Calcium in PDB 7ucy: Integrin ALAPHIIBBETA3 Complex with Gantofiban

The structure of Integrin ALAPHIIBBETA3 Complex with Gantofiban, PDB code: 7ucy was solved by F.-Y.Lin, J.Zhu, J.Zhu, T.A.Springer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.98 / 2.35
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	258.55, 144.46, 105.1, 90, 90, 90
R / Rfree (%)	22.1 / 23.1

The structure of Integrin ALAPHIIBBETA3 Complex with Gantofiban also contains other interesting chemical elements:

Manganese	(Mn)	6 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Calcium atom in the Integrin ALAPHIIBBETA3 Complex with Gantofiban (pdb code 7ucy). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Integrin ALAPHIIBBETA3 Complex with Gantofiban, PDB code: 7ucy:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in the Integrin ALAPHIIBBETA3 Complex with Gantofiban


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Integrin ALAPHIIBBETA3 Complex with Gantofiban within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:51.0 occ:1.00 OD1 A:ASP245 2.3 52.9 1.0 O A:THR250 2.3 53.8 1.0 OE1 A:GLU243 2.4 51.4 1.0 OE1 A:GLU252 2.4 48.6 1.0 O A:ASP247 2.4 60.2 1.0 OE2 A:GLU243 2.4 49.8 1.0 OE2 A:GLU252 2.4 52.5 1.0 OG1 A:THR250 2.4 58.6 1.0 CD A:GLU243 2.7 50.3 1.0 CD A:GLU252 2.7 49.4 1.0 C A:THR250 3.0 54.1 1.0 CG A:ASP245 3.1 53.5 1.0 CB A:THR250 3.4 59.3 1.0 OD2 A:ASP245 3.4 54.9 1.0 C A:ASP247 3.5 59.2 1.0 CA A:THR250 3.6 57.8 1.0 N A:THR250 3.8 59.5 1.0 N A:THR251 4.0 52.0 1.0 N A:ASP247 4.1 59.6 1.0 CG A:GLU243 4.2 49.9 1.0 CA A:ASP247 4.2 60.1 1.0 CG A:GLU252 4.2 47.7 1.0 CA A:THR251 4.4 53.1 1.0 CB A:ASP247 4.4 62.5 1.0 O A:HOH645 4.4 54.6 1.0 CB A:ASP245 4.4 52.7 1.0 N A:ASP245 4.4 54.9 1.0 N A:LEU248 4.5 59.0 1.0 N A:GLU252 4.6 49.0 1.0 O A:HOH708 4.6 55.0 1.0 CA A:GLU243 4.6 46.8 1.0 CA A:LEU248 4.6 60.2 1.0 C A:THR251 4.7 51.0 1.0 N A:PHE244 4.7 44.4 1.0 CG2 A:THR250 4.7 60.6 1.0 C A:LEU248 4.8 61.3 1.0 CB A:GLU243 4.8 48.6 1.0 N A:GLY246 4.8 57.2 1.0 CA A:ASP245 4.8 55.3 1.0 C A:ASP245 5.0 55.5 1.0

Calcium binding site 2 out of 8 in the Integrin ALAPHIIBBETA3 Complex with Gantofiban


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Integrin ALAPHIIBBETA3 Complex with Gantofiban within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:35.9 occ:1.00 OD1 A:ASN299 2.3 42.1 1.0 O A:ARG303 2.3 44.2 1.0 OD1 A:ASP305 2.4 39.8 1.0 OD1 A:ASP297 2.4 41.5 1.0 O A:HOH615 2.4 40.9 1.0 OD2 A:ASP305 2.5 41.1 1.0 OD1 A:ASP301 2.5 44.1 1.0 CG A:ASP305 2.7 38.9 1.0 CG A:ASN299 3.3 42.6 1.0 CG A:ASP301 3.3 45.3 1.0 C A:ARG303 3.5 45.0 1.0 OD2 A:ASP301 3.5 45.4 1.0 CG A:ASP297 3.5 41.5 1.0 ND2 A:ASN299 3.8 43.4 1.0 CB A:ARG303 4.1 46.1 1.0 CA A:ARG303 4.1 45.4 1.0 N A:ARG303 4.1 46.2 1.0 CB A:ASP305 4.2 37.5 1.0 CA A:ASP297 4.2 38.9 1.0 CB A:ASP297 4.3 40.3 1.0 N A:ASN299 4.4 40.8 1.0 N A:VAL298 4.4 39.1 1.0 N A:ASP305 4.4 37.8 1.0 C A:HIS304 4.4 41.0 1.0 OD2 A:ASP297 4.4 42.6 1.0 N A:HIS304 4.6 43.0 1.0 O A:HIS304 4.6 40.8 1.0 CB A:ASN299 4.6 42.5 1.0 C A:ASP297 4.7 38.9 1.0 CB A:ASP301 4.7 46.9 1.0 N A:ASP301 4.7 45.5 1.0 CA A:ASP305 4.8 37.3 1.0 CD2 A:LEU332 4.8 42.5 1.0 N A:GLN333 4.8 46.6 1.0 CA A:HIS304 4.8 41.5 1.0 CA A:ASN299 4.9 42.2 1.0

Calcium binding site 3 out of 8 in the Integrin ALAPHIIBBETA3 Complex with Gantofiban


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Integrin ALAPHIIBBETA3 Complex with Gantofiban within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca505 b:33.8 occ:1.00 O A:TYR371 2.3 39.4 1.0 O A:HOH634 2.3 35.6 1.0 OD1 A:ASP365 2.3 39.7 1.0 OD1 A:ASP367 2.3 40.8 1.0 OD1 A:ASP373 2.4 39.4 1.0 OD2 A:ASP373 2.4 39.1 1.0 OD1 A:ASP369 2.5 42.2 1.0 CG A:ASP373 2.7 40.1 1.0 C A:TYR371 3.4 40.2 1.0 CG A:ASP369 3.4 43.5 1.0 CG A:ASP367 3.5 40.6 1.0 CG A:ASP365 3.5 40.6 1.0 OD2 A:ASP369 3.8 43.6 1.0 OD2 A:ASP367 3.9 42.2 1.0 N A:LEU366 4.1 39.6 1.0 CA A:TYR371 4.2 42.3 1.0 N A:TYR371 4.2 43.5 1.0 CA A:ASP365 4.2 39.1 1.0 OD2 A:ASP365 4.2 42.5 1.0 N A:ASP367 4.2 41.0 1.0 CB A:TYR371 4.3 42.5 1.0 CB A:ASP373 4.3 39.1 1.0 CB A:ASP365 4.4 39.7 1.0 N A:ASN372 4.4 39.5 1.0 CD2 A:LEU393 4.4 37.3 1.0 C A:ASN372 4.5 36.4 1.0 C A:ASP365 4.5 38.1 1.0 N A:ASP369 4.5 44.0 1.0 N A:ASP373 4.6 38.3 1.0 N A:GLY394 4.6 37.4 1.0 CA A:ASN372 4.6 37.7 1.0 CB A:ASP369 4.7 45.2 1.0 N A:ARG368 4.7 41.0 1.0 CB A:ASP367 4.7 41.9 1.0 O A:GLY394 4.8 41.1 1.0 O A:ASN372 4.8 36.8 1.0 CA A:ASP367 4.9 41.4 1.0 CB A:LEU393 4.9 38.8 1.0 CA A:ASP373 5.0 38.6 1.0

Calcium binding site 4 out of 8 in the Integrin ALAPHIIBBETA3 Complex with Gantofiban


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Integrin ALAPHIIBBETA3 Complex with Gantofiban within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca506 b:36.1 occ:1.00 OD1 A:ASP426 2.3 43.1 1.0 O A:TYR432 2.3 40.5 1.0 OD2 A:ASP434 2.4 43.9 1.0 OD1 A:ASP434 2.4 43.0 1.0 O A:HOH660 2.4 37.1 1.0 OD1 A:ASN430 2.4 43.8 1.0 OD1 A:ASP428 2.4 40.0 1.0 CG A:ASP434 2.7 41.5 1.0 CG A:ASP426 3.4 43.9 1.0 CG A:ASN430 3.4 43.8 1.0 C A:TYR432 3.5 39.9 1.0 CG A:ASP428 3.5 41.8 1.0 OD2 A:ASP428 3.9 40.5 1.0 CA A:ASP426 4.1 41.8 1.0 ND2 A:ASN430 4.1 41.4 1.0 N A:TYR432 4.1 42.4 1.0 N A:ILE427 4.2 39.0 1.0 CB A:ASP434 4.2 40.1 1.0 CA A:TYR432 4.2 41.0 1.0 OD2 A:ASP426 4.2 45.5 1.0 CB A:ASP426 4.2 44.1 1.0 N A:ASP428 4.3 41.4 1.0 N A:ASN430 4.3 46.2 1.0 CB A:TYR432 4.3 40.6 1.0 O A:ALA450 4.3 45.0 1.0 CB A:ASN430 4.4 43.5 1.0 C A:ASP426 4.4 43.2 1.0 N A:PRO433 4.5 40.8 1.0 N A:ASP434 4.5 36.4 1.0 C A:PRO433 4.6 37.6 1.0 N A:ALA450 4.6 35.7 1.0 N A:ASP429 4.6 47.1 1.0 CA A:PRO433 4.7 38.6 1.0 CB A:ASP428 4.7 43.4 1.0 CA A:ASN430 4.8 44.5 1.0 CA A:ASP434 4.9 38.0 1.0 CA A:ASP428 4.9 43.3 1.0

Calcium binding site 5 out of 8 in the Integrin ALAPHIIBBETA3 Complex with Gantofiban


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Integrin ALAPHIIBBETA3 Complex with Gantofiban within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca505 b:75.2 occ:1.00 OD1 C:ASP245 2.3 72.2 1.0 OE1 C:GLU252 2.4 71.6 1.0 O C:THR250 2.4 76.8 1.0 O C:ASP247 2.4 78.8 1.0 OG1 C:THR250 2.4 78.8 1.0 OE2 C:GLU243 2.4 73.6 1.0 OE1 C:GLU243 2.4 73.3 1.0 OE2 C:GLU252 2.5 73.8 1.0 CD C:GLU252 2.7 71.8 1.0 CD C:GLU243 2.7 73.7 1.0 C C:THR250 3.0 75.9 1.0 CG C:ASP245 3.2 73.2 1.0 CB C:THR250 3.5 77.8 1.0 OD2 C:ASP245 3.6 73.3 1.0 C C:ASP247 3.6 80.4 1.0 CA C:THR250 3.6 77.4 1.0 N C:THR251 3.7 71.9 1.0 N C:THR250 4.0 80.2 1.0 CA C:THR251 4.1 70.4 1.0 CG C:GLU243 4.2 73.8 1.0 CG C:GLU252 4.3 69.3 1.0 C C:THR251 4.4 68.8 1.0 CA C:ASP247 4.4 83.7 1.0 N C:ASP247 4.4 83.9 1.0 CB C:ASP247 4.5 84.0 1.0 CB C:ASP245 4.5 74.7 1.0 N C:GLU252 4.5 65.0 1.0 N C:ASP245 4.5 78.7 1.0 N C:LEU248 4.6 81.3 1.0 CA C:GLU243 4.7 69.3 1.0 CA C:LEU248 4.7 80.9 1.0 CG2 C:THR250 4.8 79.1 1.0 N C:PHE244 4.8 70.4 1.0 CB C:GLU243 4.9 71.1 1.0 C C:LEU248 4.9 81.1 1.0 CA C:ASP245 4.9 77.3 1.0 O C:THR251 5.0 70.2 1.0

Calcium binding site 6 out of 8 in the Integrin ALAPHIIBBETA3 Complex with Gantofiban


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Integrin ALAPHIIBBETA3 Complex with Gantofiban within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca506 b:64.8 occ:1.00 O C:ARG303 2.3 70.4 1.0 OD1 C:ASN299 2.3 64.6 1.0 OD1 C:ASP305 2.4 64.2 1.0 OD1 C:ASP297 2.4 64.8 1.0 OD2 C:ASP305 2.4 64.1 1.0 OD1 C:ASP301 2.4 70.0 1.0 O C:HOH612 2.5 61.5 1.0 CG C:ASP305 2.7 62.6 1.0 CG C:ASP301 3.3 73.0 1.0 CG C:ASN299 3.4 65.7 1.0 CG C:ASP297 3.4 64.9 1.0 C C:ARG303 3.5 71.0 1.0 OD2 C:ASP301 3.5 73.9 1.0 ND2 C:ASN299 3.9 68.4 1.0 CA C:ASP297 4.1 60.5 1.0 CB C:ASP305 4.1 61.1 1.0 CB C:ASP297 4.2 62.2 1.0 N C:ARG303 4.2 72.8 1.0 CA C:ARG303 4.2 73.6 1.0 CB C:ARG303 4.3 75.8 1.0 OD2 C:ASP297 4.3 67.3 1.0 C C:HIS304 4.3 63.5 1.0 N C:ASP305 4.4 62.4 1.0 N C:VAL298 4.4 62.5 1.0 N C:ASN299 4.4 59.9 1.0 O C:HIS304 4.5 66.3 1.0 N C:HIS304 4.5 66.4 1.0 C C:ASP297 4.6 59.1 1.0 CD2 C:LEU332 4.7 60.9 1.0 CB C:ASP301 4.7 76.0 1.0 CB C:ASN299 4.7 64.3 1.0 N C:ASP301 4.7 71.7 1.0 CA C:ASP305 4.7 62.7 1.0 CA C:HIS304 4.7 63.3 1.0 N C:GLN333 5.0 68.0 1.0 CA C:ASN299 5.0 62.8 1.0

Calcium binding site 7 out of 8 in the Integrin ALAPHIIBBETA3 Complex with Gantofiban


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Integrin ALAPHIIBBETA3 Complex with Gantofiban within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca507 b:54.4 occ:1.00 O C:TYR371 2.2 57.8 1.0 OD1 C:ASP367 2.3 58.4 1.0 OD1 C:ASP365 2.4 58.5 1.0 OD1 C:ASP373 2.4 61.0 1.0 OD2 C:ASP373 2.4 61.3 1.0 O C:HOH645 2.5 54.3 1.0 OD1 C:ASP369 2.5 60.0 1.0 CG C:ASP373 2.8 60.1 1.0 C C:TYR371 3.4 58.9 1.0 CG C:ASP369 3.5 61.0 1.0 CG C:ASP367 3.5 60.8 1.0 CG C:ASP365 3.5 59.6 1.0 OD2 C:ASP369 3.9 61.2 1.0 OD2 C:ASP367 4.0 63.7 1.0 N C:LEU366 4.0 59.5 1.0 N C:ASP367 4.2 62.6 1.0 N C:TYR371 4.2 60.6 1.0 OD2 C:ASP365 4.2 59.7 1.0 CA C:TYR371 4.2 58.9 1.0 CA C:ASP365 4.3 58.9 1.0 CB C:ASP373 4.3 58.2 1.0 C C:ASN372 4.4 57.9 1.0 N C:ASN372 4.4 56.8 1.0 CB C:TYR371 4.4 59.0 1.0 CB C:ASP365 4.5 58.3 1.0 C C:ASP365 4.5 60.5 1.0 N C:ASP369 4.6 61.4 1.0 CA C:ASN372 4.6 54.9 1.0 O C:ASN372 4.6 58.9 1.0 N C:ASP373 4.6 55.4 1.0 N C:GLY394 4.6 59.2 1.0 CB C:ASP369 4.7 62.1 1.0 N C:ARG368 4.7 62.6 1.0 CB C:ASP367 4.7 61.2 1.0 CD2 C:LEU393 4.8 54.6 1.0 CA C:ASP367 4.9 61.7 1.0 O C:GLY394 4.9 61.0 1.0 CA C:ASP373 5.0 55.5 1.0 CA C:LEU366 5.0 58.2 1.0 CB C:LEU393 5.0 56.5 1.0

Calcium binding site 8 out of 8 in the Integrin ALAPHIIBBETA3 Complex with Gantofiban


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Integrin ALAPHIIBBETA3 Complex with Gantofiban within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca508 b:50.6 occ:1.00 O C:TYR432 2.3 54.6 1.0 OD1 C:ASP426 2.3 56.5 1.0 O C:HOH610 2.3 57.7 1.0 OD1 C:ASP434 2.4 58.6 1.0 OD2 C:ASP434 2.4 58.6 1.0 OD1 C:ASN430 2.4 60.5 1.0 OD1 C:ASP428 2.4 57.1 1.0 CG C:ASP434 2.7 55.3 1.0 CG C:ASP426 3.3 57.5 1.0 CG C:ASN430 3.4 59.2 1.0 C C:TYR432 3.4 56.3 1.0 CG C:ASP428 3.5 57.4 1.0 CA C:ASP426 3.9 56.8 1.0 OD2 C:ASP428 4.0 52.5 1.0 N C:TYR432 4.0 61.4 1.0 CB C:ASP426 4.1 58.0 1.0 ND2 C:ASN430 4.1 58.8 1.0 CA C:TYR432 4.1 58.3 1.0 CB C:ASP434 4.1 48.0 1.0 OD2 C:ASP426 4.1 57.3 1.0 CB C:TYR432 4.2 59.5 1.0 N C:ILE427 4.3 52.8 1.0 N C:ASP428 4.3 60.6 1.0 N C:ASN430 4.3 61.8 1.0 C C:ASP426 4.4 58.2 1.0 N C:ASP434 4.4 50.7 1.0 N C:ALA450 4.4 52.1 1.0 CB C:ASN430 4.4 58.1 1.0 N C:PRO433 4.5 57.4 1.0 O C:ALA450 4.5 56.9 1.0 C C:PRO433 4.5 53.8 1.0 N C:ASP429 4.7 62.7 1.0 CA C:PRO433 4.7 54.5 1.0 CB C:ASP428 4.7 59.0 1.0 CA C:ASP434 4.7 48.5 1.0 CB C:ALA450 4.7 57.0 1.0 CA C:ASN430 4.8 58.8 1.0 CA C:ASP428 4.9 61.1 1.0 O C:PRO433 5.0 56.7 1.0

J.Zhu, A.Lin, J.Zhu, T.A.Springer. Integrin Alpha Iib Beta 3 Headpiece with Fab Complex with Bms Compound 4 in MN2+. To Be Published.