Calcium in PDB 7udh: Integrin ALAPHIIBBETA3 Complex with BMS4-3

The structure of Integrin ALAPHIIBBETA3 Complex with BMS4-3, PDB code: 7udh 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)	48.99 / 2.00
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	258.33, 144.67, 105.06, 90, 90, 90
R / Rfree (%)	18.5 / 21.4

The structure of Integrin ALAPHIIBBETA3 Complex with BMS4-3 also contains other interesting chemical elements:

Chlorine	(Cl)	3 atoms
Manganese	(Mn)	6 atoms

The binding sites of Calcium atom in the Integrin ALAPHIIBBETA3 Complex with BMS4-3 (pdb code 7udh). 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 BMS4-3, PDB code: 7udh:
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 BMS4-3


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 BMS4-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:47.4 occ:1.00 OD1 A:ASP245 2.2 67.2 1.0 O A:THR250 2.3 53.1 1.0 OE1 A:GLU243 2.4 55.6 1.0 OG1 A:THR250 2.4 66.9 1.0 OE2 A:GLU252 2.4 43.1 1.0 O A:ASP247 2.4 55.4 1.0 OE1 A:GLU252 2.5 46.4 1.0 OE2 A:GLU243 2.5 55.4 1.0 CD A:GLU243 2.8 52.1 1.0 CD A:GLU252 2.8 40.9 1.0 C A:THR250 3.1 60.5 1.0 CG A:ASP245 3.2 65.2 1.0 CB A:THR250 3.5 68.9 1.0 OD2 A:ASP245 3.5 65.3 1.0 C A:ASP247 3.6 64.9 1.0 CA A:THR250 3.7 69.1 1.0 N A:THR250 3.9 73.4 1.0 N A:THR251 4.1 54.8 1.0 N A:ASP247 4.2 71.2 1.0 CG A:GLU243 4.3 48.7 1.0 CA A:ASP247 4.3 68.9 1.0 N A:ASP245 4.3 56.4 1.0 CG A:GLU252 4.3 40.2 1.0 CB A:ASP245 4.4 61.3 1.0 CB A:ASP247 4.5 70.3 1.0 CA A:THR251 4.5 56.5 1.0 O A:HOH704 4.6 76.4 1.0 N A:LEU248 4.6 65.2 1.0 N A:PHE244 4.6 41.5 1.0 CA A:GLU243 4.7 45.0 1.0 N A:GLU252 4.7 46.9 1.0 CA A:ASP245 4.8 64.1 1.0 CG2 A:THR250 4.8 73.3 1.0 CA A:LEU248 4.8 67.8 1.0 C A:THR251 4.8 53.0 1.0 N A:GLY246 4.8 66.4 1.0 CB A:GLU243 4.9 46.6 1.0 C A:ASP245 4.9 68.1 1.0 C A:LEU248 4.9 67.2 1.0

Calcium binding site 2 out of 8 in the Integrin ALAPHIIBBETA3 Complex with BMS4-3


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 BMS4-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:39.3 occ:1.00 OD1 A:ASN299 2.3 41.7 1.0 O A:ARG303 2.3 40.1 1.0 OD1 A:ASP297 2.4 44.2 1.0 O A:HOH606 2.4 45.4 1.0 OD2 A:ASP305 2.5 38.3 1.0 OD1 A:ASP305 2.5 43.3 1.0 OD1 A:ASP301 2.5 47.6 1.0 CG A:ASP305 2.8 35.3 1.0 CG A:ASP301 3.3 46.0 1.0 OD2 A:ASP301 3.4 47.5 1.0 C A:ARG303 3.4 45.3 1.0 CG A:ASN299 3.5 47.9 1.0 CG A:ASP297 3.5 40.2 1.0 CB A:ARG303 4.0 44.1 1.0 CA A:ARG303 4.1 46.3 1.0 N A:ARG303 4.1 45.6 1.0 ND2 A:ASN299 4.1 46.6 1.0 CB A:ASP297 4.2 36.4 1.0 CA A:ASP297 4.2 37.5 1.0 CB A:ASP305 4.3 33.9 1.0 N A:ASN299 4.3 37.9 1.0 OD2 A:ASP297 4.4 44.3 1.0 N A:VAL298 4.4 42.3 1.0 C A:HIS304 4.5 45.7 1.0 N A:ASP305 4.5 40.1 1.0 N A:HIS304 4.5 41.8 1.0 CB A:ASN299 4.6 54.0 1.0 C A:ASP297 4.7 45.0 1.0 N A:ASP301 4.7 48.4 1.0 O A:HIS304 4.7 46.9 1.0 CB A:ASP301 4.7 49.0 1.0 CD2 A:LEU332 4.8 36.9 1.0 N A:GLN333 4.8 46.0 1.0 CA A:ASN299 4.8 39.4 1.0 CA A:ASP305 4.9 36.8 1.0 CA A:HIS304 4.9 41.5 1.0 O A:HOH939 4.9 102.5 1.0 C A:ASN299 5.0 42.8 1.0 N A:GLY300 5.0 40.3 1.0

Calcium binding site 3 out of 8 in the Integrin ALAPHIIBBETA3 Complex with BMS4-3


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 BMS4-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca505 b:37.3 occ:1.00 O A:HOH645 2.2 34.0 1.0 O A:TYR371 2.3 43.0 1.0 OD1 A:ASP367 2.3 43.1 1.0 OD1 A:ASP365 2.3 35.2 1.0 OD1 A:ASP369 2.5 39.7 1.0 OD1 A:ASP373 2.5 39.6 1.0 OD2 A:ASP373 2.5 34.6 1.0 CG A:ASP373 2.9 35.0 1.0 CG A:ASP369 3.4 44.1 1.0 C A:TYR371 3.4 41.8 1.0 CG A:ASP365 3.4 38.7 1.0 CG A:ASP367 3.5 47.9 1.0 OD2 A:ASP369 3.8 44.8 1.0 OD2 A:ASP367 4.0 47.4 1.0 N A:TYR371 4.1 44.2 1.0 CA A:ASP365 4.1 35.3 1.0 N A:LEU366 4.2 37.8 1.0 CA A:TYR371 4.2 42.8 1.0 N A:ASP367 4.2 40.0 1.0 OD2 A:ASP365 4.2 41.3 1.0 CB A:ASP365 4.3 33.8 1.0 CB A:TYR371 4.3 36.3 1.0 C A:ASP365 4.4 39.7 1.0 CB A:ASP373 4.4 36.2 1.0 N A:ASP369 4.4 38.2 1.0 N A:ASN372 4.5 42.4 1.0 C A:ASN372 4.5 39.6 1.0 N A:ARG368 4.5 40.5 1.0 CB A:ASP369 4.6 40.7 1.0 CA A:ASN372 4.6 36.7 1.0 CB A:ASP367 4.7 44.1 1.0 N A:ASP373 4.7 34.5 1.0 N A:GLY394 4.7 33.6 1.0 CD2 A:LEU393 4.7 33.2 1.0 CA A:ASP367 4.8 39.2 1.0 O A:ASN372 4.8 40.7 1.0 C A:ASP367 4.9 39.9 1.0 CA A:ASP369 5.0 40.1 1.0 O A:GLY394 5.0 49.2 1.0 CB A:LEU393 5.0 38.2 1.0 N A:GLY370 5.0 43.1 1.0

Calcium binding site 4 out of 8 in the Integrin ALAPHIIBBETA3 Complex with BMS4-3


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 BMS4-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca506 b:39.6 occ:1.00 OD1 A:ASP428 2.3 42.8 1.0 OD1 A:ASP426 2.3 42.6 1.0 O A:TYR432 2.3 40.9 1.0 OD1 A:ASN430 2.3 43.3 1.0 O A:HOH649 2.4 35.2 1.0 OD2 A:ASP434 2.5 36.0 1.0 OD1 A:ASP434 2.5 39.1 1.0 CG A:ASP434 2.8 35.4 1.0 CG A:ASN430 3.3 43.7 1.0 CG A:ASP428 3.3 43.8 1.0 CG A:ASP426 3.4 41.2 1.0 C A:TYR432 3.5 39.1 1.0 OD2 A:ASP428 3.8 44.5 1.0 ND2 A:ASN430 3.9 40.6 1.0 N A:TYR432 4.1 36.0 1.0 CA A:ASP426 4.1 35.7 1.0 CA A:TYR432 4.2 34.7 1.0 OD2 A:ASP426 4.2 39.9 1.0 O A:ALA450 4.2 36.7 1.0 N A:ASN430 4.3 41.9 1.0 CB A:ASP426 4.3 38.8 1.0 N A:ASP428 4.3 40.3 1.0 CB A:ASP434 4.3 30.5 1.0 N A:ILE427 4.4 40.8 1.0 CB A:TYR432 4.4 30.2 1.0 CB A:ASN430 4.4 38.7 1.0 N A:PRO433 4.5 40.2 1.0 C A:ASP426 4.6 36.9 1.0 CB A:ASP428 4.6 41.9 1.0 N A:ASP429 4.6 46.2 1.0 N A:ALA450 4.6 39.4 1.0 C A:PRO433 4.7 36.8 1.0 CA A:PRO433 4.7 40.2 1.0 N A:ASP434 4.7 34.2 1.0 CA A:ASN430 4.7 45.9 1.0 CA A:ASP428 4.8 41.1 1.0 C A:ASP428 4.9 42.8 1.0 N A:GLY431 4.9 44.1 1.0 C A:ASN430 5.0 45.7 1.0

Calcium binding site 5 out of 8 in the Integrin ALAPHIIBBETA3 Complex with BMS4-3


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 BMS4-3 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca507 b:73.4 occ:1.00 OD1 C:ASP245 2.2 78.8 1.0 O C:THR250 2.3 73.8 1.0 O C:ASP247 2.3 87.7 1.0 OE2 C:GLU243 2.4 77.5 1.0 OE1 C:GLU243 2.4 76.4 1.0 OE2 C:GLU252 2.4 78.2 1.0 OG1 C:THR250 2.4 76.5 1.0 OE1 C:GLU252 2.5 77.9 1.0 CD C:GLU243 2.7 72.0 1.0 CD C:GLU252 2.8 74.2 1.0 C C:THR250 3.1 75.4 1.0 CG C:ASP245 3.1 80.5 1.0 OD2 C:ASP245 3.4 83.7 1.0 C C:ASP247 3.5 89.5 1.0 CB C:THR250 3.5 76.8 1.0 CA C:THR250 3.7 78.7 1.0 N C:THR251 4.0 74.0 1.0 N C:THR250 4.0 88.7 1.0 N C:ASP247 4.1 93.3 1.0 CA C:ASP247 4.2 93.2 1.0 CG C:GLU243 4.2 65.0 1.0 CA C:THR251 4.3 77.9 1.0 CG C:GLU252 4.3 71.9 1.0 CB C:ASP247 4.3 97.6 1.0 CB C:ASP245 4.4 78.8 1.0 N C:ASP245 4.4 74.7 1.0 N C:LEU248 4.5 92.0 1.0 C C:THR251 4.7 74.6 1.0 N C:GLU252 4.7 69.1 1.0 CA C:GLU243 4.7 65.7 1.0 CA C:LEU248 4.7 92.0 1.0 N C:PHE244 4.7 69.0 1.0 CG2 C:THR250 4.8 77.2 1.0 N C:GLY246 4.8 87.0 1.0 CA C:ASP245 4.8 82.0 1.0 CB C:GLU243 4.9 64.1 1.0 C C:LEU248 4.9 94.5 1.0

Calcium binding site 6 out of 8 in the Integrin ALAPHIIBBETA3 Complex with BMS4-3


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 BMS4-3 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca508 b:60.3 occ:1.00 OD1 C:ASN299 2.3 65.3 1.0 O C:ARG303 2.3 69.2 1.0 O C:HOH613 2.4 54.8 1.0 OD1 C:ASP297 2.4 69.9 1.0 OD1 C:ASP305 2.4 59.1 1.0 OD1 C:ASP301 2.5 76.2 1.0 OD2 C:ASP305 2.5 58.9 1.0 CG C:ASP305 2.8 60.4 1.0 CG C:ASP301 3.3 78.3 1.0 CG C:ASN299 3.4 70.0 1.0 C C:ARG303 3.4 72.0 1.0 CG C:ASP297 3.4 71.4 1.0 OD2 C:ASP301 3.5 82.2 1.0 ND2 C:ASN299 4.0 73.7 1.0 CA C:ARG303 4.0 77.2 1.0 N C:ARG303 4.0 82.0 1.0 CB C:ARG303 4.0 77.5 1.0 CA C:ASP297 4.1 62.8 1.0 CB C:ASP297 4.2 66.4 1.0 CB C:ASP305 4.2 54.5 1.0 N C:ASN299 4.3 61.0 1.0 OD2 C:ASP297 4.3 74.7 1.0 N C:VAL298 4.4 61.7 1.0 N C:ASP305 4.4 59.7 1.0 C C:HIS304 4.4 63.5 1.0 N C:HIS304 4.5 71.0 1.0 CB C:ASN299 4.6 68.3 1.0 C C:ASP297 4.6 64.5 1.0 N C:ASP301 4.7 73.9 1.0 O C:HIS304 4.7 67.6 1.0 CB C:ASP301 4.7 79.0 1.0 CA C:ASP305 4.8 60.1 1.0 CA C:HIS304 4.8 65.8 1.0 CA C:ASN299 4.8 67.1 1.0 CD2 C:LEU332 4.9 69.7 1.0 N C:GLN333 4.9 64.2 1.0 C C:ASN299 5.0 71.8 1.0

Calcium binding site 7 out of 8 in the Integrin ALAPHIIBBETA3 Complex with BMS4-3


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 BMS4-3 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca509 b:57.7 occ:1.00 O C:TYR371 2.3 60.5 1.0 O C:HOH637 2.3 50.8 1.0 OD1 C:ASP367 2.3 67.0 1.0 OD1 C:ASP365 2.4 62.9 1.0 OD1 C:ASP369 2.5 62.3 1.0 OD1 C:ASP373 2.5 58.4 1.0 OD2 C:ASP373 2.5 56.3 1.0 CG C:ASP373 2.8 56.4 1.0 CG C:ASP369 3.4 66.2 1.0 CG C:ASP365 3.4 62.6 1.0 CG C:ASP367 3.5 66.9 1.0 C C:TYR371 3.5 62.6 1.0 OD2 C:ASP369 3.7 66.7 1.0 OD2 C:ASP367 3.9 68.7 1.0 OD2 C:ASP365 4.0 68.9 1.0 N C:LEU366 4.1 60.1 1.0 N C:TYR371 4.2 67.3 1.0 N C:ASP367 4.2 68.8 1.0 CA C:TYR371 4.2 64.9 1.0 CA C:ASP365 4.2 59.4 1.0 CB C:TYR371 4.4 65.0 1.0 CB C:ASP373 4.4 49.4 1.0 CB C:ASP365 4.4 55.9 1.0 N C:ASP369 4.4 67.4 1.0 N C:ASN372 4.5 60.4 1.0 C C:ASP365 4.5 64.4 1.0 C C:ASN372 4.5 55.2 1.0 N C:ARG368 4.6 66.1 1.0 CB C:ASP369 4.6 66.5 1.0 N C:GLY394 4.6 61.2 1.0 CA C:ASN372 4.6 56.9 1.0 CB C:ASP367 4.7 65.2 1.0 N C:ASP373 4.7 51.3 1.0 CD2 C:LEU393 4.7 61.1 1.0 O C:ASN372 4.8 60.5 1.0 CA C:ASP367 4.8 66.9 1.0 O C:GLY394 4.9 65.1 1.0 CB C:LEU393 4.9 57.0 1.0 C C:ASP367 5.0 65.4 1.0

Calcium binding site 8 out of 8 in the Integrin ALAPHIIBBETA3 Complex with BMS4-3


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 BMS4-3 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca510 b:51.0 occ:1.00 OD1 C:ASP428 2.2 63.8 1.0 O C:TYR432 2.3 58.3 1.0 OD1 C:ASP426 2.4 50.6 1.0 OD1 C:ASP434 2.4 52.2 1.0 OD1 C:ASN430 2.4 63.5 1.0 OD2 C:ASP434 2.4 49.8 1.0 O C:HOH619 2.5 52.0 1.0 CG C:ASP434 2.7 52.2 1.0 CG C:ASN430 3.3 62.7 1.0 CG C:ASP428 3.3 67.2 1.0 CG C:ASP426 3.5 58.2 1.0 C C:TYR432 3.5 62.4 1.0 OD2 C:ASP428 3.8 67.5 1.0 ND2 C:ASN430 4.0 62.7 1.0 N C:TYR432 4.1 63.1 1.0 CA C:ASP426 4.1 56.2 1.0 CA C:TYR432 4.2 57.4 1.0 CB C:ASP434 4.2 47.2 1.0 N C:ASP428 4.3 64.4 1.0 N C:ASN430 4.3 72.3 1.0 CB C:ASP426 4.3 56.0 1.0 CB C:ASN430 4.3 63.4 1.0 OD2 C:ASP426 4.3 62.1 1.0 O C:ALA450 4.3 64.2 1.0 CB C:TYR432 4.3 58.8 1.0 N C:ILE427 4.3 56.3 1.0 C C:ASP426 4.5 57.4 1.0 N C:ALA450 4.5 52.4 1.0 N C:PRO433 4.5 62.4 1.0 CB C:ASP428 4.6 66.4 1.0 C C:PRO433 4.6 54.0 1.0 N C:ASP434 4.6 51.0 1.0 N C:ASP429 4.6 75.2 1.0 CA C:ASN430 4.7 69.6 1.0 CA C:PRO433 4.7 59.7 1.0 CA C:ASP428 4.8 68.3 1.0 C C:ASP428 4.9 75.3 1.0 CA C:ASP434 4.9 47.8 1.0 CB C:ALA450 4.9 51.6 1.0 N C:GLY431 4.9 71.1 1.0 O C:PRO433 5.0 54.2 1.0

F.-Y.Lin, J.Zhu, J.Zhu, T.A.Springer. Integrin Alpha Iib Beta 3 Headpiece Complex with BMS4-3 To Be Published.