 O B:ALA218 4.4 225.1 1.0 HB3 B:TYR164 4.4 232.0 1.0 C B:ALA218 4.4 225.1 1.0 CB B:ASP217 4.4 248.2 1.0 H B:ARG216 4.5 238.9 1.0 HG2 B:GLU220 4.5 233.8 1.0 OD1 B:ASP158 4.5 245.2 1.0 N B:PRO219 4.6 234.4 1.0 HD21 B:ASN215 4.6 218.6 1.0 O B:VAL157 4.6 240.9 1.0 CA B:PRO219 4.6 234.4 1.0 CB B:GLU220 4.6 233.8 1.0 HB3 B:GLU220 4.8 233.8 1.0 N B:ALA218 4.8 225.1 1.0 HB2 B:ASP217 4.8 248.2 1.0 HD2 B:PRO219 4.9 234.4 1.0 N B:ARG216 4.9 238.9 1.0 HB2 B:PRO219 4.9 234.4 1.0 H B:GLY221 5.0 235.5 1.0 HD22 B:ASN215 5.0 218.6 1.0 HA B:ALA218 5.0 225.1 1.0 HD1 B:TYR164 5.0 232.0 1.0 HA B:TYR164 5.0 232.0 1.0

B.D.Adair, C.O.Field, J.L.Alonso, J.P.Xiong, S.X.Deng, H.S.Ahn, E.Mashin, C.B.Clish, J.Van Agthoven, M.Yeager, Y.Guo, D.A.Tess, D.W.Landry, M.Poncz, M.A.Arnaout. Platelet Integrin Alpha Iib Beta 3 Plays A Key Role in A Venous Thrombogenesis Mouse Model. Nat Commun V. 15 8612 2024.
ISSN: ESSN 2041-1723
PubMed: 39366965
DOI: 10.1038/S41467-024-52869-3