Calcium in PDB 7u9v: Integrin ALAPHIIBBETA3 Complex with BMS4-1

The structure of Integrin ALAPHIIBBETA3 Complex with BMS4-1, PDB code: 7u9v was solved by J.Zhu, F.-Y.Lin, J.Zhu, T.A.Springer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.95 / 2.25
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	257.796, 143.887, 104.678, 90, 90, 90
R / Rfree (%)	20.3 / 22.6

The structure of Integrin ALAPHIIBBETA3 Complex with BMS4-1 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 BMS4-1 (pdb code 7u9v). 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 BMS4-1, PDB code: 7u9v:
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 BMS4-1


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 BMS4-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:47.4 occ:1.00 OD1 A:ASP245 2.3 61.5 1.0 O A:THR250 2.3 52.6 1.0 OE2 A:GLU252 2.4 51.9 1.0 OE1 A:GLU243 2.4 57.9 1.0 O A:ASP247 2.4 64.6 1.0 OE2 A:GLU243 2.4 54.8 1.0 OE1 A:GLU252 2.4 57.1 1.0 OG1 A:THR250 2.4 63.5 1.0 CD A:GLU243 2.7 55.7 1.0 CD A:GLU252 2.7 45.4 1.0 CG A:ASP245 3.1 59.1 1.0 C A:THR250 3.1 58.2 1.0 OD2 A:ASP245 3.3 57.2 1.0 CB A:THR250 3.5 66.2 1.0 C A:ASP247 3.5 64.2 1.0 CA A:THR250 3.7 62.8 1.0 N A:THR250 3.9 68.0 1.0 N A:THR251 4.0 53.3 1.0 N A:ASP247 4.1 66.6 1.0 CG A:GLU243 4.2 51.8 1.0 CA A:ASP247 4.2 61.5 1.0 CG A:GLU252 4.2 47.8 1.0 O A:HOH605 4.3 55.0 1.0 CB A:ASP247 4.3 64.7 1.0 CB A:ASP245 4.4 57.8 1.0 N A:ASP245 4.4 54.3 1.0 CA A:THR251 4.4 54.2 1.0 N A:LEU248 4.6 63.5 1.0 CA A:GLU243 4.6 44.0 1.0 N A:GLU252 4.6 50.5 1.0 N A:PHE244 4.7 44.0 1.0 C A:THR251 4.8 51.0 1.0 CB A:GLU243 4.8 45.5 1.0 CA A:LEU248 4.8 62.8 1.0 CG2 A:THR250 4.8 64.5 1.0 CA A:ASP245 4.8 62.6 1.0 O A:HOH628 4.8 56.0 1.0 N A:GLY246 4.9 66.2 1.0 C A:LEU248 4.9 65.2 1.0 C A:ASP245 5.0 61.0 1.0

Calcium binding site 2 out of 8 in the Integrin ALAPHIIBBETA3 Complex with BMS4-1


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 BMS4-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:37.8 occ:1.00 OD1 A:ASN299 2.3 42.4 1.0 O A:ARG303 2.3 44.2 1.0 OD1 A:ASP297 2.4 40.6 1.0 O A:HOH610 2.4 39.7 1.0 OD1 A:ASP305 2.4 42.9 1.0 OD2 A:ASP305 2.4 39.6 1.0 OD1 A:ASP301 2.5 46.2 1.0 CG A:ASP305 2.7 41.1 1.0 CG A:ASP301 3.3 45.6 1.0 CG A:ASN299 3.4 44.8 1.0 OD2 A:ASP301 3.5 45.7 1.0 CG A:ASP297 3.5 40.5 1.0 C A:ARG303 3.5 44.6 1.0 ND2 A:ASN299 4.0 44.0 1.0 CA A:ARG303 4.1 46.2 1.0 N A:ARG303 4.2 47.9 1.0 CB A:ARG303 4.2 47.0 1.0 CB A:ASP297 4.2 39.2 1.0 CB A:ASP305 4.2 37.7 1.0 CA A:ASP297 4.2 40.1 1.0 N A:ASN299 4.3 42.7 1.0 N A:VAL298 4.4 41.5 1.0 N A:ASP305 4.4 38.5 1.0 OD2 A:ASP297 4.4 41.5 1.0 C A:HIS304 4.4 40.4 1.0 N A:HIS304 4.6 45.1 1.0 C A:ASP297 4.6 38.0 1.0 CB A:ASN299 4.7 43.8 1.0 O A:HIS304 4.7 42.2 1.0 CB A:ASP301 4.7 47.1 1.0 N A:ASP301 4.7 45.6 1.0 CA A:ASP305 4.7 43.8 1.0 CD2 A:LEU332 4.8 40.8 1.0 N A:GLN333 4.8 43.9 1.0 CA A:HIS304 4.9 40.8 1.0 CA A:ASN299 4.9 43.0 1.0 N A:GLY300 5.0 43.5 1.0

Calcium binding site 3 out of 8 in the Integrin ALAPHIIBBETA3 Complex with BMS4-1


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 BMS4-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca505 b:36.7 occ:1.00 O A:TYR371 2.2 38.5 1.0 OD1 A:ASP367 2.3 40.9 1.0 O A:HOH706 2.4 33.2 1.0 OD1 A:ASP365 2.4 36.9 1.0 OD1 A:ASP373 2.4 37.8 1.0 OD2 A:ASP373 2.4 39.2 1.0 OD1 A:ASP369 2.4 44.0 1.0 CG A:ASP373 2.7 38.4 1.0 C A:TYR371 3.4 39.1 1.0 CG A:ASP369 3.4 42.0 1.0 CG A:ASP367 3.5 40.0 1.0 CG A:ASP365 3.5 37.6 1.0 OD2 A:ASP369 3.9 41.9 1.0 OD2 A:ASP367 4.0 42.1 1.0 N A:LEU366 4.0 40.0 1.0 CA A:ASP365 4.1 34.9 1.0 N A:ASP367 4.1 40.5 1.0 N A:TYR371 4.2 43.9 1.0 CA A:TYR371 4.2 41.0 1.0 CB A:ASP373 4.3 37.9 1.0 CB A:TYR371 4.3 41.4 1.0 OD2 A:ASP365 4.3 39.2 1.0 C A:ASP365 4.4 39.0 1.0 CB A:ASP365 4.4 36.6 1.0 N A:ASN372 4.5 39.5 1.0 N A:ASP369 4.5 41.6 1.0 C A:ASN372 4.5 36.7 1.0 N A:GLY394 4.6 38.7 1.0 CD2 A:LEU393 4.6 36.1 1.0 N A:ARG368 4.6 43.5 1.0 N A:ASP373 4.6 34.2 1.0 CA A:ASN372 4.6 37.8 1.0 CB A:ASP369 4.7 42.8 1.0 CB A:ASP367 4.7 43.3 1.0 O A:ASN372 4.7 38.0 1.0 CA A:ASP367 4.8 39.0 1.0 CB A:LEU393 4.9 41.2 1.0 O A:GLY394 5.0 43.0 1.0 CA A:LEU366 5.0 37.4 1.0 C A:ASP367 5.0 43.0 1.0 CA A:ASP373 5.0 35.8 1.0

Calcium binding site 4 out of 8 in the Integrin ALAPHIIBBETA3 Complex with BMS4-1


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 BMS4-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca506 b:36.4 occ:1.00 O A:TYR432 2.3 39.6 1.0 OD1 A:ASP434 2.3 38.6 1.0 OD1 A:ASP426 2.3 42.7 1.0 OD1 A:ASN430 2.4 43.3 1.0 OD1 A:ASP428 2.4 44.1 1.0 OD2 A:ASP434 2.4 35.6 1.0 O A:HOH641 2.4 35.3 1.0 CG A:ASP434 2.7 39.2 1.0 CG A:ASN430 3.4 45.8 1.0 CG A:ASP426 3.4 40.6 1.0 CG A:ASP428 3.4 40.2 1.0 C A:TYR432 3.4 36.1 1.0 OD2 A:ASP428 3.9 39.3 1.0 ND2 A:ASN430 4.0 44.1 1.0 N A:TYR432 4.0 40.9 1.0 CA A:ASP426 4.1 39.8 1.0 CA A:TYR432 4.1 40.0 1.0 CB A:ASP426 4.2 40.6 1.0 CB A:ASP434 4.2 36.5 1.0 O A:ALA450 4.2 39.2 1.0 OD2 A:ASP426 4.2 40.6 1.0 CB A:TYR432 4.2 40.6 1.0 N A:ILE427 4.3 38.6 1.0 N A:ASN430 4.3 44.0 1.0 N A:ASP428 4.4 41.2 1.0 CB A:ASN430 4.4 44.6 1.0 C A:ASP426 4.5 38.1 1.0 N A:PRO433 4.5 43.5 1.0 N A:ASP434 4.5 35.2 1.0 N A:ALA450 4.6 34.4 1.0 C A:PRO433 4.6 38.4 1.0 CA A:PRO433 4.7 32.9 1.0 N A:ASP429 4.7 51.3 1.0 CB A:ASP428 4.7 44.1 1.0 CA A:ASN430 4.8 44.7 1.0 CA A:ASP434 4.8 30.3 1.0 CA A:ASP428 4.9 45.8 1.0 N A:GLY431 4.9 47.7 1.0 CB A:ALA450 5.0 34.4 1.0 C A:ASN430 5.0 44.3 1.0 C A:ASP428 5.0 46.4 1.0

Calcium binding site 5 out of 8 in the Integrin ALAPHIIBBETA3 Complex with BMS4-1


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 BMS4-1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca506 b:81.2 occ:1.00 OD1 C:ASP245 2.3 76.3 1.0 O C:THR250 2.4 87.6 1.0 OE2 C:GLU243 2.4 83.8 1.0 OE1 C:GLU252 2.4 81.3 1.0 OE1 C:GLU243 2.4 84.2 1.0 OG1 C:THR250 2.4 88.3 1.0 O C:ASP247 2.4 89.6 1.0 OE2 C:GLU252 2.4 77.4 1.0 CD C:GLU243 2.7 83.3 1.0 CD C:GLU252 2.7 74.8 1.0 C C:THR250 2.9 87.1 1.0 CG C:ASP245 3.2 78.4 1.0 CB C:THR250 3.5 86.2 1.0 OD2 C:ASP245 3.6 81.9 1.0 CA C:THR250 3.6 85.4 1.0 C C:ASP247 3.6 92.1 1.0 N C:THR251 3.7 84.2 1.0 N C:THR250 3.9 87.7 1.0 CA C:THR251 4.0 79.4 1.0 CG C:GLU243 4.2 82.6 1.0 CG C:GLU252 4.2 73.3 1.0 N C:GLU252 4.4 70.7 1.0 CA C:ASP247 4.4 94.6 1.0 N C:ASP247 4.4 93.9 1.0 C C:THR251 4.5 76.9 1.0 CB C:ASP245 4.5 82.7 1.0 N C:ASP245 4.5 87.8 1.0 CB C:ASP247 4.6 96.0 1.0 N C:LEU248 4.6 95.0 1.0 CA C:GLU243 4.6 75.5 1.0 N C:PHE244 4.7 75.4 1.0 CA C:LEU248 4.7 92.1 1.0 CG2 C:THR250 4.7 90.7 1.0 CB C:GLU243 4.8 79.4 1.0 C C:LEU248 4.9 91.4 1.0 CA C:ASP245 5.0 87.8 1.0 N C:GLY246 5.0 91.6 1.0

Calcium binding site 6 out of 8 in the Integrin ALAPHIIBBETA3 Complex with BMS4-1


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 BMS4-1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca507 b:66.8 occ:1.00 O C:ARG303 2.3 75.1 1.0 OD1 C:ASN299 2.3 71.6 1.0 OD1 C:ASP305 2.4 67.8 1.0 OD1 C:ASP297 2.4 73.6 1.0 OD2 C:ASP305 2.4 73.9 1.0 OD1 C:ASP301 2.4 72.4 1.0 O C:HOH610 2.4 59.3 1.0 CG C:ASP305 2.7 71.6 1.0 CG C:ASP301 3.3 75.5 1.0 CG C:ASP297 3.4 73.2 1.0 CG C:ASN299 3.4 71.9 1.0 C C:ARG303 3.5 76.0 1.0 OD2 C:ASP301 3.5 76.5 1.0 ND2 C:ASN299 4.0 73.9 1.0 CA C:ASP297 4.1 72.5 1.0 CB C:ASP305 4.1 64.2 1.0 CB C:ASP297 4.1 70.8 1.0 CA C:ARG303 4.2 78.2 1.0 N C:ARG303 4.2 78.9 1.0 N C:ASP305 4.3 70.1 1.0 CB C:ARG303 4.3 86.2 1.0 OD2 C:ASP297 4.3 74.8 1.0 N C:VAL298 4.3 68.3 1.0 N C:ASN299 4.3 65.2 1.0 C C:HIS304 4.4 70.0 1.0 N C:HIS304 4.5 81.0 1.0 C C:ASP297 4.6 71.1 1.0 CA C:ASP305 4.6 68.3 1.0 CB C:ASP301 4.7 78.6 1.0 CB C:ASN299 4.7 69.7 1.0 O C:HIS304 4.7 73.3 1.0 CD2 C:LEU332 4.7 72.9 1.0 CA C:HIS304 4.7 72.7 1.0 N C:ASP301 4.8 74.3 1.0 CA C:ASN299 4.9 68.2 1.0 N C:GLN333 4.9 76.5 1.0

Calcium binding site 7 out of 8 in the Integrin ALAPHIIBBETA3 Complex with BMS4-1


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 BMS4-1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca508 b:60.0 occ:1.00 O C:TYR371 2.3 63.6 1.0 OD1 C:ASP367 2.4 59.7 1.0 OD1 C:ASP365 2.4 62.4 1.0 O C:HOH622 2.4 54.1 1.0 OD2 C:ASP373 2.4 63.5 1.0 OD1 C:ASP373 2.4 63.9 1.0 OD1 C:ASP369 2.5 73.9 1.0 CG C:ASP373 2.8 64.1 1.0 C C:TYR371 3.5 66.8 1.0 CG C:ASP369 3.5 69.7 1.0 CG C:ASP365 3.5 67.2 1.0 CG C:ASP367 3.5 61.5 1.0 OD2 C:ASP369 3.9 68.3 1.0 N C:LEU366 3.9 65.9 1.0 OD2 C:ASP367 4.0 65.3 1.0 CA C:ASP365 4.1 67.6 1.0 N C:ASP367 4.1 71.8 1.0 OD2 C:ASP365 4.2 70.1 1.0 N C:TYR371 4.2 70.0 1.0 CA C:TYR371 4.3 66.1 1.0 CB C:ASP373 4.3 60.2 1.0 C C:ASP365 4.4 66.2 1.0 CB C:ASP365 4.4 63.3 1.0 CB C:TYR371 4.5 67.0 1.0 N C:ASN372 4.5 66.8 1.0 C C:ASN372 4.5 65.0 1.0 N C:ASP369 4.5 71.5 1.0 N C:GLY394 4.6 66.0 1.0 CA C:ASN372 4.6 65.3 1.0 N C:ASP373 4.6 60.6 1.0 N C:ARG368 4.6 69.6 1.0 CB C:ASP369 4.7 69.9 1.0 CB C:ASP367 4.7 62.2 1.0 O C:ASN372 4.8 63.8 1.0 CA C:ASP367 4.8 65.7 1.0 CD2 C:LEU393 4.9 61.0 1.0 CA C:LEU366 4.9 64.2 1.0 CB C:LEU393 5.0 59.4 1.0 CA C:ASP373 5.0 59.9 1.0

Calcium binding site 8 out of 8 in the Integrin ALAPHIIBBETA3 Complex with BMS4-1


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 BMS4-1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca509 b:56.9 occ:1.00 O C:TYR432 2.3 54.8 1.0 OD1 C:ASP434 2.3 56.6 1.0 OD1 C:ASP426 2.4 62.2 1.0 OD1 C:ASN430 2.4 69.9 1.0 OD1 C:ASP428 2.4 56.9 1.0 OD2 C:ASP434 2.4 60.3 1.0 O C:HOH604 2.4 57.6 1.0 CG C:ASP434 2.7 58.0 1.0 CG C:ASP426 3.3 61.9 1.0 CG C:ASN430 3.3 62.2 1.0 C C:TYR432 3.4 57.3 1.0 CG C:ASP428 3.5 62.5 1.0 OD2 C:ASP428 3.9 61.6 1.0 ND2 C:ASN430 4.0 61.4 1.0 CA C:ASP426 4.0 57.7 1.0 N C:TYR432 4.1 66.7 1.0 OD2 C:ASP426 4.1 64.5 1.0 CB C:ASP426 4.1 61.0 1.0 CA C:TYR432 4.1 62.3 1.0 CB C:ASP434 4.1 47.8 1.0 CB C:TYR432 4.3 65.3 1.0 O C:ALA450 4.3 59.4 1.0 CB C:ASN430 4.3 63.8 1.0 N C:ASN430 4.4 67.5 1.0 N C:ILE427 4.4 55.7 1.0 N C:ASP428 4.4 60.6 1.0 N C:ASP434 4.4 52.6 1.0 N C:PRO433 4.5 56.0 1.0 C C:PRO433 4.5 57.8 1.0 C C:ASP426 4.5 57.7 1.0 N C:ALA450 4.5 53.2 1.0 CA C:PRO433 4.7 56.0 1.0 CB C:ASP428 4.7 62.9 1.0 N C:ASP429 4.7 67.3 1.0 CA C:ASP434 4.7 46.9 1.0 CA C:ASN430 4.8 65.8 1.0 CB C:ALA450 4.9 56.4 1.0 CA C:ASP428 4.9 66.1 1.0 O C:PRO433 5.0 62.3 1.0

J.Zhu, F.-Y.Lin, J.Zhu, T.A.Springer. Integrin Alpha Iib Beta 3 Headpiece with Fab Complex with BMS4-1 To Be Published.