Calcium in PDB 7uje: Integrin ALAPHIIBBETA3 Complex with UR2922 in MN2+

The structure of Integrin ALAPHIIBBETA3 Complex with UR2922 in MN2+, PDB code: 7uje 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)	48.74 / 2.50
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	259.56, 143.71, 105.17, 90, 90, 90
R / Rfree (%)	20.9 / 23.9

The structure of Integrin ALAPHIIBBETA3 Complex with UR2922 in MN2+ also contains other interesting chemical elements:

Chlorine	(Cl)	3 atoms
Manganese	(Mn)	6 atoms

The binding sites of Calcium atom in the Integrin ALAPHIIBBETA3 Complex with UR2922 in MN2+ (pdb code 7uje). 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 UR2922 in MN2+, PDB code: 7uje:
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 UR2922 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 UR2922 in MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:61.4 occ:1.00 OD1 A:ASP245 2.3 81.6 1.0 O A:THR250 2.4 71.1 1.0 O A:ASP247 2.4 94.6 1.0 OE2 A:GLU252 2.4 75.3 1.0 OE1 A:GLU252 2.4 78.0 1.0 OE2 A:GLU243 2.4 71.3 1.0 OE1 A:GLU243 2.4 75.3 1.0 OG1 A:THR250 2.4 78.3 1.0 CD A:GLU243 2.7 69.5 1.0 CD A:GLU252 2.7 75.7 1.0 C A:THR250 3.0 71.6 1.0 CG A:ASP245 3.2 74.8 1.0 OD2 A:ASP245 3.5 71.9 1.0 CB A:THR250 3.5 80.2 1.0 C A:ASP247 3.5 79.2 1.0 CA A:THR250 3.7 77.1 1.0 N A:THR251 3.9 70.2 1.0 N A:THR250 3.9 91.4 1.0 CG A:GLU243 4.2 58.7 1.0 CA A:THR251 4.2 72.8 1.0 CG A:GLU252 4.2 70.0 1.0 CA A:ASP247 4.3 66.6 1.0 N A:ASP247 4.3 73.9 1.0 CB A:ASP247 4.4 71.6 1.0 N A:GLU252 4.5 61.6 1.0 CB A:ASP245 4.5 60.3 1.0 C A:THR251 4.5 67.8 1.0 N A:ASP245 4.6 69.9 1.0 N A:LEU248 4.6 72.7 1.0 CA A:GLU243 4.6 53.7 1.0 CG2 A:THR250 4.8 82.8 1.0 N A:PHE244 4.8 58.8 1.0 CB A:GLU243 4.8 52.1 1.0 CA A:LEU248 4.8 70.4 1.0 C A:LEU248 5.0 81.9 1.0 CA A:ASP245 5.0 60.1 1.0

Calcium binding site 2 out of 8 in the Integrin ALAPHIIBBETA3 Complex with UR2922 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 UR2922 in MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:46.0 occ:1.00 O A:ARG303 2.3 52.4 1.0 OD1 A:ASN299 2.3 53.9 1.0 OD1 A:ASP297 2.4 56.7 1.0 O A:HOH646 2.4 48.2 1.0 OD1 A:ASP305 2.4 56.4 1.0 OD2 A:ASP305 2.4 66.4 1.0 OD1 A:ASP301 2.4 58.7 1.0 CG A:ASP305 2.7 61.8 1.0 CG A:ASP301 3.3 66.1 1.0 CG A:ASN299 3.3 57.2 1.0 C A:ARG303 3.4 52.7 1.0 OD2 A:ASP301 3.4 57.0 1.0 CG A:ASP297 3.5 55.0 1.0 ND2 A:ASN299 3.7 64.8 1.0 CB A:ARG303 3.9 63.4 1.0 CA A:ARG303 4.0 63.6 1.0 N A:ARG303 4.1 55.2 1.0 CB A:ASP305 4.2 52.6 1.0 CB A:ASP297 4.2 51.5 1.0 CA A:ASP297 4.3 50.3 1.0 N A:ASP305 4.4 53.6 1.0 C A:HIS304 4.4 50.7 1.0 N A:ASN299 4.5 61.5 1.0 N A:VAL298 4.5 56.2 1.0 OD2 A:ASP297 4.5 59.7 1.0 N A:HIS304 4.5 51.8 1.0 O A:HIS304 4.6 50.6 1.0 CB A:ASN299 4.7 56.5 1.0 CB A:ASP301 4.7 58.6 1.0 CA A:ASP305 4.7 53.0 1.0 C A:ASP297 4.7 50.5 1.0 N A:ASP301 4.7 75.7 1.0 CD2 A:LEU332 4.8 55.8 1.0 N A:GLN333 4.8 59.4 1.0 CA A:HIS304 4.8 50.3 1.0 O A:GLN333 5.0 64.4 1.0

Calcium binding site 3 out of 8 in the Integrin ALAPHIIBBETA3 Complex with UR2922 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 UR2922 in MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca505 b:46.2 occ:1.00 O A:TYR371 2.3 67.0 1.0 OD1 A:ASP367 2.4 61.3 1.0 OD1 A:ASP365 2.4 49.7 1.0 OD2 A:ASP373 2.4 56.1 1.0 OD1 A:ASP373 2.4 57.1 1.0 OD1 A:ASP369 2.4 59.2 1.0 O A:HOH621 2.4 39.7 1.0 CG A:ASP373 2.7 59.8 1.0 CG A:ASP369 3.4 69.9 1.0 C A:TYR371 3.5 56.2 1.0 CG A:ASP367 3.5 55.7 1.0 CG A:ASP365 3.6 63.5 1.0 OD2 A:ASP369 3.8 60.7 1.0 N A:LEU366 4.0 64.5 1.0 OD2 A:ASP367 4.0 65.7 1.0 CA A:ASP365 4.1 48.8 1.0 N A:ASP367 4.2 46.7 1.0 CB A:ASP373 4.2 50.2 1.0 N A:TYR371 4.2 64.7 1.0 CA A:TYR371 4.3 53.1 1.0 CD2 A:LEU393 4.4 46.2 1.0 OD2 A:ASP365 4.4 56.9 1.0 C A:ASP365 4.4 57.8 1.0 C A:ASN372 4.4 59.0 1.0 CB A:TYR371 4.4 53.7 1.0 CB A:ASP365 4.5 49.5 1.0 N A:ASP369 4.5 53.2 1.0 N A:ASN372 4.5 50.5 1.0 N A:ASP373 4.6 56.4 1.0 CB A:ASP369 4.6 54.4 1.0 CA A:ASN372 4.6 48.6 1.0 N A:ARG368 4.6 68.2 1.0 O A:ASN372 4.7 48.0 1.0 N A:GLY394 4.7 57.9 1.0 CB A:ASP367 4.8 48.2 1.0 CA A:ASP367 4.9 47.9 1.0 CA A:ASP373 4.9 51.3 1.0 CA A:LEU366 5.0 48.3 1.0 O A:GLY364 5.0 50.9 1.0

Calcium binding site 4 out of 8 in the Integrin ALAPHIIBBETA3 Complex with UR2922 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 UR2922 in MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca506 b:53.6 occ:1.00 O A:TYR432 2.3 58.2 1.0 OD1 A:ASP434 2.3 42.9 1.0 OD1 A:ASN430 2.3 67.6 1.0 OD1 A:ASP426 2.3 60.8 1.0 OD2 A:ASP434 2.4 43.8 1.0 OD1 A:ASP428 2.4 57.1 1.0 O A:HOH651 2.4 39.8 1.0 CG A:ASP434 2.6 43.5 1.0 CG A:ASP426 3.3 55.4 1.0 CG A:ASN430 3.4 54.8 1.0 C A:TYR432 3.5 55.1 1.0 CG A:ASP428 3.5 55.0 1.0 ND2 A:ASN430 3.9 46.8 1.0 OD2 A:ASP428 3.9 57.4 1.0 CA A:ASP426 4.0 51.6 1.0 OD2 A:ASP426 4.1 64.5 1.0 N A:TYR432 4.1 58.1 1.0 CB A:ASP426 4.1 49.7 1.0 CB A:ASP434 4.1 47.1 1.0 CA A:TYR432 4.2 54.2 1.0 O A:ALA450 4.2 47.6 1.0 N A:ILE427 4.2 48.4 1.0 CB A:TYR432 4.3 45.5 1.0 N A:ASP428 4.3 49.7 1.0 C A:ASP426 4.4 54.3 1.0 N A:ALA450 4.5 44.8 1.0 N A:ASN430 4.5 50.8 1.0 N A:ASP434 4.5 45.5 1.0 N A:PRO433 4.5 54.0 1.0 C A:PRO433 4.5 52.3 1.0 CB A:ASN430 4.5 47.2 1.0 CA A:PRO433 4.7 43.6 1.0 CB A:ASP428 4.7 45.6 1.0 N A:ASP429 4.8 58.9 1.0 CA A:ASP434 4.8 45.0 1.0 CB A:ALA450 4.9 42.6 1.0 CA A:ASN430 4.9 48.2 1.0 CA A:ASP428 4.9 48.9 1.0 O A:PRO433 5.0 55.4 1.0

Calcium binding site 5 out of 8 in the Integrin ALAPHIIBBETA3 Complex with UR2922 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 UR2922 in MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca506 b:98.3 occ:1.00 OD1 C:ASP245 2.4 104.1 1.0 OE1 C:GLU252 2.4 108.4 1.0 O C:ASP247 2.4 102.7 1.0 O C:THR250 2.4 100.0 1.0 OE1 C:GLU243 2.4 101.2 1.0 OE2 C:GLU243 2.4 104.7 1.0 OE2 C:GLU252 2.4 109.2 1.0 OG1 C:THR250 2.4 93.8 1.0 CD C:GLU252 2.7 102.2 1.0 CD C:GLU243 2.7 92.7 1.0 C C:THR250 3.0 100.7 1.0 CG C:ASP245 3.2 101.4 1.0 OD2 C:ASP245 3.4 103.9 1.0 CB C:THR250 3.5 95.5 1.0 C C:ASP247 3.6 102.0 1.0 CA C:THR250 3.7 108.6 1.0 N C:THR251 3.8 89.1 1.0 N C:THR250 4.1 118.4 1.0 CA C:THR251 4.1 91.3 1.0 CG C:GLU243 4.2 80.1 1.0 CG C:GLU252 4.2 87.3 1.0 N C:GLU252 4.4 77.0 1.0 CA C:ASP247 4.4 97.5 1.0 N C:ASP247 4.4 96.3 1.0 CB C:ASP247 4.5 111.9 1.0 C C:THR251 4.5 85.9 1.0 CB C:ASP245 4.5 94.1 1.0 N C:LEU248 4.6 111.2 1.0 N C:ASP245 4.6 105.1 1.0 CA C:GLU243 4.7 74.6 1.0 CA C:LEU248 4.7 101.0 1.0 CG2 C:THR250 4.8 92.6 1.0 N C:PHE244 4.8 84.5 1.0 C C:LEU248 4.8 99.1 1.0 CB C:GLU243 4.9 70.0 1.0 CB C:GLU252 5.0 64.2 1.0 O C:LEU248 5.0 102.0 1.0

Calcium binding site 6 out of 8 in the Integrin ALAPHIIBBETA3 Complex with UR2922 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 UR2922 in MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca507 b:80.5 occ:1.00 OD1 C:ASN299 2.3 92.4 1.0 OD1 C:ASP305 2.4 84.6 1.0 OD1 C:ASP301 2.4 97.5 1.0 OD1 C:ASP297 2.4 79.7 1.0 O C:ARG303 2.4 100.8 1.0 OD2 C:ASP305 2.4 80.2 1.0 O C:HOH602 2.4 81.8 1.0 CG C:ASP305 2.7 83.1 1.0 CG C:ASP301 3.2 96.8 1.0 OD2 C:ASP301 3.3 97.3 1.0 CG C:ASN299 3.4 85.3 1.0 CG C:ASP297 3.5 80.1 1.0 C C:ARG303 3.5 98.9 1.0 ND2 C:ASN299 3.8 85.7 1.0 CA C:ASP297 4.1 69.0 1.0 CB C:ASP305 4.2 80.2 1.0 CB C:ASP297 4.2 76.6 1.0 N C:ARG303 4.2 95.1 1.0 CA C:ARG303 4.2 101.4 1.0 CB C:ARG303 4.3 101.4 1.0 N C:VAL298 4.4 74.5 1.0 N C:ASN299 4.4 79.8 1.0 OD2 C:ASP297 4.4 83.4 1.0 N C:ASP305 4.4 71.5 1.0 C C:HIS304 4.5 83.3 1.0 C C:ASP297 4.6 84.0 1.0 CB C:ASP301 4.6 85.7 1.0 N C:HIS304 4.6 96.6 1.0 N C:ASP301 4.6 93.2 1.0 CB C:ASN299 4.7 77.3 1.0 CD2 C:LEU332 4.7 72.2 1.0 O C:HIS304 4.7 88.8 1.0 CA C:ASP305 4.8 71.2 1.0 CA C:HIS304 4.8 88.1 1.0 N C:GLN333 4.9 79.5 1.0 CA C:ASN299 4.9 79.2 1.0 N C:GLY300 5.0 91.7 1.0

Calcium binding site 7 out of 8 in the Integrin ALAPHIIBBETA3 Complex with UR2922 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 UR2922 in MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca508 b:75.1 occ:1.00 O C:TYR371 2.3 70.2 1.0 OD1 C:ASP365 2.4 69.8 1.0 OD1 C:ASP367 2.4 73.0 1.0 OD1 C:ASP373 2.4 89.4 1.0 OD2 C:ASP373 2.4 80.9 1.0 OD1 C:ASP369 2.4 96.0 1.0 O C:HOH616 2.4 58.0 1.0 CG C:ASP373 2.7 83.0 1.0 CG C:ASP369 3.4 91.0 1.0 CG C:ASP365 3.5 76.5 1.0 CG C:ASP367 3.5 85.3 1.0 C C:TYR371 3.5 73.5 1.0 OD2 C:ASP369 3.8 87.0 1.0 OD2 C:ASP367 3.8 89.0 1.0 N C:LEU366 4.0 75.7 1.0 CA C:ASP365 4.1 79.9 1.0 OD2 C:ASP365 4.2 78.8 1.0 CB C:ASP373 4.2 67.9 1.0 N C:TYR371 4.2 74.9 1.0 N C:ASP367 4.2 75.4 1.0 CA C:TYR371 4.3 70.4 1.0 C C:ASP365 4.4 84.9 1.0 CB C:ASP365 4.4 71.5 1.0 C C:ASN372 4.4 73.5 1.0 CB C:TYR371 4.5 70.4 1.0 N C:ASN372 4.5 76.6 1.0 N C:ASP373 4.5 74.7 1.0 N C:GLY394 4.6 64.0 1.0 N C:ASP369 4.6 81.7 1.0 CA C:ASN372 4.6 63.4 1.0 CB C:ASP369 4.7 79.9 1.0 O C:ASN372 4.7 78.7 1.0 N C:ARG368 4.7 79.0 1.0 CB C:ASP367 4.7 71.0 1.0 CD2 C:LEU393 4.8 73.5 1.0 CA C:ASP373 4.9 73.9 1.0 O C:GLY364 4.9 70.1 1.0 CA C:ASP367 4.9 65.5 1.0 CB C:LEU393 5.0 70.5 1.0 CA C:LEU366 5.0 73.0 1.0

Calcium binding site 8 out of 8 in the Integrin ALAPHIIBBETA3 Complex with UR2922 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 UR2922 in MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca509 b:65.2 occ:1.00 O C:TYR432 2.3 79.5 1.0 OD1 C:ASP426 2.3 69.6 1.0 OD1 C:ASN430 2.4 97.7 1.0 OD1 C:ASP434 2.4 79.3 1.0 OD2 C:ASP434 2.4 80.8 1.0 OD1 C:ASP428 2.4 63.4 1.0 O C:HOH603 2.4 68.6 1.0 CG C:ASP434 2.7 76.8 1.0 CG C:ASP426 3.3 74.2 1.0 CG C:ASN430 3.4 80.7 1.0 C C:TYR432 3.5 75.4 1.0 CG C:ASP428 3.5 70.8 1.0 OD2 C:ASP428 3.9 72.7 1.0 N C:TYR432 4.0 77.9 1.0 OD2 C:ASP426 4.1 76.2 1.0 CA C:ASP426 4.1 67.4 1.0 CA C:TYR432 4.1 81.8 1.0 ND2 C:ASN430 4.1 73.8 1.0 CB C:ASP434 4.1 66.6 1.0 CB C:ASP426 4.2 74.8 1.0 CB C:TYR432 4.3 79.6 1.0 O C:ALA450 4.3 79.4 1.0 N C:ILE427 4.4 60.3 1.0 N C:ASN430 4.4 86.5 1.0 CB C:ASN430 4.4 71.0 1.0 N C:ASP434 4.4 55.3 1.0 N C:ASP428 4.5 85.1 1.0 N C:ALA450 4.5 74.3 1.0 N C:PRO433 4.5 71.4 1.0 C C:PRO433 4.5 64.0 1.0 C C:ASP426 4.6 64.9 1.0 CA C:PRO433 4.7 69.3 1.0 CA C:ASP434 4.8 59.6 1.0 CB C:ASP428 4.8 67.8 1.0 N C:ASP429 4.8 88.3 1.0 CA C:ASN430 4.8 78.8 1.0 CB C:ALA450 4.9 57.4 1.0 N C:GLY431 5.0 86.2 1.0 O C:PRO433 5.0 63.2 1.0

J.Zhu, F.-Y.Lin, J.Zhu, T.A.Springer. Integrin Alpha Iib Beta 3 Headpiece with Fab Complex with UR2922 in MN2+. To Be Published.