Calcium in PDB 7uko: Integrin ALAPHIIBBETA3 Complex with Sibrafiban (Mn)

The structure of Integrin ALAPHIIBBETA3 Complex with Sibrafiban (Mn), PDB code: 7uko 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)	49.29 / 2.60
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	258.388, 144.599, 104.854, 90, 90, 90
R / Rfree (%)	21.4 / 23.9

The structure of Integrin ALAPHIIBBETA3 Complex with Sibrafiban (Mn) also contains other interesting chemical elements:

Manganese	(Mn)	6 atoms
Chlorine	(Cl)	1 atom

The binding sites of Calcium atom in the Integrin ALAPHIIBBETA3 Complex with Sibrafiban (Mn) (pdb code 7uko). 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 Sibrafiban (Mn), PDB code: 7uko:
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 Sibrafiban (Mn)


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 Sibrafiban (Mn) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:44.2 occ:1.00 OG1 A:THR250 2.3 48.1 1.0 OD1 A:ASP245 2.3 46.6 1.0 O A:THR250 2.4 45.9 1.0 O A:ASP247 2.4 47.2 1.0 OE2 A:GLU243 2.4 44.2 1.0 OE1 A:GLU243 2.4 43.6 1.0 OE1 A:GLU252 2.4 43.3 1.0 OE2 A:GLU252 2.4 44.1 1.0 CD A:GLU243 2.7 43.7 1.0 CD A:GLU252 2.8 42.9 1.0 CG A:ASP245 2.9 46.0 1.0 OD2 A:ASP245 3.0 46.0 1.0 C A:THR250 3.1 45.9 1.0 CB A:THR250 3.4 48.0 1.0 C A:ASP247 3.5 49.2 1.0 CA A:THR250 3.6 48.0 1.0 N A:THR250 3.9 50.1 1.0 N A:ASP247 4.1 49.1 1.0 N A:THR251 4.1 45.0 1.0 CA A:ASP247 4.2 50.5 1.0 CG A:GLU243 4.2 43.2 1.0 CB A:ASP245 4.2 45.4 1.0 CG A:GLU252 4.3 41.1 1.0 N A:ASP245 4.3 43.6 1.0 CB A:ASP247 4.4 50.6 1.0 CA A:THR251 4.5 43.0 1.0 N A:LEU248 4.5 51.1 1.0 N A:PHE244 4.6 41.2 1.0 CG2 A:THR250 4.7 50.1 1.0 CA A:GLU243 4.7 39.3 1.0 N A:GLY246 4.7 46.2 1.0 CA A:ASP245 4.7 45.4 1.0 C A:THR251 4.7 41.5 1.0 CA A:LEU248 4.7 50.2 1.0 N A:GLU252 4.8 40.3 1.0 O A:HOH734 4.8 48.2 1.0 CB A:GLU243 4.9 41.1 1.0 C A:LEU248 4.9 50.2 1.0 C A:ASP245 4.9 47.8 1.0

Calcium binding site 2 out of 8 in the Integrin ALAPHIIBBETA3 Complex with Sibrafiban (Mn)


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 Sibrafiban (Mn) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:33.4 occ:1.00 OD1 A:ASN299 2.2 36.6 1.0 O A:ARG303 2.3 37.0 1.0 OD1 A:ASP297 2.4 37.4 1.0 O A:HOH604 2.4 37.7 1.0 OD1 A:ASP301 2.5 39.0 1.0 OD1 A:ASP305 2.5 37.5 1.0 OD2 A:ASP305 2.5 37.0 1.0 CG A:ASP305 2.8 36.4 1.0 CG A:ASP301 3.3 40.6 1.0 CG A:ASN299 3.3 37.3 1.0 OD2 A:ASP301 3.4 40.4 1.0 C A:ARG303 3.5 37.6 1.0 CG A:ASP297 3.5 37.5 1.0 ND2 A:ASN299 3.8 38.5 1.0 N A:ARG303 4.1 41.2 1.0 CA A:ARG303 4.1 39.9 1.0 CB A:ARG303 4.2 40.8 1.0 CB A:ASP297 4.2 35.9 1.0 CA A:ASP297 4.2 34.0 1.0 CB A:ASP305 4.3 34.5 1.0 N A:ASN299 4.3 35.0 1.0 N A:VAL298 4.4 35.1 1.0 OD2 A:ASP297 4.4 39.2 1.0 C A:HIS304 4.5 34.7 1.0 N A:ASP305 4.5 35.0 1.0 CB A:ASN299 4.6 37.2 1.0 N A:HIS304 4.6 37.6 1.0 N A:ASP301 4.6 41.3 1.0 O A:HIS304 4.6 35.2 1.0 CB A:ASP301 4.7 42.9 1.0 C A:ASP297 4.7 34.0 1.0 CD2 A:LEU332 4.7 35.4 1.0 N A:GLN333 4.8 38.4 1.0 CA A:ASP305 4.8 34.1 1.0 CA A:ASN299 4.9 36.9 1.0 CA A:HIS304 4.9 35.6 1.0 N A:GLY300 4.9 38.3 1.0 O A:GLN333 4.9 42.1 1.0

Calcium binding site 3 out of 8 in the Integrin ALAPHIIBBETA3 Complex with Sibrafiban (Mn)


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 Sibrafiban (Mn) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:31.9 occ:1.00 O A:TYR371 2.3 32.9 1.0 OD1 A:ASP365 2.3 33.5 1.0 O A:HOH672 2.4 31.5 1.0 OD1 A:ASP369 2.4 33.7 1.0 OD1 A:ASP367 2.4 34.3 1.0 OD1 A:ASP373 2.5 34.2 1.0 OD2 A:ASP373 2.5 33.7 1.0 CG A:ASP373 2.8 33.4 1.0 CG A:ASP369 3.4 34.6 1.0 CG A:ASP365 3.4 34.1 1.0 C A:TYR371 3.4 33.4 1.0 CG A:ASP367 3.5 34.6 1.0 OD2 A:ASP369 3.8 34.9 1.0 OD2 A:ASP367 4.0 35.3 1.0 OD2 A:ASP365 4.1 35.4 1.0 N A:TYR371 4.1 35.9 1.0 CA A:ASP365 4.1 31.9 1.0 CA A:TYR371 4.2 35.0 1.0 N A:LEU366 4.2 32.7 1.0 N A:ASP367 4.3 33.1 1.0 CB A:ASP365 4.3 33.4 1.0 CB A:TYR371 4.3 35.1 1.0 CB A:ASP373 4.3 32.2 1.0 C A:ASP365 4.4 31.5 1.0 N A:ASN372 4.4 33.9 1.0 N A:ASP369 4.4 34.8 1.0 C A:ASN372 4.5 31.6 1.0 CB A:ASP369 4.5 35.6 1.0 N A:GLY394 4.5 34.1 1.0 CD2 A:LEU393 4.6 32.9 1.0 CA A:ASN372 4.6 32.6 1.0 N A:ASP373 4.7 33.1 1.0 N A:ARG368 4.7 34.3 1.0 O A:ASN372 4.7 31.9 1.0 O A:HOH627 4.7 36.6 1.0 CB A:ASP367 4.8 34.3 1.0 O A:GLY394 4.8 37.0 1.0 CB A:LEU393 4.9 34.1 1.0 CA A:ASP367 4.9 34.1 1.0 CA A:ASP369 4.9 36.1 1.0

Calcium binding site 4 out of 8 in the Integrin ALAPHIIBBETA3 Complex with Sibrafiban (Mn)


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 Sibrafiban (Mn) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca505 b:31.1 occ:1.00 OD1 A:ASP428 2.2 32.9 1.0 O A:TYR432 2.2 31.4 1.0 OD1 A:ASP426 2.3 32.7 1.0 OD1 A:ASN430 2.3 31.8 1.0 O A:HOH609 2.4 30.8 1.0 OD2 A:ASP434 2.4 32.6 1.0 OD1 A:ASP434 2.5 32.1 1.0 CG A:ASP434 2.8 31.9 1.0 CG A:ASP428 3.3 33.0 1.0 CG A:ASP426 3.3 33.2 1.0 CG A:ASN430 3.3 32.4 1.0 C A:TYR432 3.4 31.7 1.0 OD2 A:ASP428 3.6 32.9 1.0 CA A:ASP426 4.0 31.7 1.0 N A:TYR432 4.0 33.6 1.0 CB A:ASP426 4.0 32.7 1.0 ND2 A:ASN430 4.0 32.2 1.0 CA A:TYR432 4.1 32.6 1.0 OD2 A:ASP426 4.1 34.2 1.0 O A:ALA450 4.3 33.7 1.0 N A:ILE427 4.3 33.0 1.0 N A:ASP428 4.3 33.1 1.0 CB A:TYR432 4.3 32.4 1.0 N A:ASN430 4.3 33.8 1.0 CB A:ASP434 4.3 31.0 1.0 CB A:ASN430 4.3 33.5 1.0 C A:ASP426 4.4 32.0 1.0 N A:PRO433 4.5 31.8 1.0 CB A:ASP428 4.6 33.5 1.0 N A:ALA450 4.6 31.8 1.0 N A:ASP434 4.6 31.3 1.0 C A:PRO433 4.6 30.1 1.0 N A:ASP429 4.6 34.2 1.0 CA A:PRO433 4.7 31.0 1.0 CA A:ASN430 4.7 34.2 1.0 CA A:ASP428 4.8 33.9 1.0 N A:GLY431 4.9 35.5 1.0 C A:ASP428 4.9 34.9 1.0 CA A:ASP434 4.9 30.6 1.0 C A:ASN430 5.0 34.3 1.0 CB A:ALA450 5.0 32.2 1.0

Calcium binding site 5 out of 8 in the Integrin ALAPHIIBBETA3 Complex with Sibrafiban (Mn)


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 Sibrafiban (Mn) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:68.0 occ:1.00 O C:THR250 2.3 67.3 1.0 O C:ASP247 2.3 68.4 1.0 OG1 C:THR250 2.3 70.9 1.0 OE1 C:GLU252 2.4 66.6 1.0 OD1 C:ASP245 2.4 69.8 1.0 OE2 C:GLU252 2.4 66.2 1.0 OE2 C:GLU243 2.4 68.5 1.0 OE1 C:GLU243 2.4 66.4 1.0 OD2 C:ASP245 2.5 69.3 1.0 CG C:ASP245 2.6 69.5 1.0 CD C:GLU252 2.7 65.8 1.0 CD C:GLU243 2.7 67.1 1.0 C C:THR250 3.1 67.4 1.0 CB C:THR250 3.5 70.7 1.0 C C:ASP247 3.5 70.6 1.0 CA C:THR250 3.7 69.9 1.0 N C:THR250 4.0 71.8 1.0 CB C:ASP245 4.0 69.3 1.0 N C:THR251 4.1 67.5 1.0 N C:ASP247 4.2 71.9 1.0 CG C:GLU243 4.2 66.2 1.0 CG C:GLU252 4.2 64.2 1.0 CA C:ASP247 4.3 72.8 1.0 N C:ASP245 4.3 66.4 1.0 N C:GLY246 4.4 68.7 1.0 CB C:ASP247 4.5 73.5 1.0 CA C:THR251 4.5 65.2 1.0 N C:LEU248 4.5 72.3 1.0 CA C:ASP245 4.6 68.8 1.0 N C:GLU252 4.7 62.0 1.0 N C:PHE244 4.7 64.1 1.0 CA C:LEU248 4.7 70.4 1.0 CA C:GLU243 4.7 62.2 1.0 CG2 C:THR250 4.7 73.5 1.0 C C:THR251 4.8 64.1 1.0 CB C:GLU243 4.8 63.7 1.0 C C:GLY246 4.9 72.1 1.0 C C:LEU248 5.0 70.1 1.0

Calcium binding site 6 out of 8 in the Integrin ALAPHIIBBETA3 Complex with Sibrafiban (Mn)


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 Sibrafiban (Mn) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca504 b:55.9 occ:1.00 OD1 C:ASP301 2.3 61.7 1.0 OD1 C:ASN299 2.3 59.7 1.0 O C:ARG303 2.4 59.7 1.0 OD1 C:ASP297 2.4 58.8 1.0 OD2 C:ASP305 2.4 55.7 1.0 OD1 C:ASP305 2.4 57.5 1.0 O C:HOH601 2.5 61.7 1.0 OD2 C:ASP301 2.6 62.3 1.0 CG C:ASP305 2.7 55.7 1.0 CG C:ASP301 2.7 62.9 1.0 CG C:ASN299 3.4 60.2 1.0 C C:ARG303 3.5 60.9 1.0 CG C:ASP297 3.5 59.0 1.0 ND2 C:ASN299 3.9 61.6 1.0 N C:ARG303 4.1 64.4 1.0 CA C:ARG303 4.1 63.7 1.0 CA C:ASP297 4.2 55.0 1.0 CB C:ARG303 4.2 65.0 1.0 CB C:ASP305 4.2 53.7 1.0 CB C:ASP301 4.2 65.3 1.0 CB C:ASP297 4.2 57.2 1.0 N C:ASN299 4.3 56.6 1.0 N C:VAL298 4.3 55.6 1.0 OD2 C:ASP297 4.3 60.8 1.0 C C:HIS304 4.4 56.0 1.0 N C:ASP305 4.4 54.9 1.0 O C:HIS304 4.5 57.2 1.0 N C:HIS304 4.5 59.2 1.0 N C:ASP301 4.6 63.2 1.0 CD2 C:LEU332 4.6 55.6 1.0 C C:ASP297 4.6 54.2 1.0 CB C:ASN299 4.6 59.4 1.0 CA C:ASP305 4.8 54.0 1.0 CA C:HIS304 4.8 56.8 1.0 CA C:ASP301 4.9 65.5 1.0 CA C:ASN299 4.9 58.6 1.0 N C:GLN333 4.9 61.6 1.0

Calcium binding site 7 out of 8 in the Integrin ALAPHIIBBETA3 Complex with Sibrafiban (Mn)


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 Sibrafiban (Mn) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca505 b:50.6 occ:1.00 O C:TYR371 2.2 52.2 1.0 OD1 C:ASP365 2.3 53.6 1.0 OD1 C:ASP367 2.4 53.3 1.0 O C:HOH608 2.4 52.9 1.0 OD1 C:ASP369 2.4 53.2 1.0 OD2 C:ASP373 2.5 50.9 1.0 OD1 C:ASP373 2.5 51.1 1.0 CG C:ASP373 2.8 50.2 1.0 CG C:ASP365 3.4 54.8 1.0 CG C:ASP369 3.4 54.3 1.0 C C:TYR371 3.4 53.1 1.0 CG C:ASP367 3.5 53.9 1.0 OD2 C:ASP369 3.8 54.0 1.0 OD2 C:ASP367 3.9 54.6 1.0 N C:LEU366 4.0 52.3 1.0 OD2 C:ASP365 4.0 56.8 1.0 N C:TYR371 4.1 56.9 1.0 CA C:ASP365 4.1 51.5 1.0 CA C:TYR371 4.2 55.4 1.0 N C:ASP367 4.2 52.3 1.0 CB C:ASP373 4.3 48.3 1.0 CB C:ASP365 4.3 53.9 1.0 CB C:TYR371 4.4 55.2 1.0 C C:ASP365 4.4 50.9 1.0 N C:GLY394 4.5 53.2 1.0 N C:ASN372 4.5 52.9 1.0 C C:ASN372 4.5 49.3 1.0 N C:ASP369 4.5 56.0 1.0 CB C:ASP369 4.6 56.4 1.0 CA C:ASN372 4.7 51.0 1.0 N C:ASP373 4.7 49.9 1.0 O C:ASN372 4.7 49.5 1.0 N C:ARG368 4.7 54.4 1.0 CD2 C:LEU393 4.7 49.9 1.0 CB C:ASP367 4.8 53.9 1.0 CB C:LEU393 4.8 51.4 1.0 O C:GLY394 4.9 57.1 1.0 CA C:ASP367 4.9 53.9 1.0 CA C:LEU366 5.0 51.6 1.0

Calcium binding site 8 out of 8 in the Integrin ALAPHIIBBETA3 Complex with Sibrafiban (Mn)


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 Sibrafiban (Mn) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca506 b:49.6 occ:1.00 O C:TYR432 2.2 50.2 1.0 OD1 C:ASN430 2.3 51.5 1.0 OD1 C:ASP428 2.3 52.5 1.0 OD1 C:ASP426 2.3 51.4 1.0 OD1 C:ASP434 2.4 47.7 1.0 OD2 C:ASP434 2.4 48.6 1.0 O C:HOH602 2.4 50.4 1.0 CG C:ASP434 2.7 47.4 1.0 CG C:ASP428 3.1 52.2 1.0 CG C:ASN430 3.3 52.4 1.0 OD2 C:ASP428 3.3 51.6 1.0 C C:TYR432 3.3 50.7 1.0 CG C:ASP426 3.3 52.5 1.0 N C:TYR432 3.9 54.2 1.0 CA C:TYR432 4.0 52.5 1.0 ND2 C:ASN430 4.0 52.1 1.0 CA C:ASP426 4.0 49.7 1.0 CB C:ASP426 4.0 51.6 1.0 CB C:TYR432 4.1 52.1 1.0 CB C:ASP434 4.2 45.8 1.0 OD2 C:ASP426 4.2 54.4 1.0 O C:ALA450 4.3 51.1 1.0 CB C:ASN430 4.3 54.3 1.0 N C:ASP428 4.3 52.2 1.0 N C:ILE427 4.3 50.3 1.0 N C:PRO433 4.4 49.9 1.0 N C:ASN430 4.4 55.1 1.0 N C:ASP434 4.4 46.5 1.0 N C:ALA450 4.4 47.4 1.0 C C:PRO433 4.5 46.7 1.0 C C:ASP426 4.5 50.0 1.0 CB C:ASP428 4.5 52.8 1.0 CA C:PRO433 4.7 48.4 1.0 CA C:ASP434 4.8 45.2 1.0 CB C:ALA450 4.8 48.5 1.0 CA C:ASN430 4.8 55.8 1.0 CA C:ASP428 4.9 53.6 1.0 O C:PRO433 4.9 46.2 1.0 N C:ASP429 4.9 54.7 1.0 N C:GLY431 4.9 54.9 1.0 C C:ASN430 4.9 56.0 1.0 CG C:ARG449 5.0 46.5 1.0

J.Zhu, F.-Y.Lin, J.Zhu, T.A.Springer. Integrin Alpha Iib Beta 3 Headpiece with Fab Complex with Sibrafiban (Mn) To Be Published.