Calcium in PDB 7ukp: Integrin ALAPHIIBBETA3 Complex with A Gantofiban Analog

The structure of Integrin ALAPHIIBBETA3 Complex with A Gantofiban Analog, PDB code: 7ukp 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)	48.25 / 2.80
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	259.322, 144.495, 104.848, 90, 90, 90
R / Rfree (%)	21.9 / 24.1

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

Manganese	(Mn)	4 atoms
Chlorine	(Cl)	1 atom

The binding sites of Calcium atom in the Integrin ALAPHIIBBETA3 Complex with A Gantofiban Analog (pdb code 7ukp). 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 A Gantofiban Analog, PDB code: 7ukp:
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 A Gantofiban Analog


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 A Gantofiban Analog within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:81.1 occ:1.00 OD1 A:ASP245 2.3 84.0 1.0 O A:ASP247 2.3 87.1 1.0 OG1 A:THR250 2.3 87.5 1.0 O A:THR250 2.4 84.4 1.0 OE2 A:GLU252 2.4 82.5 1.0 OE2 A:GLU243 2.4 82.5 1.0 OE1 A:GLU243 2.4 81.2 1.0 OE1 A:GLU252 2.4 81.9 1.0 CD A:GLU243 2.8 81.6 1.0 CD A:GLU252 2.8 81.5 1.0 C A:THR250 3.0 84.5 1.0 CG A:ASP245 3.2 84.6 1.0 CB A:THR250 3.4 87.3 1.0 OD2 A:ASP245 3.4 85.5 1.0 C A:ASP247 3.5 89.2 1.0 CA A:THR250 3.6 86.8 1.0 N A:THR250 3.8 88.9 1.0 N A:THR251 3.9 83.4 1.0 N A:ASP247 4.2 89.5 1.0 CA A:ASP247 4.2 90.8 1.0 CB A:ASP247 4.2 91.2 1.0 CA A:THR251 4.2 81.2 1.0 CG A:GLU243 4.3 80.9 1.0 CG A:GLU252 4.3 79.8 1.0 CB A:ASP245 4.5 84.3 1.0 N A:GLU252 4.5 78.2 1.0 N A:LEU248 4.5 91.9 1.0 C A:THR251 4.6 80.0 1.0 N A:ASP245 4.6 81.9 1.0 CG2 A:THR250 4.7 89.8 1.0 CA A:GLU243 4.7 76.9 1.0 O A:HOH678 4.7 82.9 1.0 CA A:LEU248 4.7 90.7 1.0 N A:PHE244 4.8 77.6 1.0 C A:LEU248 4.9 90.7 1.0 CB A:GLU243 4.9 78.5 1.0 CG A:ASP247 5.0 92.8 1.0 CA A:ASP245 5.0 84.1 1.0

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


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 A Gantofiban Analog within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:69.3 occ:1.00 OD1 A:ASN299 2.2 68.7 1.0 O A:ARG303 2.2 71.2 1.0 O A:HOH617 2.2 66.3 1.0 OD1 A:ASP297 2.4 68.3 1.0 OD1 A:ASP301 2.5 71.7 1.0 OD2 A:ASP305 2.5 68.0 1.0 OD1 A:ASP305 2.5 69.0 1.0 CG A:ASP305 2.8 67.7 1.0 CG A:ASN299 3.3 69.2 1.0 C A:ARG303 3.4 71.9 1.0 CG A:ASP301 3.4 73.4 1.0 CG A:ASP297 3.5 68.4 1.0 OD2 A:ASP301 3.7 73.6 1.0 ND2 A:ASN299 3.7 70.2 1.0 CA A:ARG303 4.1 74.2 1.0 N A:ARG303 4.1 75.3 1.0 CA A:ASP297 4.1 64.8 1.0 CB A:ASP297 4.2 66.7 1.0 CB A:ARG303 4.2 75.2 1.0 N A:ASN299 4.3 66.8 1.0 CB A:ASP305 4.3 65.9 1.0 C A:HIS304 4.3 67.5 1.0 N A:VAL298 4.3 65.2 1.0 N A:ASP305 4.4 66.5 1.0 O A:HIS304 4.4 68.3 1.0 N A:HIS304 4.5 70.3 1.0 OD2 A:ASP297 4.5 69.9 1.0 C A:ASP297 4.5 64.7 1.0 CB A:ASN299 4.5 68.9 1.0 N A:ASP301 4.6 73.5 1.0 CA A:HIS304 4.7 68.2 1.0 CB A:ASP301 4.7 75.4 1.0 CD2 A:LEU332 4.8 66.8 1.0 CA A:ASP305 4.8 65.8 1.0 CA A:ASN299 4.8 68.5 1.0 N A:GLY300 4.8 70.2 1.0 C A:ASN299 4.9 70.4 1.0 N A:GLN333 5.0 71.5 1.0

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


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 A Gantofiban Analog within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:62.7 occ:1.00 O A:TYR371 2.2 64.6 1.0 OD1 A:ASP369 2.3 69.6 1.0 O A:HOH638 2.3 62.5 1.0 OD1 A:ASP365 2.3 68.3 1.0 OD1 A:ASP367 2.4 67.2 1.0 OD1 A:ASP373 2.5 66.2 1.0 OD2 A:ASP373 2.5 66.0 1.0 CG A:ASP373 2.9 65.2 1.0 CG A:ASP369 3.4 71.1 1.0 C A:TYR371 3.4 65.3 1.0 CG A:ASP367 3.5 68.3 1.0 CG A:ASP365 3.5 69.5 1.0 OD2 A:ASP369 3.9 71.1 1.0 OD2 A:ASP367 4.0 69.4 1.0 N A:LEU366 4.1 67.8 1.0 N A:TYR371 4.1 69.4 1.0 CA A:TYR371 4.1 67.6 1.0 N A:ASP367 4.2 66.7 1.0 CA A:ASP365 4.2 66.2 1.0 OD2 A:ASP365 4.3 71.7 1.0 CB A:TYR371 4.3 67.5 1.0 N A:ASP369 4.4 72.7 1.0 CB A:ASP373 4.4 63.3 1.0 CB A:ASP365 4.5 68.6 1.0 N A:ASN372 4.5 66.4 1.0 C A:ASP365 4.5 65.9 1.0 C A:ASN372 4.6 62.8 1.0 CD2 A:LEU393 4.6 64.6 1.0 N A:GLY394 4.6 65.7 1.0 CB A:ASP369 4.6 73.3 1.0 N A:ARG368 4.6 70.4 1.0 N A:ASP373 4.7 64.5 1.0 CA A:ASN372 4.7 64.5 1.0 CB A:ASP367 4.7 68.5 1.0 CA A:ASP367 4.8 68.6 1.0 O A:ASN372 4.9 62.9 1.0 CA A:ASP369 4.9 74.3 1.0 O A:GLY394 4.9 69.8 1.0 N A:GLY370 5.0 72.3 1.0 C A:ASP367 5.0 70.8 1.0

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


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 A Gantofiban Analog within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca505 b:63.2 occ:1.00 OD1 A:ASP426 2.3 69.5 1.0 OD1 A:ASP428 2.3 69.6 1.0 O A:TYR432 2.4 67.8 1.0 OD1 A:ASN430 2.4 70.4 1.0 OD1 A:ASP434 2.4 67.9 1.0 OD2 A:ASP434 2.4 69.0 1.0 O A:HOH634 2.5 66.6 1.0 CG A:ASP434 2.7 67.6 1.0 CG A:ASP426 3.4 70.4 1.0 CG A:ASN430 3.4 71.9 1.0 CG A:ASP428 3.4 70.6 1.0 C A:TYR432 3.6 67.7 1.0 OD2 A:ASP428 3.9 70.8 1.0 CA A:ASP426 4.1 67.1 1.0 N A:TYR432 4.2 71.8 1.0 ND2 A:ASN430 4.2 71.5 1.0 OD2 A:ASP426 4.2 72.5 1.0 O A:ALA450 4.2 69.9 1.0 CB A:ASP434 4.2 65.6 1.0 N A:ILE427 4.2 68.6 1.0 CB A:ASP426 4.2 69.1 1.0 CA A:TYR432 4.2 69.5 1.0 N A:ASP428 4.3 70.4 1.0 N A:ASN430 4.3 75.1 1.0 CB A:TYR432 4.4 69.2 1.0 CB A:ASN430 4.4 74.6 1.0 C A:ASP426 4.5 68.2 1.0 N A:ASP434 4.6 65.4 1.0 N A:PRO433 4.6 67.1 1.0 N A:ASP429 4.6 74.1 1.0 C A:PRO433 4.6 64.0 1.0 N A:ALA450 4.7 65.9 1.0 CB A:ASP428 4.7 72.0 1.0 CA A:PRO433 4.7 65.6 1.0 CA A:ASN430 4.8 75.8 1.0 CA A:ASP428 4.9 72.7 1.0 CA A:ASP434 4.9 64.3 1.0 C A:ASP428 5.0 74.6 1.0

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


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 A Gantofiban Analog within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca505 b:122.7 occ:1.00 OD1 C:ASP245 2.3 121.3 1.0 O C:ASP247 2.3 122.3 1.0 OE2 C:GLU243 2.4 123.6 1.0 OE1 C:GLU252 2.4 117.7 1.0 OG1 C:THR250 2.4 127.2 1.0 OE2 C:GLU252 2.4 120.8 1.0 O C:THR250 2.4 120.7 1.0 OE1 C:GLU243 2.4 119.5 1.0 CD C:GLU243 2.7 121.0 1.0 CD C:GLU252 2.7 118.4 1.0 C C:THR250 3.0 120.8 1.0 CG C:ASP245 3.2 123.0 1.0 CB C:THR250 3.4 126.4 1.0 OD2 C:ASP245 3.5 124.6 1.0 C C:ASP247 3.6 125.8 1.0 CA C:THR250 3.6 124.5 1.0 N C:THR251 3.7 119.7 1.0 N C:THR250 3.9 127.3 1.0 CA C:THR251 4.1 116.2 1.0 CG C:GLU243 4.2 119.8 1.0 CG C:GLU252 4.2 116.4 1.0 CA C:ASP247 4.4 129.6 1.0 N C:ASP247 4.4 128.9 1.0 N C:GLU252 4.5 111.4 1.0 CB C:ASP245 4.5 123.3 1.0 CB C:ASP247 4.5 130.6 1.0 C C:THR251 4.5 115.1 1.0 N C:LEU248 4.5 129.9 1.0 N C:ASP245 4.6 119.3 1.0 CA C:LEU248 4.7 126.8 1.0 CA C:GLU243 4.7 113.8 1.0 CG2 C:THR250 4.7 130.3 1.0 N C:PHE244 4.8 116.0 1.0 C C:LEU248 4.8 125.8 1.0 CB C:GLU243 4.8 115.7 1.0 N C:GLY246 5.0 124.0 1.0 CA C:ASP245 5.0 123.3 1.0 O C:LEU248 5.0 122.6 1.0

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


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 A Gantofiban Analog within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca506 b:104.2 occ:1.00 O C:ARG303 2.3 107.9 1.0 OD1 C:ASP301 2.3 108.8 1.0 OD1 C:ASN299 2.3 105.4 1.0 O C:HOH605 2.4 107.8 1.0 OD1 C:ASP297 2.4 106.9 1.0 OD1 C:ASP305 2.4 106.9 1.0 OD2 C:ASP305 2.4 103.5 1.0 CG C:ASP305 2.7 103.9 1.0 CG C:ASP301 3.2 112.0 1.0 OD2 C:ASP301 3.3 112.8 1.0 CG C:ASN299 3.4 106.5 1.0 C C:ARG303 3.5 109.5 1.0 CG C:ASP297 3.5 106.2 1.0 ND2 C:ASN299 3.9 109.0 1.0 CA C:ASP297 4.0 99.9 1.0 CB C:ASP297 4.1 103.2 1.0 N C:ARG303 4.1 115.0 1.0 CB C:ASP305 4.2 100.8 1.0 CA C:ARG303 4.2 113.9 1.0 N C:VAL298 4.3 99.8 1.0 N C:ASN299 4.3 100.2 1.0 CB C:ARG303 4.3 116.4 1.0 N C:ASP305 4.4 102.2 1.0 C C:HIS304 4.4 103.4 1.0 C C:ASP297 4.5 98.9 1.0 OD2 C:ASP297 4.5 108.2 1.0 CB C:ASP301 4.5 115.4 1.0 N C:HIS304 4.5 108.1 1.0 N C:ASP301 4.5 110.8 1.0 CB C:ASN299 4.7 105.4 1.0 CD2 C:LEU332 4.7 102.7 1.0 O C:HIS304 4.8 105.6 1.0 CA C:HIS304 4.8 104.2 1.0 CA C:ASP305 4.8 101.2 1.0 N C:GLY300 4.8 104.8 1.0 CA C:ASN299 4.9 103.6 1.0 CA C:ASP301 5.0 114.7 1.0 C C:ASN299 5.0 106.6 1.0

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


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 A Gantofiban Analog within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca507 b:90.2 occ:1.00 O C:TYR371 2.2 91.2 1.0 OD1 C:ASP367 2.4 92.1 1.0 OD1 C:ASP369 2.4 93.7 1.0 OD1 C:ASP365 2.4 94.0 1.0 O C:HOH616 2.4 89.5 1.0 OD2 C:ASP373 2.5 90.2 1.0 OD1 C:ASP373 2.5 92.0 1.0 CG C:ASP373 2.8 89.8 1.0 CG C:ASP369 3.4 96.0 1.0 C C:TYR371 3.4 92.8 1.0 CG C:ASP365 3.5 95.6 1.0 CG C:ASP367 3.5 93.4 1.0 N C:LEU366 3.9 91.1 1.0 OD2 C:ASP369 3.9 96.4 1.0 OD2 C:ASP367 4.0 95.2 1.0 N C:ASP367 4.1 89.7 1.0 CA C:ASP365 4.1 90.1 1.0 N C:TYR371 4.2 98.6 1.0 CA C:TYR371 4.2 96.6 1.0 OD2 C:ASP365 4.3 98.8 1.0 CB C:ASP373 4.3 87.1 1.0 C C:ASP365 4.4 88.8 1.0 CB C:ASP365 4.4 93.7 1.0 CB C:TYR371 4.4 96.9 1.0 N C:ASN372 4.5 93.9 1.0 N C:ASP369 4.5 97.1 1.0 C C:ASN372 4.5 88.4 1.0 N C:ARG368 4.6 93.6 1.0 CB C:ASP369 4.6 98.8 1.0 N C:GLY394 4.6 93.0 1.0 CA C:ASN372 4.6 90.7 1.0 N C:ASP373 4.7 89.5 1.0 CB C:ASP367 4.7 92.9 1.0 CD2 C:LEU393 4.8 88.5 1.0 CA C:ASP367 4.8 92.3 1.0 O C:ASN372 4.8 89.3 1.0 CA C:LEU366 4.9 89.7 1.0 C C:LEU366 5.0 91.9 1.0 C C:ASP367 5.0 95.5 1.0

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


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 A Gantofiban Analog within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca508 b:81.6 occ:1.00 OD1 C:ASP428 2.3 85.7 1.0 O C:TYR432 2.3 85.5 1.0 OD1 C:ASP426 2.3 86.7 1.0 OD1 C:ASN430 2.3 85.8 1.0 OD1 C:ASP434 2.4 83.9 1.0 O C:HOH611 2.4 85.4 1.0 OD2 C:ASP434 2.4 84.7 1.0 CG C:ASP434 2.7 83.3 1.0 CG C:ASN430 3.3 86.9 1.0 CG C:ASP428 3.3 85.6 1.0 CG C:ASP426 3.4 88.3 1.0 C C:TYR432 3.4 86.5 1.0 OD2 C:ASP428 3.7 85.5 1.0 ND2 C:ASN430 4.0 86.5 1.0 CA C:ASP426 4.0 84.6 1.0 N C:TYR432 4.0 91.3 1.0 CA C:TYR432 4.1 89.2 1.0 CB C:ASP426 4.1 87.4 1.0 OD2 C:ASP426 4.2 91.0 1.0 CB C:ASP434 4.2 81.2 1.0 CB C:TYR432 4.3 88.6 1.0 N C:ILE427 4.3 85.1 1.0 N C:ASP428 4.3 85.2 1.0 N C:ASN430 4.3 89.9 1.0 CB C:ASN430 4.3 89.2 1.0 O C:ALA450 4.4 87.3 1.0 N C:ASP434 4.4 82.9 1.0 C C:ASP426 4.4 84.5 1.0 N C:PRO433 4.5 87.8 1.0 C C:PRO433 4.5 83.2 1.0 N C:ALA450 4.5 82.2 1.0 CB C:ASP428 4.6 86.0 1.0 N C:ASP429 4.7 88.8 1.0 CA C:PRO433 4.7 85.6 1.0 CA C:ASN430 4.8 91.3 1.0 CA C:ASP434 4.8 81.0 1.0 CB C:ALA450 4.8 84.6 1.0 CA C:ASP428 4.9 87.0 1.0 O C:PRO433 4.9 82.8 1.0 C C:ASP428 5.0 89.8 1.0 C C:ASN430 5.0 92.2 1.0

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