Calcium in PDB 3fcs: Structure of Complete Ectodomain of Integrin AIIBB3

The structure of Structure of Complete Ectodomain of Integrin AIIBB3, PDB code: 3fcs 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)	45.31 / 2.55
Space group	P 41
Cell size a, b, c (Å), α, β, γ (°)	81.300, 81.300, 654.623, 90.00, 90.00, 90.00
R / Rfree (%)	23.3 / 26.8

The structure of Structure of Complete Ectodomain of Integrin AIIBB3 also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Calcium atom in the Structure of Complete Ectodomain of Integrin AIIBB3 (pdb code 3fcs). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 14 binding sites of Calcium where determined in the Structure of Complete Ectodomain of Integrin AIIBB3, PDB code: 3fcs:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 14 in the Structure of Complete Ectodomain of Integrin AIIBB3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Complete Ectodomain of Integrin AIIBB3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2004 b:25.9 occ:1.00 O A:ASP247 2.1 28.9 1.0 OE1 A:GLU243 2.4 23.0 1.0 O A:THR250 2.4 31.8 1.0 OD1 A:ASP245 2.5 27.2 1.0 OE1 A:GLU252 2.6 23.1 1.0 OG1 A:THR250 2.7 30.3 1.0 OE2 A:GLU252 2.9 23.8 1.0 C A:THR250 3.0 30.7 1.0 CD A:GLU252 3.1 24.0 1.0 CD A:GLU243 3.1 24.1 1.0 OE2 A:GLU243 3.2 24.3 1.0 C A:ASP247 3.4 28.8 1.0 CG A:ASP245 3.4 27.7 1.0 CB A:THR250 3.6 31.1 1.0 CA A:THR250 3.7 31.2 1.0 OD2 A:ASP245 3.8 28.3 1.0 N A:THR251 3.8 29.0 1.0 N A:THR250 3.9 32.3 1.0 O A:HOH1076 4.0 24.4 1.0 CA A:THR251 4.0 28.2 1.0 CA A:ASP247 4.3 29.5 1.0 N A:LEU248 4.3 29.0 1.0 N A:ASP247 4.4 28.8 1.0 CA A:LEU248 4.4 29.5 1.0 CB A:ASP247 4.5 30.7 1.0 C A:LEU248 4.5 30.9 1.0 C A:THR251 4.6 27.0 1.0 CG A:GLU243 4.6 24.8 1.0 CG A:GLU252 4.6 25.2 1.0 CB A:ASP245 4.6 27.4 1.0 N A:GLU252 4.7 25.9 1.0 O A:LEU248 4.7 31.4 1.0 N A:ASN249 4.9 32.3 1.0 N A:ASP245 4.9 26.4 1.0 C A:ASN249 4.9 33.5 1.0 CA A:GLU243 4.9 25.5 1.0 CG2 A:THR250 5.0 31.1 1.0

Calcium binding site 2 out of 14 in the Structure of Complete Ectodomain of Integrin AIIBB3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Complete Ectodomain of Integrin AIIBB3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2005 b:17.5 occ:1.00 O A:ARG303 2.2 26.8 1.0 OD1 A:ASN299 2.3 25.9 1.0 OD1 A:ASP305 2.4 25.5 1.0 O A:HOH960 2.5 13.8 1.0 OD1 A:ASP301 2.5 26.3 1.0 OD1 A:ASP297 2.5 25.7 1.0 OD2 A:ASP305 2.8 27.1 1.0 CG A:ASP305 2.9 26.4 1.0 C A:ARG303 3.3 26.6 1.0 CG A:ASN299 3.4 26.3 1.0 CG A:ASP301 3.5 26.7 1.0 CG A:ASP297 3.5 25.1 1.0 OD2 A:ASP301 3.8 26.8 1.0 ND2 A:ASN299 3.9 27.2 1.0 CA A:ARG303 4.0 27.1 1.0 CB A:ARG303 4.1 26.9 1.0 N A:ARG303 4.1 26.6 1.0 CA A:ASP297 4.1 24.8 1.0 CB A:ASP297 4.2 25.0 1.0 C A:HIS304 4.3 25.3 1.0 CB A:ASP305 4.3 25.5 1.0 N A:ASP305 4.4 24.8 1.0 N A:HIS304 4.4 26.7 1.0 OD2 A:ASP297 4.4 23.8 1.0 N A:ASN299 4.4 25.0 1.0 N A:VAL298 4.5 25.1 1.0 O A:HIS304 4.5 24.8 1.0 CB A:ASN299 4.6 25.8 1.0 C A:ASP297 4.7 25.2 1.0 N A:ASP301 4.7 25.4 1.0 CA A:HIS304 4.7 26.5 1.0 O A:GLN333 4.8 27.9 1.0 CD2 A:LEU332 4.8 24.2 1.0 CA A:ASP305 4.8 24.8 1.0 CB A:ASP301 4.8 25.9 1.0 N A:GLN333 4.8 27.1 1.0 N A:GLY300 4.9 26.2 1.0 CA A:ASN299 4.9 25.7 1.0

Calcium binding site 3 out of 14 in the Structure of Complete Ectodomain of Integrin AIIBB3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of Complete Ectodomain of Integrin AIIBB3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2006 b:29.7 occ:1.00 OD1 A:ASP367 2.1 24.3 1.0 OD1 A:ASP369 2.2 25.4 1.0 OD1 A:ASP365 2.2 24.7 1.0 O A:HOH961 2.3 17.4 1.0 O A:TYR371 2.5 25.0 1.0 OD2 A:ASP373 2.7 27.3 1.0 OD1 A:ASP373 2.7 26.9 1.0 CG A:ASP373 3.1 26.9 1.0 CG A:ASP367 3.2 24.3 1.0 CG A:ASP365 3.3 25.4 1.0 CG A:ASP369 3.3 25.5 1.0 C A:TYR371 3.7 24.9 1.0 OD2 A:ASP367 3.7 24.8 1.0 N A:ASP367 3.9 24.2 1.0 OD2 A:ASP365 4.0 24.6 1.0 OD2 A:ASP369 4.0 25.1 1.0 N A:LEU366 4.0 25.1 1.0 CA A:ASP365 4.1 25.4 1.0 N A:ASP369 4.1 26.7 1.0 N A:TYR371 4.2 24.9 1.0 N A:ARG368 4.3 25.5 1.0 C A:ASP365 4.3 24.7 1.0 CB A:ASP365 4.3 25.5 1.0 CB A:ASP369 4.3 25.5 1.0 CA A:TYR371 4.4 24.9 1.0 CB A:ASP367 4.4 24.1 1.0 CA A:ASP367 4.5 24.5 1.0 CB A:ASP373 4.6 26.5 1.0 CD2 A:LEU393 4.6 22.7 1.0 C A:ASP367 4.6 24.6 1.0 CA A:ASP369 4.7 25.8 1.0 N A:ASN372 4.7 24.5 1.0 CB A:TYR371 4.7 25.3 1.0 C A:ASN372 4.8 24.6 1.0 N A:GLY370 4.8 25.0 1.0 N A:GLY394 4.8 25.9 1.0 CA A:ASN372 4.9 25.6 1.0 N A:ASP373 4.9 25.2 1.0 C A:LEU366 4.9 23.8 1.0 CA A:LEU366 4.9 24.9 1.0

Calcium binding site 4 out of 14 in the Structure of Complete Ectodomain of Integrin AIIBB3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of Complete Ectodomain of Integrin AIIBB3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2007 b:20.7 occ:1.00 OD1 A:ASN430 2.3 25.9 1.0 OD1 A:ASP426 2.3 24.2 1.0 OD1 A:ASP428 2.3 24.2 1.0 O A:TYR432 2.4 26.0 1.0 O A:HOH962 2.4 17.1 1.0 OD1 A:ASP434 2.5 25.3 1.0 OD2 A:ASP434 2.6 26.6 1.0 CG A:ASP434 2.9 25.5 1.0 CG A:ASN430 3.3 24.8 1.0 CG A:ASP426 3.4 24.1 1.0 CG A:ASP428 3.5 25.0 1.0 C A:TYR432 3.6 25.1 1.0 OD2 A:ASP428 3.9 23.8 1.0 ND2 A:ASN430 4.0 25.0 1.0 CA A:ASP426 4.1 24.7 1.0 OD2 A:ASP426 4.1 24.7 1.0 N A:TYR432 4.2 25.7 1.0 N A:ILE427 4.3 25.7 1.0 CB A:ASP426 4.3 24.3 1.0 N A:ASP428 4.3 25.7 1.0 CA A:TYR432 4.3 25.7 1.0 N A:ASN430 4.3 25.8 1.0 CB A:ASN430 4.4 24.9 1.0 CB A:ASP434 4.4 25.0 1.0 O A:ALA450 4.4 24.1 1.0 CB A:TYR432 4.5 25.7 1.0 N A:ALA450 4.5 26.7 1.0 C A:ASP426 4.5 25.9 1.0 C A:PRO433 4.6 25.0 1.0 N A:PRO433 4.6 24.8 1.0 N A:ASP429 4.7 25.8 1.0 N A:ASP434 4.7 25.5 1.0 CB A:ASP428 4.7 25.4 1.0 CA A:PRO433 4.8 24.4 1.0 CA A:ASN430 4.8 25.2 1.0 CA A:ASP428 4.8 25.4 1.0 CB A:ALA450 4.9 25.5 1.0 N A:GLY431 4.9 24.1 1.0 O A:PRO433 4.9 25.9 1.0 C A:ASP428 4.9 25.5 1.0

Calcium binding site 5 out of 14 in the Structure of Complete Ectodomain of Integrin AIIBB3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of Complete Ectodomain of Integrin AIIBB3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2008 b:23.4 occ:1.00 O A:HOH1045 2.2 29.6 1.0 O A:CYS602 2.2 29.5 1.0 O A:HOH1044 2.3 46.8 1.0 OD1 A:ASP605 2.5 32.3 1.0 OE1 A:GLU642 2.6 25.4 1.0 O A:VAL607 2.6 28.9 1.0 OE2 A:GLU642 2.9 26.3 1.0 CD A:GLU642 3.1 26.1 1.0 CG A:ASP605 3.3 32.3 1.0 OD2 A:ASP605 3.3 32.1 1.0 C A:CYS602 3.3 30.4 1.0 C A:VAL607 3.6 28.9 1.0 N A:VAL607 4.1 30.3 1.0 CA A:CYS602 4.2 30.2 1.0 N A:GLY603 4.2 30.9 1.0 CA A:GLY603 4.3 31.9 1.0 CA A:VAL607 4.4 29.4 1.0 CB A:CYS602 4.4 31.4 1.0 N A:CYS608 4.5 28.4 1.0 CA A:CYS608 4.6 28.3 1.0 CG A:GLU642 4.6 25.9 1.0 N A:VAL609 4.6 26.7 1.0 CB A:ASP605 4.7 32.2 1.0 CG2 A:VAL609 4.8 25.4 1.0 CB A:VAL607 4.9 29.2 1.0 C A:GLY603 4.9 32.9 1.0 N A:ASP606 4.9 31.9 1.0

Calcium binding site 6 out of 14 in the Structure of Complete Ectodomain of Integrin AIIBB3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of Complete Ectodomain of Integrin AIIBB3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2002 b:34.7 occ:1.00 O B:MET335 2.4 40.8 1.0 O B:SER123 2.5 40.5 1.0 OD1 B:ASP127 2.5 40.7 1.0 O B:HOH693 2.6 17.6 1.0 OD1 B:ASP126 2.6 39.4 1.0 O B:HOH694 2.7 27.1 1.0 OD2 B:ASP126 3.3 39.3 1.0 CG B:ASP126 3.3 39.5 1.0 CG B:ASP127 3.5 40.5 1.0 C B:MET335 3.6 41.4 1.0 C B:SER123 3.6 40.5 1.0 OD2 B:ASP127 3.9 40.5 1.0 CA B:MET124 4.2 40.9 1.0 N B:MET124 4.3 40.5 1.0 SD B:MET124 4.5 42.0 1.0 CA B:ASP336 4.5 43.0 1.0 N B:ASP336 4.5 41.8 1.0 CA B:MET335 4.5 41.6 1.0 N B:ASP127 4.7 40.2 1.0 CA B:SER123 4.7 40.6 1.0 OD2 B:ASP251 4.7 32.4 1.0 CB B:ASP127 4.8 40.4 1.0 CB B:MET335 4.8 43.0 1.0 CB B:ASP126 4.8 39.6 1.0 CB B:SER123 4.8 40.1 1.0 C B:MET124 4.9 41.1 1.0

Calcium binding site 7 out of 14 in the Structure of Complete Ectodomain of Integrin AIIBB3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Structure of Complete Ectodomain of Integrin AIIBB3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2003 b:37.5 occ:1.00 OD1 B:ASN215 2.1 32.6 1.0 OD1 B:ASP217 2.2 31.1 1.0 O B:PRO219 2.4 33.4 1.0 OD2 B:ASP158 2.4 31.2 1.0 O B:ASP217 2.6 31.2 1.0 OE1 B:GLU220 2.7 38.6 1.0 CG B:ASP217 3.2 30.8 1.0 CG B:ASN215 3.3 33.5 1.0 CG B:ASP158 3.5 30.9 1.0 C B:ASP217 3.6 31.8 1.0 CD B:GLU220 3.6 38.8 1.0 C B:PRO219 3.6 34.3 1.0 CB B:ASP158 3.8 30.5 1.0 OD2 B:ASP217 3.8 28.9 1.0 OE2 B:GLU220 4.0 39.5 1.0 N B:ASP217 4.1 31.5 1.0 CA B:ASP217 4.1 31.8 1.0 CA B:GLU220 4.2 36.9 1.0 ND2 B:ASN215 4.2 35.0 1.0 CB B:ASN215 4.3 32.5 1.0 CB B:ASP217 4.3 31.4 1.0 N B:GLU220 4.4 35.5 1.0 NE2 B:HIS255 4.5 30.9 1.0 C B:ALA218 4.5 32.3 1.0 N B:PRO219 4.6 33.7 1.0 N B:ALA218 4.6 32.3 1.0 OD1 B:ASP158 4.6 31.1 1.0 O B:ALA218 4.6 32.2 1.0 CG B:GLU220 4.7 38.5 1.0 CA B:PRO219 4.7 33.9 1.0 CD2 B:HIS255 4.8 31.8 1.0 CD1 B:TYR164 4.9 33.5 1.0 CB B:GLU220 4.9 37.7 1.0 O B:TYR164 4.9 33.2 1.0 C B:ARG216 5.0 30.6 1.0 CA B:ALA218 5.0 32.1 1.0

Calcium binding site 8 out of 14 in the Structure of Complete Ectodomain of Integrin AIIBB3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Structure of Complete Ectodomain of Integrin AIIBB3 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca2004 b:29.4 occ:1.00 O C:THR250 2.1 31.8 1.0 O C:ASP247 2.3 29.0 1.0 OD1 C:ASP245 2.4 27.2 1.0 OE1 C:GLU243 2.5 23.0 1.0 OG1 C:THR250 2.5 30.3 1.0 OE2 C:GLU252 2.5 23.8 1.0 OE1 C:GLU252 2.5 23.1 1.0 CD C:GLU252 2.9 24.0 1.0 C C:THR250 2.9 30.7 1.0 OE2 C:GLU243 3.0 24.2 1.0 CD C:GLU243 3.1 24.1 1.0 CG C:ASP245 3.3 27.8 1.0 C C:ASP247 3.5 28.8 1.0 CB C:THR250 3.5 31.0 1.0 OD2 C:ASP245 3.6 28.4 1.0 CA C:THR250 3.6 31.2 1.0 N C:THR251 3.8 28.9 1.0 N C:THR250 3.9 32.3 1.0 CA C:THR251 4.1 28.2 1.0 O C:HOH986 4.2 29.6 1.0 CA C:ASP247 4.3 29.4 1.0 N C:ASP247 4.3 28.8 1.0 CG C:GLU252 4.4 25.2 1.0 O C:HOH1092 4.5 16.9 1.0 CB C:ASP247 4.5 30.7 1.0 N C:LEU248 4.5 29.0 1.0 CB C:ASP245 4.5 27.4 1.0 CG C:GLU243 4.6 24.8 1.0 C C:THR251 4.6 27.0 1.0 N C:GLU252 4.6 25.9 1.0 CA C:LEU248 4.6 29.5 1.0 N C:ASP245 4.7 26.4 1.0 C C:LEU248 4.8 30.9 1.0 CG2 C:THR250 4.8 31.0 1.0 CA C:GLU243 4.9 25.5 1.0 N C:GLY246 5.0 26.2 1.0 C C:ASN249 5.0 33.5 1.0

Calcium binding site 9 out of 14 in the Structure of Complete Ectodomain of Integrin AIIBB3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Structure of Complete Ectodomain of Integrin AIIBB3 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca2005 b:41.4 occ:1.00 O C:HOH961 2.0 5.7 1.0 O C:ARG303 2.2 26.8 1.0 OD1 C:ASP297 2.3 25.7 1.0 OD1 C:ASN299 2.3 25.9 1.0 OD1 C:ASP305 2.4 25.5 1.0 OD1 C:ASP301 2.4 26.2 1.0 OD2 C:ASP305 2.9 27.0 1.0 CG C:ASP305 3.0 26.3 1.0 CG C:ASP297 3.3 25.1 1.0 C C:ARG303 3.3 26.6 1.0 CG C:ASN299 3.5 26.3 1.0 CG C:ASP301 3.5 26.8 1.0 N C:ARG303 3.9 26.6 1.0 CA C:ARG303 4.0 27.0 1.0 OD2 C:ASP301 4.0 26.9 1.0 CA C:ASP297 4.0 24.8 1.0 CB C:ASP297 4.0 25.0 1.0 ND2 C:ASN299 4.1 27.2 1.0 CB C:ARG303 4.1 26.9 1.0 OD2 C:ASP297 4.2 23.6 1.0 N C:ASN299 4.3 25.0 1.0 N C:HIS304 4.4 26.6 1.0 C C:HIS304 4.4 25.3 1.0 N C:VAL298 4.4 25.1 1.0 CB C:ASP305 4.4 25.5 1.0 N C:ASP301 4.5 25.4 1.0 N C:ASP305 4.5 24.8 1.0 C C:ASP297 4.5 25.2 1.0 CB C:ASN299 4.7 25.8 1.0 O C:HIS304 4.7 24.7 1.0 N C:GLY300 4.7 26.2 1.0 CA C:HIS304 4.7 26.4 1.0 CB C:ASP301 4.8 25.9 1.0 CA C:ASN299 4.8 25.7 1.0 C C:ASN299 4.9 25.4 1.0 N C:GLY302 4.9 25.5 1.0 CD2 C:LEU332 4.9 24.2 1.0 C C:GLY302 4.9 26.6 1.0 CA C:ASP305 4.9 24.8 1.0 O C:GLN333 5.0 27.9 1.0 CA C:ASP301 5.0 25.4 1.0

Calcium binding site 10 out of 14 in the Structure of Complete Ectodomain of Integrin AIIBB3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Structure of Complete Ectodomain of Integrin AIIBB3 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca2006 b:30.0 occ:1.00 OD1 C:ASP369 2.2 25.5 1.0 O C:TYR371 2.3 25.0 1.0 OD1 C:ASP367 2.3 24.4 1.0 OD1 C:ASP365 2.4 24.8 1.0 OD2 C:ASP373 2.6 27.3 1.0 O C:HOH1012 2.6 10.5 1.0 OD1 C:ASP373 2.6 26.9 1.0 CG C:ASP373 3.0 27.0 1.0 CG C:ASP369 3.3 25.4 1.0 CG C:ASP365 3.4 25.4 1.0 CG C:ASP367 3.5 24.3 1.0 C C:TYR371 3.5 24.9 1.0 OD2 C:ASP369 3.9 25.1 1.0 CA C:ASP365 4.0 25.4 1.0 OD2 C:ASP365 4.0 24.6 1.0 OD2 C:ASP367 4.0 24.7 1.0 N C:LEU366 4.1 25.0 1.0 N C:ASP367 4.1 24.2 1.0 N C:TYR371 4.2 24.9 1.0 N C:ASP369 4.2 26.6 1.0 CB C:ASP365 4.3 25.5 1.0 CA C:TYR371 4.3 24.9 1.0 C C:ASP365 4.3 24.8 1.0 CB C:ASP369 4.4 25.5 1.0 CB C:ASP373 4.5 26.5 1.0 N C:ASN372 4.5 24.5 1.0 N C:ARG368 4.5 25.5 1.0 C C:ASN372 4.5 24.6 1.0 CB C:TYR371 4.6 25.2 1.0 CA C:ASN372 4.6 25.6 1.0 CB C:ASP367 4.7 24.1 1.0 N C:GLY394 4.7 25.9 1.0 O C:ASN372 4.7 23.2 1.0 N C:ASP373 4.8 25.2 1.0 N C:GLY370 4.8 25.0 1.0 CA C:ASP367 4.8 24.5 1.0 CA C:ASP369 4.8 25.7 1.0 C C:ASP367 4.9 24.6 1.0 CD2 C:LEU393 4.9 22.8 1.0 O C:GLY364 4.9 26.2 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