Calcium in PDB 7u9f: Integrin ALAPHIIBBETA3 Complex with Bms Compound 4 in MN2+

The structure of Integrin ALAPHIIBBETA3 Complex with Bms Compound 4 in MN2+, PDB code: 7u9f 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)	46.09 / 2.70
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	259.397, 144.292, 104.923, 90, 90, 90
R / Rfree (%)	21.7 / 23.7

The structure of Integrin ALAPHIIBBETA3 Complex with Bms Compound 4 in MN2+ also contains other interesting chemical elements:

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

The binding sites of Calcium atom in the Integrin ALAPHIIBBETA3 Complex with Bms Compound 4 in MN2+ (pdb code 7u9f). 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 Bms Compound 4 in MN2+, PDB code: 7u9f:
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 Bms Compound 4 in MN2+


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 Bms Compound 4 in MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:48.9 occ:1.00 OD1 A:ASP245 2.3 53.5 1.0 O A:THR250 2.3 55.8 1.0 O A:ASP247 2.3 57.8 1.0 OE1 A:GLU252 2.4 51.1 1.0 OE2 A:GLU252 2.4 51.7 1.0 OE2 A:GLU243 2.4 51.6 1.0 OE1 A:GLU243 2.4 50.8 1.0 OG1 A:THR250 2.4 58.0 1.0 CD A:GLU243 2.7 50.9 1.0 CD A:GLU252 2.7 51.0 1.0 C A:THR250 3.1 56.0 1.0 CG A:ASP245 3.2 53.8 1.0 C A:ASP247 3.5 59.1 1.0 OD2 A:ASP245 3.5 54.3 1.0 CB A:THR250 3.5 58.0 1.0 CA A:THR250 3.7 57.6 1.0 N A:THR250 3.9 58.8 1.0 N A:THR251 4.1 54.5 1.0 N A:ASP247 4.1 59.6 1.0 CG A:GLU243 4.2 50.3 1.0 CA A:ASP247 4.2 60.4 1.0 CG A:GLU252 4.2 50.0 1.0 CB A:ASP247 4.4 60.8 1.0 O A:HOH630 4.4 55.7 1.0 CA A:THR251 4.4 53.0 1.0 N A:ASP245 4.4 52.0 1.0 CB A:ASP245 4.5 53.7 1.0 N A:LEU248 4.5 61.4 1.0 N A:GLU252 4.6 48.8 1.0 CA A:GLU243 4.6 47.8 1.0 N A:PHE244 4.6 47.1 1.0 CA A:LEU248 4.7 60.5 1.0 C A:THR251 4.7 52.3 1.0 CB A:GLU243 4.8 48.7 1.0 CG2 A:THR250 4.8 59.7 1.0 CA A:ASP245 4.9 53.6 1.0 C A:LEU248 4.9 60.5 1.0 N A:GLY246 4.9 55.7 1.0 O A:HOH666 5.0 54.5 1.0

Calcium binding site 2 out of 8 in the Integrin ALAPHIIBBETA3 Complex with Bms Compound 4 in MN2+


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 Bms Compound 4 in MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:40.6 occ:1.00 OD1 A:ASN299 2.3 42.8 1.0 O A:ARG303 2.3 45.0 1.0 O A:HOH635 2.3 44.0 1.0 OD1 A:ASP297 2.4 42.3 1.0 OD1 A:ASP305 2.4 44.1 1.0 OD2 A:ASP305 2.4 42.2 1.0 OD1 A:ASP301 2.4 44.7 1.0 CG A:ASP305 2.7 42.4 1.0 CG A:ASP301 3.3 45.9 1.0 CG A:ASN299 3.4 43.3 1.0 OD2 A:ASP301 3.4 46.2 1.0 C A:ARG303 3.5 45.4 1.0 CG A:ASP297 3.5 42.1 1.0 ND2 A:ASN299 3.8 44.2 1.0 CB A:ARG303 4.1 47.8 1.0 CA A:ARG303 4.1 47.0 1.0 CB A:ASP305 4.2 40.8 1.0 N A:ARG303 4.2 47.5 1.0 CA A:ASP297 4.2 39.8 1.0 CB A:ASP297 4.2 41.0 1.0 N A:ASP305 4.4 41.6 1.0 N A:ASN299 4.4 41.4 1.0 C A:HIS304 4.4 42.2 1.0 N A:VAL298 4.4 41.2 1.0 OD2 A:ASP297 4.5 43.0 1.0 N A:HIS304 4.6 43.9 1.0 O A:HIS304 4.6 42.9 1.0 CB A:ASN299 4.7 43.1 1.0 CD2 A:LEU332 4.7 41.0 1.0 C A:ASP297 4.7 39.7 1.0 CB A:ASP301 4.7 47.3 1.0 CA A:ASP305 4.7 41.1 1.0 N A:ASP301 4.8 45.8 1.0 N A:GLN333 4.8 44.8 1.0 CA A:HIS304 4.9 42.5 1.0 CA A:ASN299 4.9 42.6 1.0

Calcium binding site 3 out of 8 in the Integrin ALAPHIIBBETA3 Complex with Bms Compound 4 in MN2+


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 Bms Compound 4 in MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca505 b:38.9 occ:1.00 O A:TYR371 2.3 39.0 1.0 OD1 A:ASP367 2.4 40.6 1.0 OD1 A:ASP365 2.4 41.2 1.0 O A:HOH644 2.4 40.0 1.0 OD1 A:ASP373 2.4 40.4 1.0 OD1 A:ASP369 2.4 40.6 1.0 OD2 A:ASP373 2.5 39.7 1.0 CG A:ASP373 2.8 39.4 1.0 C A:TYR371 3.5 39.7 1.0 CG A:ASP369 3.5 41.9 1.0 CG A:ASP367 3.5 41.4 1.0 CG A:ASP365 3.5 42.0 1.0 OD2 A:ASP367 3.9 42.5 1.0 OD2 A:ASP369 4.0 42.2 1.0 N A:LEU366 4.1 40.2 1.0 CA A:ASP365 4.2 39.3 1.0 N A:TYR371 4.2 42.7 1.0 N A:ASP367 4.2 39.6 1.0 CA A:TYR371 4.2 41.6 1.0 CB A:ASP373 4.3 38.0 1.0 CB A:TYR371 4.3 41.9 1.0 OD2 A:ASP365 4.3 43.6 1.0 CD2 A:LEU393 4.4 39.6 1.0 CB A:ASP365 4.4 41.1 1.0 C A:ASP365 4.5 38.9 1.0 N A:ASP369 4.5 42.3 1.0 C A:ASN372 4.5 38.2 1.0 N A:ASN372 4.5 40.9 1.0 N A:GLY394 4.6 39.9 1.0 CB A:ASP369 4.6 43.4 1.0 N A:ASP373 4.6 39.0 1.0 N A:ARG368 4.6 42.0 1.0 CA A:ASN372 4.7 39.3 1.0 CB A:ASP367 4.7 41.4 1.0 O A:ASN372 4.7 38.6 1.0 CA A:ASP367 4.8 41.1 1.0 O A:GLY394 4.9 43.4 1.0 CB A:LEU393 4.9 40.9 1.0 C A:ASP367 5.0 42.6 1.0 CA A:ASP373 5.0 38.0 1.0 CA A:LEU366 5.0 39.8 1.0 CA A:ASP369 5.0 43.8 1.0

Calcium binding site 4 out of 8 in the Integrin ALAPHIIBBETA3 Complex with Bms Compound 4 in MN2+


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 Bms Compound 4 in MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca506 b:39.0 occ:1.00 O A:TYR432 2.3 39.5 1.0 OD1 A:ASP426 2.3 42.7 1.0 OD1 A:ASP434 2.3 40.3 1.0 OD1 A:ASN430 2.3 41.2 1.0 OD1 A:ASP428 2.3 41.7 1.0 OD2 A:ASP434 2.4 41.1 1.0 O A:HOH622 2.4 38.5 1.0 CG A:ASP434 2.7 40.1 1.0 CG A:ASN430 3.3 42.1 1.0 CG A:ASP426 3.4 43.3 1.0 CG A:ASP428 3.4 42.2 1.0 C A:TYR432 3.5 39.5 1.0 OD2 A:ASP428 3.8 42.1 1.0 ND2 A:ASN430 4.0 41.8 1.0 CA A:ASP426 4.0 41.2 1.0 N A:TYR432 4.1 42.3 1.0 OD2 A:ASP426 4.2 44.7 1.0 CB A:ASP434 4.2 38.8 1.0 N A:ILE427 4.2 41.2 1.0 CA A:TYR432 4.2 40.8 1.0 CB A:ASP426 4.2 42.6 1.0 N A:ASP428 4.3 42.3 1.0 O A:ALA450 4.3 41.6 1.0 N A:ASN430 4.3 44.5 1.0 CB A:TYR432 4.3 40.5 1.0 CB A:ASN430 4.4 43.9 1.0 N A:ASP434 4.5 38.8 1.0 C A:ASP426 4.5 42.0 1.0 N A:PRO433 4.5 39.9 1.0 C A:PRO433 4.5 37.7 1.0 CA A:PRO433 4.6 38.8 1.0 N A:ALA450 4.7 38.8 1.0 N A:ASP429 4.7 45.8 1.0 CB A:ASP428 4.7 43.3 1.0 CA A:ASP434 4.8 38.0 1.0 CA A:ASN430 4.8 44.9 1.0 CA A:ASP428 4.9 43.8 1.0 N A:GLY431 5.0 44.9 1.0

Calcium binding site 5 out of 8 in the Integrin ALAPHIIBBETA3 Complex with Bms Compound 4 in MN2+


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 Bms Compound 4 in MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca505 b:94.3 occ:1.00 OD1 C:ASP245 2.3 90.6 1.0 O C:THR250 2.4 90.2 1.0 O C:ASP247 2.4 92.5 1.0 OE1 C:GLU243 2.4 88.4 1.0 OE2 C:GLU243 2.4 91.5 1.0 OE1 C:GLU252 2.4 86.1 1.0 OE2 C:GLU252 2.4 89.0 1.0 OG1 C:THR250 2.4 95.8 1.0 CD C:GLU243 2.7 89.2 1.0 CD C:GLU252 2.8 86.8 1.0 C C:THR250 3.0 90.7 1.0 CG C:ASP245 3.2 92.1 1.0 CB C:THR250 3.5 95.9 1.0 C C:ASP247 3.6 95.2 1.0 OD2 C:ASP245 3.6 93.7 1.0 CA C:THR250 3.7 94.3 1.0 N C:THR251 3.8 89.3 1.0 N C:THR250 4.0 96.5 1.0 CA C:THR251 4.1 86.0 1.0 CG C:GLU243 4.2 87.5 1.0 CG C:GLU252 4.3 85.1 1.0 N C:ASP247 4.3 97.4 1.0 CA C:ASP247 4.4 98.5 1.0 N C:ASP245 4.4 87.9 1.0 N C:GLU252 4.5 81.3 1.0 C C:THR251 4.5 85.2 1.0 CB C:ASP245 4.5 92.3 1.0 N C:LEU248 4.5 98.5 1.0 CB C:ASP247 4.6 99.9 1.0 CA C:GLU243 4.6 82.5 1.0 N C:PHE244 4.6 85.6 1.0 CA C:LEU248 4.6 95.8 1.0 CG2 C:THR250 4.8 99.8 1.0 CB C:GLU243 4.8 83.9 1.0 C C:LEU248 4.8 95.4 1.0 N C:GLY246 4.8 94.1 1.0 CA C:ASP245 4.9 91.6 1.0

Calcium binding site 6 out of 8 in the Integrin ALAPHIIBBETA3 Complex with Bms Compound 4 in MN2+


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 Bms Compound 4 in MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca506 b:75.7 occ:1.00 OD1 C:ASP301 2.3 80.7 1.0 O C:ARG303 2.3 76.9 1.0 OD1 C:ASP297 2.3 79.6 1.0 OD2 C:ASP305 2.4 74.2 1.0 OD1 C:ASP305 2.4 77.9 1.0 OD1 C:ASN299 2.4 77.7 1.0 O C:HOH620 2.4 78.1 1.0 CG C:ASP305 2.7 74.8 1.0 CG C:ASP301 3.3 84.0 1.0 CG C:ASN299 3.5 78.2 1.0 CG C:ASP297 3.5 79.2 1.0 C C:ARG303 3.5 78.9 1.0 OD2 C:ASP301 3.6 85.1 1.0 ND2 C:ASN299 4.0 80.5 1.0 CA C:ASP297 4.0 73.1 1.0 CB C:ASP297 4.0 76.6 1.0 N C:ARG303 4.1 84.1 1.0 CB C:ASP305 4.1 71.8 1.0 CA C:ARG303 4.2 83.4 1.0 N C:VAL298 4.2 73.4 1.0 CB C:ARG303 4.3 85.7 1.0 N C:ASN299 4.3 72.1 1.0 N C:ASP305 4.4 73.9 1.0 C C:ASP297 4.5 71.6 1.0 OD2 C:ASP297 4.5 81.1 1.0 C C:HIS304 4.5 75.0 1.0 N C:HIS304 4.6 80.1 1.0 N C:ASP301 4.6 82.3 1.0 CB C:ASP301 4.6 87.0 1.0 CD2 C:LEU332 4.6 71.8 1.0 CB C:ASN299 4.7 76.5 1.0 CA C:ASP305 4.8 72.6 1.0 CA C:HIS304 4.9 76.2 1.0 CA C:ASN299 4.9 75.0 1.0 O C:HIS304 4.9 77.1 1.0 CA C:ASP301 5.0 86.3 1.0

Calcium binding site 7 out of 8 in the Integrin ALAPHIIBBETA3 Complex with Bms Compound 4 in MN2+


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 Bms Compound 4 in MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca507 b:66.7 occ:1.00 O C:TYR371 2.3 66.0 1.0 OD1 C:ASP365 2.4 68.7 1.0 OD1 C:ASP367 2.4 67.0 1.0 OD2 C:ASP373 2.4 65.2 1.0 O C:HOH626 2.4 65.8 1.0 OD1 C:ASP369 2.5 67.8 1.0 OD1 C:ASP373 2.5 66.5 1.0 CG C:ASP373 2.8 64.7 1.0 CG C:ASP369 3.5 69.5 1.0 C C:TYR371 3.5 67.7 1.0 CG C:ASP365 3.5 70.6 1.0 CG C:ASP367 3.6 67.7 1.0 N C:LEU366 3.9 65.0 1.0 OD2 C:ASP369 4.0 69.5 1.0 OD2 C:ASP367 4.1 69.0 1.0 N C:ASP367 4.2 64.7 1.0 N C:TYR371 4.2 73.1 1.0 CA C:ASP365 4.2 65.7 1.0 CA C:TYR371 4.3 71.1 1.0 OD2 C:ASP365 4.3 73.7 1.0 CB C:ASP373 4.3 62.1 1.0 C C:ASP365 4.4 64.3 1.0 CB C:ASP365 4.5 69.3 1.0 CB C:TYR371 4.5 70.8 1.0 N C:ASP369 4.5 71.2 1.0 N C:ASN372 4.5 69.7 1.0 C C:ASN372 4.6 64.1 1.0 N C:GLY394 4.6 65.9 1.0 N C:ARG368 4.6 66.6 1.0 CB C:ASP369 4.7 72.0 1.0 N C:ASP373 4.7 65.0 1.0 CA C:ASN372 4.7 66.7 1.0 CD2 C:LEU393 4.7 60.6 1.0 CB C:ASP367 4.8 67.1 1.0 CA C:LEU366 4.8 63.6 1.0 CA C:ASP367 4.9 67.0 1.0 O C:ASN372 4.9 64.7 1.0 C C:LEU366 5.0 65.6 1.0

Calcium binding site 8 out of 8 in the Integrin ALAPHIIBBETA3 Complex with Bms Compound 4 in MN2+


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 Bms Compound 4 in MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca508 b:59.7 occ:1.00 O C:TYR432 2.3 60.4 1.0 OD1 C:ASP426 2.3 62.3 1.0 OD1 C:ASP434 2.4 58.8 1.0 OD1 C:ASN430 2.4 61.8 1.0 OD2 C:ASP434 2.4 59.9 1.0 OD1 C:ASP428 2.4 61.1 1.0 O C:HOH602 2.4 61.1 1.0 CG C:ASP434 2.7 58.4 1.0 CG C:ASP426 3.3 64.1 1.0 CG C:ASN430 3.4 63.1 1.0 C C:TYR432 3.5 61.2 1.0 CG C:ASP428 3.5 61.3 1.0 CA C:ASP426 4.0 60.6 1.0 OD2 C:ASP428 4.0 61.2 1.0 OD2 C:ASP426 4.1 66.7 1.0 N C:TYR432 4.1 66.0 1.0 CB C:ASP426 4.1 63.4 1.0 CA C:TYR432 4.1 63.7 1.0 CB C:ASP434 4.1 56.3 1.0 ND2 C:ASN430 4.2 62.6 1.0 CB C:TYR432 4.3 62.8 1.0 N C:ILE427 4.3 60.5 1.0 N C:ASN430 4.3 66.7 1.0 N C:ASP428 4.3 61.5 1.0 O C:ALA450 4.4 61.9 1.0 CB C:ASN430 4.4 65.6 1.0 N C:ASP434 4.4 57.9 1.0 C C:ASP426 4.4 60.7 1.0 N C:PRO433 4.5 62.2 1.0 N C:ALA450 4.5 57.0 1.0 C C:PRO433 4.5 57.6 1.0 N C:ASP429 4.7 64.0 1.0 CA C:PRO433 4.7 60.2 1.0 CB C:ASP428 4.7 61.8 1.0 CA C:ASP434 4.8 55.8 1.0 CA C:ASN430 4.8 67.8 1.0 CB C:ALA450 4.8 58.9 1.0 CA C:ASP428 4.9 63.2 1.0 C C:ASP428 5.0 66.0 1.0 N C:GLY431 5.0 67.3 1.0 O C:PRO433 5.0 56.8 1.0

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