Calcium in PDB 3fcu: Structure of Headpiece of Integrin AIIBB3 in Open Conformation

The structure of Structure of Headpiece of Integrin AIIBB3 in Open Conformation, PDB code: 3fcu was solved by J.Zhu, B.-H.Luo, T.Xiao, C.Zhang, N.Nishida, T.A.Springer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.59 / 2.90
Space group	P 62
Cell size a, b, c (Å), α, β, γ (°)	332.093, 332.093, 88.288, 90.00, 90.00, 120.00
R / Rfree (%)	17.4 / 19.7

The structure of Structure of Headpiece of Integrin AIIBB3 in Open Conformation also contains other interesting chemical elements:

Magnesium	(Mg)	6 atoms
Arsenic	(As)	3 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Calcium atom in the Structure of Headpiece of Integrin AIIBB3 in Open Conformation (pdb code 3fcu). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 18 binding sites of Calcium where determined in the Structure of Headpiece of Integrin AIIBB3 in Open Conformation, PDB code: 3fcu:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 18 in the Structure of Headpiece of Integrin AIIBB3 in Open Conformation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Headpiece of Integrin AIIBB3 in Open Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2004 b:57.0 occ:1.00 O A:ASP247 2.3 77.1 1.0 OD2 A:ASP245 2.3 68.0 1.0 O A:THR250 2.4 63.6 1.0 OE1 A:GLU243 2.4 64.3 1.0 OE2 A:GLU252 2.4 59.7 1.0 OG1 A:THR250 2.4 60.1 1.0 OE2 A:GLU243 2.8 63.1 1.0 OE1 A:GLU252 2.9 56.0 1.0 CD A:GLU243 2.9 62.6 1.0 CD A:GLU252 3.0 58.3 1.0 C A:THR250 3.0 64.9 1.0 C A:ASP247 3.4 79.0 1.0 CG A:ASP245 3.4 68.5 1.0 CB A:THR250 3.5 62.9 1.0 CA A:THR250 3.7 65.8 1.0 OD1 A:ASP245 3.8 69.1 1.0 N A:THR251 3.9 66.8 1.0 N A:THR250 3.9 72.5 1.0 N A:ASP247 4.0 77.5 1.0 CA A:ASP247 4.0 78.3 1.0 CB A:ASP247 4.1 79.3 1.0 CA A:THR251 4.2 65.7 1.0 CG A:GLU243 4.4 59.4 1.0 N A:LEU248 4.5 80.5 1.0 CG A:GLU252 4.5 55.3 1.0 N A:ASP245 4.7 64.2 1.0 C A:THR251 4.7 61.1 1.0 CB A:ASP245 4.7 68.2 1.0 CA A:LEU248 4.8 83.3 1.0 CG2 A:THR250 4.8 61.5 1.0 CG A:ASP247 4.8 81.0 1.0 N A:GLU252 4.8 54.5 1.0 CA A:GLU243 4.9 55.9 1.0 N A:PHE244 4.9 57.9 1.0 C A:LEU248 4.9 81.2 1.0 N A:GLY246 5.0 71.7 1.0

Calcium binding site 2 out of 18 in the Structure of Headpiece of Integrin AIIBB3 in Open Conformation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Headpiece of Integrin AIIBB3 in Open Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2005 b:66.8 occ:1.00 OD1 A:ASN299 2.3 52.2 1.0 O A:HOH583 2.3 83.1 1.0 O A:ARG303 2.3 62.6 1.0 OD1 A:ASP301 2.4 62.9 1.0 OD1 A:ASP297 2.4 59.4 1.0 OD2 A:ASP305 2.6 57.5 1.0 OD1 A:ASP305 2.9 57.3 1.0 CG A:ASP305 3.0 58.5 1.0 CG A:ASP301 3.3 62.1 1.0 CG A:ASN299 3.4 48.8 1.0 C A:ARG303 3.4 62.7 1.0 CG A:ASP297 3.5 59.5 1.0 OD2 A:ASP301 3.5 65.2 1.0 ND2 A:ASN299 3.9 47.2 1.0 N A:ARG303 3.9 61.8 1.0 CA A:ARG303 4.0 64.9 1.0 CB A:ARG303 4.1 69.7 1.0 CA A:ASP297 4.2 57.0 1.0 CB A:ASP297 4.2 58.0 1.0 OD2 A:ASP297 4.4 57.9 1.0 N A:ASN299 4.4 53.3 1.0 CB A:ASP305 4.5 55.2 1.0 N A:HIS304 4.5 60.9 1.0 N A:VAL298 4.5 54.4 1.0 C A:HIS304 4.5 55.6 1.0 N A:ASP305 4.6 53.3 1.0 N A:ASP301 4.6 53.5 1.0 CB A:ASN299 4.6 51.0 1.0 C A:ASP297 4.6 55.9 1.0 CB A:ASP301 4.7 58.3 1.0 O A:HIS304 4.8 52.8 1.0 CA A:HIS304 4.8 58.7 1.0 O A:GLN333 4.9 64.8 1.0 N A:GLY300 4.9 56.0 1.0 N A:GLY302 4.9 57.1 1.0 CA A:ASN299 4.9 52.1 1.0 C A:ASN299 5.0 54.0 1.0

Calcium binding site 3 out of 18 in the Structure of Headpiece of Integrin AIIBB3 in Open Conformation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of Headpiece of Integrin AIIBB3 in Open Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2006 b:61.0 occ:1.00 OD1 A:ASP367 2.3 73.5 1.0 O A:HOH512 2.3 86.5 1.0 O A:TYR371 2.4 59.7 1.0 OD1 A:ASP369 2.5 66.4 1.0 OD2 A:ASP365 2.6 74.3 1.0 OD2 A:ASP373 2.7 67.2 1.0 OD1 A:ASP373 2.8 63.0 1.0 CG A:ASP373 3.1 62.7 1.0 CG A:ASP367 3.4 73.6 1.0 CG A:ASP369 3.5 66.5 1.0 C A:TYR371 3.5 60.1 1.0 CG A:ASP365 3.7 73.7 1.0 OD2 A:ASP369 3.9 65.9 1.0 OD2 A:ASP367 3.9 73.7 1.0 N A:ASP367 4.0 70.1 1.0 N A:LEU366 4.1 63.5 1.0 N A:TYR371 4.2 60.5 1.0 CA A:TYR371 4.3 60.5 1.0 N A:ASP369 4.3 67.3 1.0 CA A:ASP365 4.4 67.0 1.0 CB A:TYR371 4.4 61.7 1.0 OD1 A:ASP365 4.4 74.5 1.0 C A:ASP365 4.5 65.2 1.0 N A:ARG368 4.5 73.6 1.0 CD2 A:LEU393 4.5 55.2 1.0 CB A:ASP373 4.6 59.1 1.0 N A:ASN372 4.6 58.2 1.0 CB A:ASP369 4.6 66.3 1.0 CB A:ASP367 4.6 72.7 1.0 CB A:ASP365 4.6 70.3 1.0 C A:ASN372 4.7 53.7 1.0 CA A:ASP367 4.7 71.1 1.0 C A:ASP367 4.8 70.9 1.0 CA A:ASN372 4.8 55.0 1.0 N A:ASP373 4.8 54.0 1.0 CA A:ASP369 4.9 65.2 1.0 N A:GLY394 4.9 58.6 1.0 O A:GLY394 4.9 59.8 1.0 CA A:LEU366 5.0 63.0 1.0 O A:ASN372 5.0 54.0 1.0 N A:GLY370 5.0 64.6 1.0

Calcium binding site 4 out of 18 in the Structure of Headpiece of Integrin AIIBB3 in Open Conformation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of Headpiece of Integrin AIIBB3 in Open Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2007 b:74.6 occ:1.00 OD1 A:ASN430 2.3 81.4 1.0 OD1 A:ASP426 2.3 67.0 1.0 OD1 A:ASP428 2.3 62.4 1.0 O A:HOH589 2.3 50.7 1.0 O A:TYR432 2.4 71.6 1.0 OD2 A:ASP434 2.7 67.2 1.0 OD1 A:ASP434 2.8 65.8 1.0 CG A:ASP434 3.1 66.6 1.0 CG A:ASN430 3.4 76.2 1.0 CG A:ASP426 3.4 67.5 1.0 CG A:ASP428 3.5 66.4 1.0 C A:TYR432 3.5 75.6 1.0 N A:TYR432 4.1 79.4 1.0 OD2 A:ASP428 4.1 67.5 1.0 CA A:ASP426 4.1 65.5 1.0 N A:ASN430 4.1 76.3 1.0 ND2 A:ASN430 4.1 74.4 1.0 N A:ASP428 4.1 70.7 1.0 N A:ILE427 4.2 64.0 1.0 CA A:TYR432 4.2 79.0 1.0 OD2 A:ASP426 4.3 65.2 1.0 CB A:ASP426 4.3 68.4 1.0 CB A:TYR432 4.3 81.7 1.0 CB A:ASN430 4.4 75.7 1.0 C A:ASP426 4.4 64.8 1.0 N A:ASP429 4.4 80.9 1.0 CB A:ASP434 4.5 65.0 1.0 O A:ALA450 4.6 76.8 1.0 N A:PRO433 4.6 74.9 1.0 CA A:ASN430 4.7 76.0 1.0 C A:PRO433 4.7 68.6 1.0 CB A:ASP428 4.7 68.8 1.0 C A:ASP428 4.7 76.2 1.0 N A:ASP434 4.7 66.6 1.0 CA A:ASP428 4.7 72.2 1.0 N A:GLY431 4.8 77.4 1.0 N A:ALA450 4.8 65.2 1.0 CA A:PRO433 4.9 72.2 1.0 C A:ASN430 4.9 76.6 1.0 O A:PRO433 5.0 68.2 1.0

Calcium binding site 5 out of 18 in the Structure of Headpiece of Integrin AIIBB3 in Open Conformation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of Headpiece of Integrin AIIBB3 in Open Conformation within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2002 b:72.6 occ:1.00 O A:HOH550 2.2 57.4 1.0 O A:HOH590 2.2 42.4 1.0 O B:SER123 2.2 53.8 1.0 OD1 B:ASP127 2.3 58.5 1.0 OD2 B:ASP251 2.3 56.8 1.0 OD1 B:ASP126 2.7 92.6 1.0 OD2 B:ASP126 3.3 94.6 1.0 CG B:ASP126 3.4 91.5 1.0 CG B:ASP127 3.4 61.7 1.0 C B:SER123 3.4 53.8 1.0 CG B:ASP251 3.5 56.5 1.0 OD2 B:ASP127 3.9 65.5 1.0 CB B:ASP251 4.1 54.4 1.0 CA B:SER123 4.3 52.6 1.0 N B:MET124 4.3 57.1 1.0 CB B:SER123 4.4 52.8 1.0 CA B:MET124 4.4 59.8 1.0 OD1 B:ASP251 4.5 60.0 1.0 CB B:ASP127 4.6 60.1 1.0 N B:ASP127 4.8 64.9 1.0 CB B:ASP126 4.8 83.0 1.0 OG B:SER123 4.9 51.9 1.0 C B:MET124 5.0 60.5 1.0

Calcium binding site 6 out of 18 in the Structure of Headpiece of Integrin AIIBB3 in Open Conformation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of Headpiece of Integrin AIIBB3 in Open Conformation within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2003 b:38.0 occ:1.00 O B:PRO219 2.1 51.2 1.0 OD1 B:ASN215 2.2 50.8 1.0 OD1 B:ASP217 2.2 54.0 1.0 OD2 B:ASP158 2.3 47.1 1.0 O B:ASP217 2.3 46.3 1.0 OE2 B:GLU220 2.4 46.7 1.0 CG B:ASN215 3.2 49.1 1.0 CG B:ASP217 3.2 55.4 1.0 C B:PRO219 3.2 48.9 1.0 CG B:ASP158 3.3 49.6 1.0 C B:ASP217 3.4 49.4 1.0 CD B:GLU220 3.5 49.3 1.0 ND2 B:ASN215 3.5 52.5 1.0 CA B:GLU220 3.7 48.1 1.0 CB B:ASP158 3.8 47.7 1.0 OD2 B:ASP217 3.8 57.9 1.0 N B:GLU220 3.9 47.0 1.0 N B:ASP217 4.0 47.9 1.0 CA B:ASP217 4.0 49.0 1.0 CB B:ASP217 4.2 52.2 1.0 C B:ALA218 4.2 51.4 1.0 OE1 B:GLU220 4.3 45.4 1.0 N B:PRO219 4.3 49.0 1.0 NE2 B:HIS255 4.3 49.3 1.0 O B:ALA218 4.3 56.9 1.0 C1 B:CAC462 4.3 0.8 1.0 CG B:GLU220 4.4 50.4 1.0 CA B:PRO219 4.4 49.9 1.0 CB B:GLU220 4.4 48.3 1.0 OD1 B:ASP158 4.4 49.8 1.0 N B:ALA218 4.4 49.5 1.0 CB B:ASN215 4.5 48.3 1.0 CD2 B:HIS255 4.6 50.2 1.0 CA B:ALA218 4.8 47.4 1.0 C B:GLU220 4.9 48.5 1.0 CD B:PRO219 5.0 48.3 1.0

Calcium binding site 7 out of 18 in the Structure of Headpiece of Integrin AIIBB3 in Open Conformation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Structure of Headpiece of Integrin AIIBB3 in Open Conformation within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca2004 b:53.9 occ:1.00 OD2 C:ASP245 2.3 68.1 1.0 O C:THR250 2.4 63.8 1.0 OG1 C:THR250 2.4 59.7 1.0 O C:ASP247 2.4 77.3 1.0 OE1 C:GLU243 2.4 64.2 1.0 OE1 C:GLU252 2.6 55.4 1.0 OE2 C:GLU243 2.6 63.4 1.0 OE2 C:GLU252 2.8 58.9 1.0 CD C:GLU243 2.8 63.2 1.0 CD C:GLU252 3.0 57.7 1.0 C C:THR250 3.1 64.8 1.0 CG C:ASP245 3.4 68.6 1.0 CB C:THR250 3.5 62.7 1.0 C C:ASP247 3.5 78.5 1.0 CA C:THR250 3.6 66.0 1.0 OD1 C:ASP245 3.8 68.7 1.0 N C:THR250 3.9 72.2 1.0 N C:THR251 4.0 66.0 1.0 N C:ASP247 4.1 77.5 1.0 CA C:ASP247 4.2 77.8 1.0 CB C:ASP247 4.2 79.1 1.0 CA C:THR251 4.3 65.5 1.0 CG C:GLU243 4.4 60.0 1.0 N C:ASP245 4.5 63.8 1.0 N C:LEU248 4.5 80.3 1.0 CG C:GLU252 4.6 55.4 1.0 C C:THR251 4.6 60.5 1.0 CB C:ASP245 4.7 68.3 1.0 CG2 C:THR250 4.7 61.1 1.0 N C:PHE244 4.8 57.5 1.0 CA C:LEU248 4.8 83.2 1.0 CA C:GLU243 4.8 55.8 1.0 N C:GLU252 4.9 54.6 1.0 CA C:ASP245 4.9 67.2 1.0 C C:LEU248 4.9 81.2 1.0 C C:ASP245 4.9 69.0 1.0

Calcium binding site 8 out of 18 in the Structure of Headpiece of Integrin AIIBB3 in Open Conformation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Structure of Headpiece of Integrin AIIBB3 in Open Conformation within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca2005 b:43.4 occ:1.00 OD1 C:ASN299 2.1 52.2 1.0 O C:ARG303 2.3 62.6 1.0 OD1 C:ASP297 2.3 59.0 1.0 O A:HOH582 2.3 56.6 1.0 OD1 C:ASP301 2.3 62.2 1.0 OD2 C:ASP305 2.4 56.2 1.0 OD1 C:ASP305 2.8 55.5 1.0 CG C:ASP305 2.9 57.1 1.0 CG C:ASN299 3.2 48.9 1.0 CG C:ASP301 3.3 62.0 1.0 CG C:ASP297 3.4 59.3 1.0 C C:ARG303 3.4 62.7 1.0 OD2 C:ASP301 3.6 65.5 1.0 ND2 C:ASN299 3.7 47.3 1.0 N C:ARG303 3.9 62.0 1.0 CA C:ARG303 4.0 64.8 1.0 CA C:ASP297 4.1 57.2 1.0 CB C:ASP297 4.1 57.8 1.0 N C:ASN299 4.2 53.1 1.0 CB C:ARG303 4.2 69.2 1.0 N C:VAL298 4.2 54.7 1.0 OD2 C:ASP297 4.3 58.7 1.0 CB C:ASP305 4.4 55.6 1.0 N C:ASP301 4.5 53.6 1.0 C C:ASP297 4.5 56.2 1.0 CB C:ASN299 4.5 50.9 1.0 C C:HIS304 4.5 55.5 1.0 N C:HIS304 4.5 61.7 1.0 CB C:ASP301 4.6 58.7 1.0 N C:ASP305 4.6 53.4 1.0 CA C:ASN299 4.7 52.3 1.0 O C:HIS304 4.7 52.6 1.0 N C:GLY302 4.7 57.3 1.0 N C:GLY300 4.7 55.3 1.0 CA C:HIS304 4.8 58.8 1.0 O C:GLN333 4.8 64.2 1.0 C C:ASN299 4.9 54.2 1.0 CA C:ASP301 4.9 55.4 1.0 C C:ASP301 5.0 54.7 1.0 CA C:ASP305 5.0 53.1 1.0

Calcium binding site 9 out of 18 in the Structure of Headpiece of Integrin AIIBB3 in Open Conformation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Structure of Headpiece of Integrin AIIBB3 in Open Conformation within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca2006 b:63.1 occ:1.00 O C:TYR371 2.3 59.2 1.0 O A:HOH591 2.3 74.4 1.0 OD1 C:ASP367 2.4 73.7 1.0 OD2 C:ASP365 2.4 73.9 1.0 OD1 C:ASP369 2.5 67.3 1.0 OD2 C:ASP373 2.6 66.4 1.0 OD1 C:ASP373 2.8 62.8 1.0 CG C:ASP373 3.1 62.7 1.0 C C:TYR371 3.4 59.7 1.0 CG C:ASP365 3.5 73.7 1.0 CG C:ASP367 3.5 73.4 1.0 CG C:ASP369 3.6 67.0 1.0 OD2 C:ASP367 4.1 73.8 1.0 N C:LEU366 4.1 64.0 1.0 N C:ASP367 4.1 70.3 1.0 N C:TYR371 4.1 60.6 1.0 OD1 C:ASP365 4.2 74.9 1.0 CA C:TYR371 4.2 60.2 1.0 OD2 C:ASP369 4.2 66.8 1.0 N C:ASP369 4.3 67.4 1.0 CA C:ASP365 4.3 67.1 1.0 CB C:TYR371 4.3 61.8 1.0 N C:ARG368 4.4 73.2 1.0 N C:ASN372 4.5 57.6 1.0 C C:ASP365 4.5 65.3 1.0 CB C:ASP365 4.5 70.4 1.0 CB C:ASP373 4.6 59.4 1.0 C C:ASN372 4.6 54.1 1.0 CA C:ASN372 4.7 55.6 1.0 CB C:ASP369 4.7 66.4 1.0 CB C:ASP367 4.7 72.2 1.0 CA C:ASP367 4.7 71.2 1.0 N C:ASP373 4.7 53.3 1.0 N C:GLY394 4.8 58.5 1.0 C C:ASP367 4.8 70.8 1.0 CD2 C:LEU393 4.8 55.5 1.0 N C:GLY370 4.9 64.1 1.0 CA C:ASP369 4.9 65.4 1.0

Calcium binding site 10 out of 18 in the Structure of Headpiece of Integrin AIIBB3 in Open Conformation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Structure of Headpiece of Integrin AIIBB3 in Open Conformation within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca2007 b:78.0 occ:1.00 O C:TYR432 2.2 71.6 1.0 OD1 C:ASN430 2.2 81.6 1.0 OD1 C:ASP426 2.4 67.8 1.0 O A:HOH592 2.4 67.0 1.0 OD1 C:ASP428 2.4 61.8 1.0 OD1 C:ASP434 2.7 66.0 1.0 OD2 C:ASP434 2.7 67.0 1.0 CG C:ASP434 3.0 66.7 1.0 CG C:ASN430 3.3 76.5 1.0 C C:TYR432 3.4 75.4 1.0 CG C:ASP426 3.5 67.8 1.0 CG C:ASP428 3.6 66.5 1.0 N C:TYR432 3.9 79.4 1.0 CA C:TYR432 4.0 79.0 1.0 CB C:TYR432 4.0 81.8 1.0 ND2 C:ASN430 4.0 74.8 1.0 OD2 C:ASP428 4.0 67.9 1.0 CA C:ASP426 4.2 65.5 1.0 OD2 C:ASP426 4.2 65.8 1.0 N C:ASN430 4.3 76.4 1.0 CB C:ASP426 4.4 68.3 1.0 N C:ILE427 4.4 64.0 1.0 N C:ASP428 4.4 70.7 1.0 CB C:ASN430 4.4 75.5 1.0 C C:PRO433 4.5 69.2 1.0 N C:PRO433 4.5 74.9 1.0 CB C:ASP434 4.5 65.2 1.0 C C:ASP426 4.6 64.9 1.0 O C:PRO433 4.6 68.7 1.0 N C:ASP429 4.6 80.5 1.0 O C:ALA450 4.6 77.7 1.0 N C:ASP434 4.7 66.6 1.0 CA C:ASN430 4.8 75.9 1.0 CA C:PRO433 4.8 72.5 1.0 CB C:ASP428 4.8 68.7 1.0 N C:ALA450 4.9 65.0 1.0 N C:GLY431 4.9 77.3 1.0 C C:ASN430 4.9 76.5 1.0 CA C:ASP428 4.9 72.1 1.0 C C:ASP428 5.0 76.0 1.0

J.Zhu, B.H.Luo, T.Xiao, C.Zhang, N.Nishida, T.A.Springer. Structure of A Complete Integrin Ectodomain in A Physiologic Resting State and Activation and Deactivation By Applied Forces. Mol.Cell V. 32 849 2008.
ISSN: ISSN 1097-2765
PubMed: 19111664
DOI: 10.1016/J.MOLCEL.2008.11.018