Calcium in PDB 7ufh: Integrin ALAPHIIBBETA3 Complex with Fradafiban (Mn/Ca)

The structure of Integrin ALAPHIIBBETA3 Complex with Fradafiban (Mn/Ca), PDB code: 7ufh 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)	42.05 / 3.00
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	258.581, 144.453, 104.764, 90, 90, 90
R / Rfree (%)	22.5 / 24.5

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

Manganese	(Mn)	6 atoms
Chlorine	(Cl)	4 atoms

The binding sites of Calcium atom in the Integrin ALAPHIIBBETA3 Complex with Fradafiban (Mn/Ca) (pdb code 7ufh). 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 Fradafiban (Mn/Ca), PDB code: 7ufh:
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 Fradafiban (Mn/Ca)


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 Fradafiban (Mn/Ca) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca505 b:76.1 occ:1.00 OD1 A:ASP245 2.3 75.7 1.0 O A:ASP247 2.4 77.8 1.0 OE2 A:GLU243 2.4 73.6 1.0 O A:THR250 2.4 76.0 1.0 OE1 A:GLU252 2.4 73.5 1.0 OG1 A:THR250 2.4 78.8 1.0 OE2 A:GLU252 2.4 74.2 1.0 OD2 A:ASP245 2.5 76.9 1.0 OE1 A:GLU243 2.5 72.6 1.0 CG A:ASP245 2.7 76.2 1.0 CD A:GLU252 2.7 73.2 1.0 CD A:GLU243 2.8 72.7 1.0 C A:THR250 3.1 76.3 1.0 C A:ASP247 3.5 79.8 1.0 CB A:THR250 3.5 79.0 1.0 CA A:THR250 3.7 78.5 1.0 N A:THR250 3.9 80.2 1.0 N A:THR251 4.1 75.7 1.0 CB A:ASP245 4.2 76.2 1.0 CB A:ASP247 4.2 82.0 1.0 CA A:ASP247 4.2 81.3 1.0 CG A:GLU252 4.3 71.8 1.0 CG A:GLU243 4.3 71.8 1.0 N A:ASP247 4.3 80.2 1.0 CA A:THR251 4.5 73.7 1.0 N A:LEU248 4.6 83.2 1.0 N A:ASP245 4.6 73.6 1.0 N A:GLU252 4.7 70.7 1.0 C A:THR251 4.7 72.7 1.0 CG2 A:THR250 4.8 81.3 1.0 CG A:ASP247 4.8 83.2 1.0 CA A:LEU248 4.8 82.2 1.0 CA A:GLU243 4.8 68.5 1.0 CA A:ASP245 4.9 75.6 1.0 N A:PHE244 4.9 69.9 1.0 CB A:GLU243 5.0 69.8 1.0 O A:HOH635 5.0 72.2 1.0

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


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 Fradafiban (Mn/Ca) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca506 b:64.0 occ:1.00 O A:ARG303 2.2 64.6 1.0 O A:HOH603 2.2 58.4 1.0 OD1 A:ASN299 2.3 61.4 1.0 OD1 A:ASP297 2.4 62.6 1.0 OD2 A:ASP305 2.4 62.1 1.0 OD1 A:ASP301 2.4 65.0 1.0 OD1 A:ASP305 2.5 63.0 1.0 CG A:ASP305 2.7 62.0 1.0 CG A:ASP301 3.3 66.0 1.0 CG A:ASN299 3.3 61.5 1.0 C A:ARG303 3.3 65.4 1.0 CG A:ASP297 3.5 62.9 1.0 OD2 A:ASP301 3.5 65.8 1.0 ND2 A:ASN299 3.7 62.1 1.0 CA A:ARG303 4.1 67.4 1.0 N A:ARG303 4.1 68.1 1.0 CB A:ARG303 4.1 68.0 1.0 CB A:ASP305 4.1 60.7 1.0 CA A:ASP297 4.2 60.2 1.0 CB A:ASP297 4.2 61.8 1.0 N A:ASP305 4.2 61.7 1.0 C A:HIS304 4.3 61.8 1.0 N A:ASN299 4.4 59.6 1.0 N A:HIS304 4.4 64.3 1.0 OD2 A:ASP297 4.4 64.2 1.0 N A:VAL298 4.4 59.4 1.0 N A:ASP301 4.5 66.0 1.0 O A:HIS304 4.5 62.4 1.0 CB A:ASP301 4.6 67.6 1.0 CB A:ASN299 4.6 60.9 1.0 CA A:ASP305 4.6 60.9 1.0 C A:ASP297 4.7 59.8 1.0 CA A:HIS304 4.7 62.6 1.0 N A:GLY300 4.8 61.6 1.0 N A:GLN333 4.9 65.3 1.0 CD2 A:LEU332 4.9 60.8 1.0 CA A:ASN299 4.9 60.7 1.0 CA A:ASP301 4.9 67.7 1.0

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


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 Fradafiban (Mn/Ca) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca507 b:59.4 occ:1.00 OD1 A:ASP365 2.3 63.0 1.0 O A:HOH608 2.3 57.2 1.0 O A:TYR371 2.3 58.4 1.0 OD1 A:ASP373 2.4 60.6 1.0 OD1 A:ASP369 2.4 63.3 1.0 OD2 A:ASP373 2.4 60.1 1.0 OD1 A:ASP367 2.4 61.6 1.0 CG A:ASP373 2.8 59.5 1.0 C A:TYR371 3.5 59.0 1.0 CG A:ASP365 3.5 64.0 1.0 CG A:ASP369 3.5 64.8 1.0 CG A:ASP367 3.6 62.4 1.0 N A:LEU366 4.0 59.8 1.0 OD2 A:ASP369 4.1 65.0 1.0 OD2 A:ASP367 4.1 63.4 1.0 CA A:ASP365 4.1 60.8 1.0 N A:ASP367 4.3 60.5 1.0 N A:TYR371 4.3 62.7 1.0 CB A:ASP373 4.3 57.9 1.0 CA A:TYR371 4.3 61.2 1.0 OD2 A:ASP365 4.3 66.0 1.0 CD2 A:LEU393 4.4 58.2 1.0 C A:ASN372 4.4 56.2 1.0 CB A:ASP365 4.4 63.0 1.0 C A:ASP365 4.4 60.4 1.0 N A:ASP369 4.4 65.7 1.0 CB A:TYR371 4.5 61.1 1.0 N A:ASN372 4.5 59.5 1.0 N A:ASP373 4.5 59.1 1.0 N A:GLY394 4.6 59.8 1.0 CA A:ASN372 4.6 57.6 1.0 N A:ARG368 4.6 64.4 1.0 CB A:ASP369 4.7 66.7 1.0 O A:ASN372 4.7 56.5 1.0 CB A:ASP367 4.8 62.5 1.0 O A:GLY364 4.8 57.7 1.0 CA A:ASP373 4.9 57.8 1.0 CA A:ASP367 4.9 62.3 1.0 O A:GLY394 5.0 63.9 1.0

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


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 Fradafiban (Mn/Ca) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca508 b:57.0 occ:1.00 O A:TYR432 2.2 60.3 1.0 OD1 A:ASP426 2.3 61.5 1.0 O A:HOH605 2.3 60.8 1.0 OD1 A:ASP434 2.3 58.9 1.0 OD1 A:ASP428 2.3 60.9 1.0 OD1 A:ASN430 2.3 60.7 1.0 OD2 A:ASP434 2.4 59.9 1.0 CG A:ASP434 2.7 58.7 1.0 CG A:ASP428 3.4 61.4 1.0 C A:TYR432 3.4 60.4 1.0 CG A:ASN430 3.4 61.7 1.0 CG A:ASP426 3.4 62.4 1.0 OD2 A:ASP428 3.7 61.2 1.0 ND2 A:ASN430 4.0 61.2 1.0 CA A:ASP426 4.1 60.0 1.0 N A:TYR432 4.1 63.8 1.0 CA A:TYR432 4.1 62.0 1.0 CB A:ASP434 4.1 57.1 1.0 N A:ILE427 4.2 60.5 1.0 CB A:ASP426 4.3 61.6 1.0 OD2 A:ASP426 4.3 64.1 1.0 O A:ALA450 4.3 61.8 1.0 CB A:TYR432 4.3 61.6 1.0 N A:ASP428 4.3 61.8 1.0 N A:PRO433 4.4 60.3 1.0 N A:ASN430 4.4 64.4 1.0 N A:ASP434 4.5 57.2 1.0 C A:PRO433 4.5 57.6 1.0 N A:ALA450 4.5 58.5 1.0 C A:ASP426 4.6 60.8 1.0 CB A:ASN430 4.6 63.9 1.0 CA A:PRO433 4.6 59.0 1.0 N A:ASP429 4.7 63.6 1.0 CB A:ASP428 4.7 62.6 1.0 CA A:ASP434 4.8 56.3 1.0 CB A:ALA450 4.9 58.9 1.0 CA A:ASP428 4.9 63.4 1.0 O A:PRO433 4.9 57.1 1.0 CA A:ASN430 4.9 65.0 1.0

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


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 Fradafiban (Mn/Ca) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca504 b:119.2 occ:1.00 O C:ASP247 2.4 118.0 1.0 OD1 C:ASP245 2.4 117.5 1.0 OE2 C:GLU243 2.4 120.0 1.0 OE1 C:GLU252 2.4 116.1 1.0 OE2 C:GLU252 2.4 116.3 1.0 O C:THR250 2.5 116.8 1.0 OE1 C:GLU243 2.5 116.1 1.0 OG1 C:THR250 2.5 122.8 1.0 CD C:GLU252 2.7 115.2 1.0 CD C:GLU243 2.8 117.5 1.0 C C:THR250 3.0 116.7 1.0 CG C:ASP245 3.3 119.4 1.0 OD2 C:ASP245 3.5 120.8 1.0 CB C:THR250 3.6 121.9 1.0 C C:ASP247 3.6 121.5 1.0 CA C:THR250 3.7 120.3 1.0 N C:THR251 3.7 116.2 1.0 CA C:THR251 4.0 112.9 1.0 N C:THR250 4.0 123.3 1.0 CG C:GLU243 4.2 116.3 1.0 CG C:GLU252 4.3 112.9 1.0 CA C:ASP247 4.3 125.3 1.0 N C:ASP247 4.4 124.5 1.0 CB C:ASP247 4.4 126.2 1.0 C C:THR251 4.4 111.7 1.0 N C:GLU252 4.4 108.0 1.0 N C:LEU248 4.6 125.0 1.0 CB C:ASP245 4.6 120.0 1.0 N C:ASP245 4.7 115.8 1.0 CA C:LEU248 4.8 121.8 1.0 CG2 C:THR250 4.8 125.8 1.0 CA C:GLU243 4.8 110.2 1.0 N C:PHE244 4.9 112.8 1.0 CB C:GLU243 4.9 112.2 1.0 C C:LEU248 4.9 121.0 1.0 CB C:GLU252 5.0 109.0 1.0

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


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 Fradafiban (Mn/Ca) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca505 b:104.0 occ:1.00 OD1 C:ASN299 2.3 102.9 1.0 OD1 C:ASP301 2.3 106.7 1.0 OD2 C:ASP305 2.3 99.7 1.0 OD1 C:ASP305 2.4 102.5 1.0 OD1 C:ASP297 2.4 103.7 1.0 O C:ARG303 2.4 104.3 1.0 O C:HOH601 2.4 104.5 1.0 CG C:ASP305 2.7 99.9 1.0 CG C:ASP301 3.2 109.2 1.0 CG C:ASN299 3.3 103.2 1.0 OD2 C:ASP301 3.4 109.3 1.0 C C:ARG303 3.6 105.8 1.0 CG C:ASP297 3.6 103.5 1.0 ND2 C:ASN299 3.7 104.4 1.0 N C:ARG303 4.2 111.2 1.0 CB C:ASP305 4.2 97.0 1.0 CA C:ASP297 4.2 97.3 1.0 CA C:ARG303 4.2 109.9 1.0 CB C:ASP297 4.3 100.6 1.0 CB C:ARG303 4.3 111.7 1.0 N C:ASN299 4.3 98.2 1.0 N C:VAL298 4.4 97.8 1.0 N C:ASP305 4.5 98.3 1.0 OD2 C:ASP297 4.5 105.9 1.0 CD2 C:LEU332 4.5 98.3 1.0 CB C:ASP301 4.5 112.5 1.0 N C:ASP301 4.6 108.8 1.0 C C:HIS304 4.6 100.0 1.0 C C:ASP297 4.6 96.5 1.0 CB C:ASN299 4.6 102.5 1.0 N C:HIS304 4.6 104.8 1.0 CA C:ASP305 4.8 97.1 1.0 CA C:ASN299 4.9 101.3 1.0 CA C:HIS304 4.9 101.1 1.0 O C:HIS304 4.9 101.7 1.0 CA C:ASP301 4.9 112.3 1.0 N C:GLY300 5.0 102.6 1.0

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


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 Fradafiban (Mn/Ca) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca506 b:89.3 occ:1.00 O C:TYR371 2.3 90.3 1.0 OD1 C:ASP369 2.4 92.0 1.0 OD2 C:ASP373 2.4 89.4 1.0 O C:HOH606 2.4 88.7 1.0 OD1 C:ASP367 2.4 90.0 1.0 OD1 C:ASP365 2.4 92.3 1.0 OD1 C:ASP373 2.5 90.5 1.0 CG C:ASP373 2.8 88.7 1.0 CG C:ASP369 3.4 93.9 1.0 C C:TYR371 3.5 91.6 1.0 CG C:ASP365 3.6 93.9 1.0 CG C:ASP367 3.6 90.8 1.0 OD2 C:ASP369 3.7 93.5 1.0 N C:LEU366 3.8 87.6 1.0 CA C:ASP365 4.1 88.5 1.0 OD2 C:ASP367 4.1 91.9 1.0 N C:ASP367 4.1 87.8 1.0 N C:TYR371 4.3 97.4 1.0 CB C:ASP373 4.3 85.8 1.0 C C:ASP365 4.3 87.3 1.0 OD2 C:ASP365 4.3 97.1 1.0 CA C:TYR371 4.4 95.2 1.0 CB C:ASP365 4.4 92.1 1.0 C C:ASN372 4.5 88.2 1.0 N C:ASN372 4.5 93.7 1.0 N C:ASP369 4.5 96.1 1.0 CA C:ASN372 4.6 90.7 1.0 N C:ASP373 4.6 88.2 1.0 N C:ARG368 4.6 91.4 1.0 N C:GLY394 4.6 91.1 1.0 CB C:ASP369 4.7 97.1 1.0 CB C:TYR371 4.7 95.3 1.0 CA C:LEU366 4.8 86.2 1.0 CB C:ASP367 4.8 90.7 1.0 O C:ASN372 4.8 88.7 1.0 CA C:ASP367 4.8 90.4 1.0 O C:GLY364 4.9 85.9 1.0 CD2 C:LEU393 4.9 87.3 1.0 C C:LEU366 4.9 88.5 1.0 CB C:LEU366 4.9 83.7 1.0

Calcium binding site 8 out of 8 in the Integrin ALAPHIIBBETA3 Complex with Fradafiban (Mn/Ca)


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 Fradafiban (Mn/Ca) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca507 b:81.2 occ:1.00 O C:TYR432 2.3 82.7 1.0 OD1 C:ASP434 2.3 79.3 1.0 OD2 C:ASP434 2.3 79.9 1.0 OD1 C:ASP428 2.4 82.2 1.0 OD1 C:ASP426 2.4 83.7 1.0 OD1 C:ASN430 2.4 82.2 1.0 O C:HOH603 2.4 81.8 1.0 CG C:ASP434 2.6 78.6 1.0 CG C:ASP426 3.4 85.4 1.0 CG C:ASN430 3.4 83.5 1.0 C C:TYR432 3.4 83.7 1.0 CG C:ASP428 3.5 82.3 1.0 CA C:ASP426 3.9 81.3 1.0 OD2 C:ASP428 4.0 82.6 1.0 ND2 C:ASN430 4.1 83.0 1.0 CB C:ASP434 4.1 76.3 1.0 N C:TYR432 4.1 88.7 1.0 CB C:ASP426 4.1 84.4 1.0 CA C:TYR432 4.1 86.5 1.0 N C:ILE427 4.2 81.7 1.0 OD2 C:ASP426 4.2 88.2 1.0 N C:ASP428 4.3 81.6 1.0 CB C:TYR432 4.3 85.9 1.0 N C:ASP434 4.3 78.2 1.0 C C:PRO433 4.3 78.9 1.0 C C:ASP426 4.3 81.1 1.0 N C:PRO433 4.4 83.8 1.0 N C:ASN430 4.4 86.7 1.0 CB C:ASN430 4.5 86.0 1.0 O C:ALA450 4.5 84.5 1.0 CA C:PRO433 4.6 81.5 1.0 N C:ALA450 4.7 79.1 1.0 CA C:ASP434 4.7 76.1 1.0 CB C:ASP428 4.7 82.4 1.0 O C:PRO433 4.7 78.6 1.0 N C:ASP429 4.7 84.7 1.0 CA C:ASN430 4.9 88.1 1.0 CA C:ASP428 4.9 83.5 1.0 O C:VAL425 4.9 78.1 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.