Calcium in PDB 7tho: Integrin ALAPHIIBBETA3 Complex with Eptifibatide

The structure of Integrin ALAPHIIBBETA3 Complex with Eptifibatide, PDB code: 7tho 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)	48.44 / 2.75
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	260.34, 145.04, 104.87, 90, 90, 90
R / Rfree (%)	18.9 / 22.2

The structure of Integrin ALAPHIIBBETA3 Complex with Eptifibatide also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Calcium atom in the Integrin ALAPHIIBBETA3 Complex with Eptifibatide (pdb code 7tho). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 12 binding sites of Calcium where determined in the Integrin ALAPHIIBBETA3 Complex with Eptifibatide, PDB code: 7tho:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 12 in the Integrin ALAPHIIBBETA3 Complex with Eptifibatide


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 Eptifibatide within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:67.8 occ:1.00 O A:ASP247 2.3 85.6 1.0 OD1 A:ASP245 2.3 83.1 1.0 O A:THR250 2.4 78.5 1.0 OE1 A:GLU252 2.4 60.5 1.0 OE2 A:GLU252 2.4 68.7 1.0 OE2 A:GLU243 2.5 66.8 1.0 OG1 A:THR250 2.5 81.9 1.0 CD A:GLU252 2.7 68.2 1.0 OE1 A:GLU243 3.0 72.4 1.0 CG A:ASP245 3.1 80.8 1.0 CD A:GLU243 3.1 67.8 1.0 C A:THR250 3.1 74.3 1.0 OD2 A:ASP245 3.2 84.1 1.0 CB A:THR250 3.5 86.6 1.0 C A:ASP247 3.5 83.8 1.0 CA A:THR250 3.7 88.5 1.0 N A:THR250 4.0 98.8 1.0 N A:THR251 4.0 71.1 1.0 N A:ASP247 4.2 88.3 1.0 CA A:ASP247 4.2 83.0 1.0 CB A:ASP247 4.2 92.8 1.0 CG A:GLU252 4.2 64.3 1.0 CA A:THR251 4.4 73.4 1.0 CB A:ASP245 4.4 72.7 1.0 CG A:GLU243 4.5 54.6 1.0 N A:ASP245 4.5 72.6 1.0 N A:LEU248 4.6 83.3 1.0 N A:GLU252 4.7 57.9 1.0 C A:THR251 4.7 67.6 1.0 O A:HOH686 4.8 71.8 1.0 CA A:LEU248 4.8 80.1 1.0 CG2 A:THR250 4.8 88.0 1.0 CA A:GLU243 4.9 61.7 1.0 CA A:ASP245 4.9 74.2 1.0 N A:PHE244 4.9 63.2 1.0 N A:GLY246 4.9 81.8 1.0

Calcium binding site 2 out of 12 in the Integrin ALAPHIIBBETA3 Complex with Eptifibatide


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 Eptifibatide within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:52.9 occ:1.00 OD1 A:ASN299 2.4 63.2 1.0 O A:ARG303 2.4 64.5 1.0 O A:HOH605 2.4 79.2 1.0 OD1 A:ASP301 2.4 64.0 1.0 OD1 A:ASP305 2.5 59.8 1.0 OD2 A:ASP305 2.6 62.4 1.0 OD1 A:ASP297 2.6 57.2 1.0 CG A:ASP305 2.8 49.6 1.0 CG A:ASP301 3.2 70.7 1.0 CG A:ASN299 3.3 57.7 1.0 OD2 A:ASP301 3.3 79.3 1.0 C A:ARG303 3.5 62.9 1.0 ND2 A:ASN299 3.6 53.9 1.0 CG A:ASP297 3.8 58.7 1.0 CB A:ARG303 4.0 64.2 1.0 CA A:ARG303 4.0 66.5 1.0 N A:ARG303 4.0 62.1 1.0 CB A:ASP305 4.3 48.3 1.0 N A:ASN299 4.4 50.3 1.0 CA A:ASP297 4.4 51.4 1.0 CB A:ASP297 4.5 49.7 1.0 C A:HIS304 4.5 57.6 1.0 N A:ASP305 4.5 50.9 1.0 N A:VAL298 4.6 48.1 1.0 N A:HIS304 4.6 65.1 1.0 N A:ASP301 4.6 60.9 1.0 OD2 A:ASP297 4.6 63.0 1.0 CB A:ASN299 4.6 52.6 1.0 CB A:ASP301 4.6 66.1 1.0 O A:HIS304 4.7 61.0 1.0 CD2 A:LEU332 4.7 50.6 1.0 N A:GLN333 4.7 64.7 1.0 C A:ASP297 4.8 49.9 1.0 CA A:ASP305 4.9 51.6 1.0 O A:GLN333 4.9 59.5 1.0 N A:GLY300 4.9 59.8 1.0 CA A:HIS304 4.9 61.1 1.0 CA A:ASN299 4.9 51.7 1.0

Calcium binding site 3 out of 12 in the Integrin ALAPHIIBBETA3 Complex with Eptifibatide


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 Eptifibatide within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:47.0 occ:1.00 O A:TYR371 2.4 58.7 1.0 OD1 A:ASP369 2.4 49.2 1.0 OD1 A:ASP367 2.4 57.0 1.0 OD1 A:ASP373 2.4 55.0 1.0 OD1 A:ASP365 2.4 47.7 1.0 O A:HOH630 2.4 45.7 1.0 OD2 A:ASP373 2.5 66.1 1.0 CG A:ASP373 2.8 49.6 1.0 CG A:ASP369 3.3 57.5 1.0 C A:TYR371 3.5 48.1 1.0 CG A:ASP367 3.6 55.1 1.0 CG A:ASP365 3.6 50.1 1.0 OD2 A:ASP369 3.7 65.0 1.0 N A:TYR371 4.1 50.3 1.0 OD2 A:ASP367 4.1 55.3 1.0 N A:LEU366 4.2 55.3 1.0 CA A:TYR371 4.2 49.6 1.0 N A:ASP367 4.2 54.7 1.0 CA A:ASP365 4.3 49.5 1.0 CB A:ASP373 4.3 46.6 1.0 CB A:TYR371 4.4 53.6 1.0 OD2 A:ASP365 4.4 49.5 1.0 N A:ASP369 4.4 56.2 1.0 CD2 A:LEU393 4.5 44.5 1.0 CB A:ASP365 4.5 47.5 1.0 CB A:ASP369 4.5 62.4 1.0 C A:ASP365 4.5 56.3 1.0 C A:ASN372 4.6 52.9 1.0 N A:ASN372 4.6 47.7 1.0 N A:GLY394 4.6 49.4 1.0 N A:ARG368 4.6 52.4 1.0 N A:ASP373 4.7 58.7 1.0 O A:GLY394 4.7 48.9 1.0 CB A:ASP367 4.7 47.4 1.0 CA A:ASN372 4.8 48.7 1.0 O A:ASN372 4.8 46.3 1.0 CA A:ASP367 4.8 50.7 1.0 CB A:LEU393 4.9 49.2 1.0 N A:GLY370 4.9 55.9 1.0 C A:ASP367 4.9 59.3 1.0 O A:HOH652 4.9 56.1 1.0 CA A:ASP369 5.0 59.1 1.0

Calcium binding site 4 out of 12 in the Integrin ALAPHIIBBETA3 Complex with Eptifibatide


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 Eptifibatide within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:55.3 occ:1.00 OD1 A:ASP428 2.3 53.6 1.0 OD1 A:ASN430 2.4 55.2 1.0 OD1 A:ASP434 2.4 54.7 1.0 OD1 A:ASP426 2.5 62.5 1.0 OD2 A:ASP434 2.5 47.4 1.0 O A:TYR432 2.5 53.0 1.0 O A:HOH650 2.5 43.0 1.0 CG A:ASP434 2.7 50.3 1.0 CG A:ASN430 3.3 49.1 1.0 CG A:ASP428 3.4 53.8 1.0 CG A:ASP426 3.5 53.6 1.0 C A:TYR432 3.6 47.4 1.0 OD2 A:ASP428 3.8 55.0 1.0 ND2 A:ASN430 4.0 57.2 1.0 N A:TYR432 4.2 51.8 1.0 CA A:ASP426 4.2 52.3 1.0 O A:ALA450 4.2 44.9 1.0 CB A:ASP434 4.2 42.1 1.0 CA A:TYR432 4.3 51.0 1.0 N A:ASP428 4.3 49.8 1.0 CB A:ASN430 4.3 48.0 1.0 N A:ILE427 4.3 52.2 1.0 OD2 A:ASP426 4.4 64.6 1.0 CB A:ASP426 4.4 53.6 1.0 N A:ASN430 4.4 55.4 1.0 CB A:TYR432 4.4 45.8 1.0 N A:ALA450 4.5 43.0 1.0 C A:ASP426 4.6 53.5 1.0 C A:PRO433 4.6 51.4 1.0 N A:ASP434 4.6 44.9 1.0 CB A:ASP428 4.6 51.2 1.0 N A:PRO433 4.6 44.7 1.0 N A:ASP429 4.7 66.5 1.0 CA A:PRO433 4.8 57.8 1.0 CA A:ASN430 4.8 51.6 1.0 CA A:ASP428 4.8 50.2 1.0 CA A:ASP434 4.9 47.4 1.0 C A:ASP428 4.9 62.1 1.0 O A:PRO433 5.0 50.0 1.0 CG A:ARG449 5.0 50.0 1.0 N A:GLY431 5.0 53.5 1.0

Calcium binding site 5 out of 12 in the Integrin ALAPHIIBBETA3 Complex with Eptifibatide


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 Eptifibatide within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2002 b:181.5 occ:1.00 O B:SER123 2.5 77.9 1.0 OD1 B:ASP127 3.0 110.2 1.0 OD1 B:ASP126 3.3 126.6 1.0 OD2 B:ASP251 3.3 80.6 1.0 C B:SER123 3.7 76.2 1.0 CG B:ASP127 3.8 102.2 1.0 O B:MET335 3.8 102.3 1.0 CA B:MET124 3.9 65.0 1.0 OD2 B:ASP127 4.1 110.9 1.0 CG B:ASP251 4.1 71.4 1.0 N B:MET124 4.2 66.0 1.0 CG B:ASP126 4.3 129.4 1.0 CB M:PRO6 4.4 100.8 1.0 CB B:ASP251 4.4 56.0 1.0 SD B:MET124 4.5 53.3 1.0 O B:HOH2101 4.5 102.9 1.0 OD2 B:ASP126 4.6 136.7 1.0 C B:MET124 4.6 74.5 1.0 N B:LYS125 4.8 85.7 1.0 CA B:SER123 4.8 77.4 1.0 CG M:PRO6 4.9 98.5 1.0 CB B:MET124 5.0 63.9 1.0 CB B:ASP127 5.0 87.7 1.0 CA M:PRO6 5.0 103.0 1.0

Calcium binding site 6 out of 12 in the Integrin ALAPHIIBBETA3 Complex with Eptifibatide


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 Eptifibatide within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2003 b:61.0 occ:1.00 O B:PRO219 2.2 53.1 1.0 OD1 B:ASN215 2.3 55.9 1.0 OD1 B:ASP217 2.4 51.2 1.0 OD2 B:ASP158 2.5 58.2 1.0 O B:ASP217 2.5 65.8 1.0 OE1 B:GLU220 2.5 46.5 1.0 CG B:ASP217 3.1 57.1 1.0 CG B:ASN215 3.3 54.5 1.0 C B:PRO219 3.3 49.3 1.0 CD B:GLU220 3.4 46.0 1.0 C B:ASP217 3.5 62.5 1.0 OD2 B:ASP217 3.5 56.6 1.0 CG B:ASP158 3.6 50.8 1.0 ND2 B:ASN215 3.8 58.3 1.0 CA B:GLU220 3.9 43.7 1.0 CB B:ASP158 4.0 51.3 1.0 OE2 B:GLU220 4.0 46.3 1.0 N B:GLU220 4.1 43.5 1.0 CA B:ASP217 4.1 69.8 1.0 N B:ASP217 4.1 62.4 1.0 CB B:ASP217 4.1 62.5 1.0 O B:ALA218 4.2 49.9 1.0 C B:ALA218 4.2 57.8 1.0 N B:PRO219 4.3 60.2 1.0 NE2 B:HIS255 4.3 43.4 1.0 CA B:PRO219 4.4 54.1 1.0 CG B:GLU220 4.4 43.0 1.0 N B:ALA218 4.4 49.6 1.0 CD2 B:HIS255 4.6 47.4 1.0 CB B:GLU220 4.6 41.6 1.0 CB B:ASN215 4.6 53.8 1.0 OD1 B:ASP158 4.7 54.3 1.0 CA B:ALA218 4.8 49.6 1.0 CD B:PRO219 4.9 49.8 1.0 CD1 B:TYR164 4.9 55.6 1.0 C B:GLU220 5.0 56.3 1.0

Calcium binding site 7 out of 12 in the Integrin ALAPHIIBBETA3 Complex with Eptifibatide


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 Eptifibatide within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca501 b:114.5 occ:1.00 OD1 C:ASP245 2.4 111.7 1.0 O C:ASP247 2.4 126.6 1.0 O C:THR250 2.4 132.1 1.0 OE2 C:GLU252 2.4 97.6 1.0 OE1 C:GLU252 2.5 99.2 1.0 OE1 C:GLU243 2.5 120.8 1.0 OE2 C:GLU243 2.6 120.1 1.0 OG1 C:THR250 2.7 145.4 1.0 CD C:GLU252 2.8 94.3 1.0 CD C:GLU243 2.9 119.5 1.0 C C:THR250 3.0 130.4 1.0 CG C:ASP245 3.3 112.0 1.0 C C:ASP247 3.5 127.0 1.0 OD2 C:ASP245 3.6 108.6 1.0 CB C:THR250 3.6 144.7 1.0 CA C:THR250 3.7 141.3 1.0 N C:THR251 3.9 118.0 1.0 N C:THR250 4.0 146.0 1.0 N C:ASP247 4.2 130.1 1.0 CA C:THR251 4.2 105.8 1.0 CA C:ASP247 4.2 129.5 1.0 CG C:GLU252 4.3 84.8 1.0 CG C:GLU243 4.3 115.3 1.0 CB C:ASP247 4.4 136.8 1.0 N C:GLU252 4.6 86.2 1.0 CB C:ASP245 4.6 118.3 1.0 N C:ASP245 4.6 121.4 1.0 N C:LEU248 4.6 124.9 1.0 C C:THR251 4.6 99.3 1.0 CA C:GLU243 4.8 109.1 1.0 CA C:LEU248 4.8 125.5 1.0 N C:PHE244 4.8 106.0 1.0 C C:LEU248 4.9 133.8 1.0 CB C:GLU243 5.0 108.6 1.0 CG2 C:THR250 5.0 146.7 1.0

Calcium binding site 8 out of 12 in the Integrin ALAPHIIBBETA3 Complex with Eptifibatide


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 Eptifibatide within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca502 b:87.0 occ:1.00 OD1 C:ASN299 2.4 104.5 1.0 OD1 C:ASP301 2.4 105.8 1.0 OD1 C:ASP305 2.4 95.1 1.0 O C:ARG303 2.5 111.9 1.0 OD2 C:ASP305 2.5 102.6 1.0 OD1 C:ASP297 2.7 96.0 1.0 CG C:ASP305 2.8 90.4 1.0 OD2 C:ASP301 2.9 113.9 1.0 CG C:ASP301 3.0 105.7 1.0 CG C:ASN299 3.2 95.1 1.0 ND2 C:ASN299 3.5 87.3 1.0 C C:ARG303 3.5 106.6 1.0 CG C:ASP297 3.8 89.9 1.0 CB C:ARG303 3.9 105.3 1.0 CA C:ARG303 4.1 104.2 1.0 N C:ARG303 4.1 97.5 1.0 CB C:ASP305 4.3 76.8 1.0 CB C:ASP301 4.5 95.7 1.0 CD2 C:LEU332 4.5 81.4 1.0 C C:HIS304 4.5 97.3 1.0 CA C:ASP297 4.6 74.9 1.0 N C:ASN299 4.6 87.0 1.0 N C:ASP305 4.6 87.2 1.0 N C:GLN333 4.6 99.1 1.0 CB C:ASP297 4.6 82.3 1.0 CB C:ASN299 4.6 88.9 1.0 N C:HIS304 4.6 106.4 1.0 N C:ASP301 4.7 96.5 1.0 O C:HIS304 4.7 100.6 1.0 N C:VAL298 4.7 84.4 1.0 OD2 C:ASP297 4.7 84.8 1.0 O C:GLN333 4.8 106.0 1.0 CA C:ASP305 4.9 84.8 1.0 CA C:HIS304 5.0 95.8 1.0 C C:ASP297 5.0 80.7 1.0

Calcium binding site 9 out of 12 in the Integrin ALAPHIIBBETA3 Complex with Eptifibatide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Integrin ALAPHIIBBETA3 Complex with Eptifibatide within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:80.0 occ:1.00 O C:TYR371 2.3 83.2 1.0 OD1 C:ASP367 2.3 87.3 1.0 OD1 C:ASP369 2.4 95.2 1.0 O C:HOH647 2.5 70.0 1.0 OD1 C:ASP365 2.5 88.2 1.0 OD1 C:ASP373 2.5 80.6 1.0 OD2 C:ASP373 2.5 78.8 1.0 CG C:ASP373 2.9 78.4 1.0 CG C:ASP369 3.4 95.8 1.0 CG C:ASP367 3.5 84.8 1.0 C C:TYR371 3.5 86.0 1.0 CG C:ASP365 3.7 91.4 1.0 OD2 C:ASP369 3.9 101.9 1.0 N C:LEU366 3.9 81.8 1.0 OD2 C:ASP367 4.0 88.0 1.0 N C:ASP367 4.1 71.2 1.0 CA C:ASP365 4.1 83.0 1.0 N C:TYR371 4.1 87.8 1.0 CA C:TYR371 4.3 88.1 1.0 C C:ASP365 4.3 84.5 1.0 CB C:ASP373 4.4 71.9 1.0 N C:ASP369 4.5 73.2 1.0 OD2 C:ASP365 4.5 93.6 1.0 N C:ASN372 4.5 92.8 1.0 CB C:ASP365 4.5 89.3 1.0 C C:ASN372 4.5 86.6 1.0 CB C:TYR371 4.6 89.7 1.0 CB C:ASP369 4.6 81.2 1.0 CA C:ASN372 4.6 90.6 1.0 N C:ASP373 4.7 90.7 1.0 N C:ARG368 4.7 85.9 1.0 N C:GLY394 4.7 79.1 1.0 CB C:ASP367 4.7 89.6 1.0 CD2 C:LEU393 4.7 63.6 1.0 CA C:ASP367 4.8 82.3 1.0 N C:GLY370 4.8 92.6 1.0 CA C:LEU366 4.9 77.3 1.0 O C:ASN372 4.9 78.7 1.0 C C:ASP367 5.0 88.4 1.0 C C:LEU366 5.0 76.0 1.0 O C:GLY364 5.0 74.9 1.0 O C:GLY394 5.0 84.6 1.0

Calcium binding site 10 out of 12 in the Integrin ALAPHIIBBETA3 Complex with Eptifibatide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Integrin ALAPHIIBBETA3 Complex with Eptifibatide within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca504 b:64.5 occ:1.00 OD1 C:ASN430 2.4 74.5 1.0 OD1 C:ASP428 2.4 71.1 1.0 O C:TYR432 2.4 80.6 1.0 O C:HOH611 2.5 61.9 1.0 OD1 C:ASP426 2.5 72.8 1.0 OD2 C:ASP434 2.5 74.5 1.0 OD1 C:ASP434 2.5 78.3 1.0 CG C:ASP434 2.8 74.4 1.0 CG C:ASP428 3.4 74.3 1.0 CG C:ASN430 3.4 74.7 1.0 CG C:ASP426 3.5 80.3 1.0 C C:TYR432 3.5 79.1 1.0 OD2 C:ASP428 3.7 69.7 1.0 O C:ALA450 4.0 74.5 1.0 N C:TYR432 4.1 83.7 1.0 ND2 C:ASN430 4.1 75.2 1.0 CA C:TYR432 4.2 79.6 1.0 CA C:ASP426 4.2 70.2 1.0 CB C:ASP434 4.3 68.2 1.0 CB C:TYR432 4.3 80.9 1.0 OD2 C:ASP426 4.3 85.5 1.0 CB C:ASP426 4.3 79.3 1.0 C C:PRO433 4.4 80.2 1.0 N C:ILE427 4.4 75.9 1.0 N C:ASP428 4.4 75.7 1.0 O C:PRO433 4.4 101.5 1.0 CB C:ASN430 4.4 73.0 1.0 N C:ASN430 4.4 89.3 1.0 N C:ALA450 4.5 70.8 1.0 N C:PRO433 4.5 85.0 1.0 N C:ASP434 4.6 68.0 1.0 C C:ASP426 4.6 73.4 1.0 CB C:ASP428 4.7 74.3 1.0 CA C:PRO433 4.7 76.6 1.0 N C:ASP429 4.8 86.2 1.0 CA C:ASN430 4.9 79.5 1.0 CA C:ASP434 4.9 65.5 1.0 N C:GLY431 4.9 96.8 1.0 CA C:ASP428 4.9 79.2 1.0 C C:ALA450 5.0 77.3 1.0

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