Calcium in PDB 2vdl: Re-Refinement of Integrin ALPHAIIBBETA3 Headpiece

The structure of Re-Refinement of Integrin ALPHAIIBBETA3 Headpiece, PDB code: 2vdl was solved by T.A.Springer, J.Zhu, T.Xiao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.99 / 2.75
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	148.927, 148.927, 176.398, 90.00, 90.00, 120.00
R / Rfree (%)	14.4 / 19.1

The structure of Re-Refinement of Integrin ALPHAIIBBETA3 Headpiece also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Arsenic	(As)	1 atom

The binding sites of Calcium atom in the Re-Refinement of Integrin ALPHAIIBBETA3 Headpiece (pdb code 2vdl). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Re-Refinement of Integrin ALPHAIIBBETA3 Headpiece, PDB code: 2vdl:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Re-Refinement of Integrin ALPHAIIBBETA3 Headpiece


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Re-Refinement of Integrin ALPHAIIBBETA3 Headpiece within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2004 b:57.3 occ:1.00 OD2 A:ASP245 2.2 50.3 1.0 O A:ASP247 2.3 57.5 1.0 OE1 A:GLU243 2.5 32.0 1.0 OG1 A:THR250 2.5 44.0 1.0 OE1 A:GLU252 2.6 44.4 1.0 OE2 A:GLU252 2.6 44.3 1.0 O A:THR250 2.6 41.6 1.0 OE2 A:GLU243 2.7 37.1 1.0 CD A:GLU252 2.9 42.7 1.0 CD A:GLU243 2.9 35.6 1.0 CG A:ASP245 3.2 50.8 1.0 C A:THR250 3.2 42.0 1.0 C A:ASP247 3.4 56.4 1.0 CB A:THR250 3.6 45.7 1.0 OD1 A:ASP245 3.6 51.3 1.0 CA A:THR250 3.8 45.9 1.0 N A:THR250 4.0 50.6 1.0 N A:THR251 4.1 42.2 1.0 CA A:ASP247 4.1 56.9 1.0 N A:ASP247 4.1 57.2 1.0 CB A:ASP247 4.2 56.7 1.0 CG A:GLU252 4.4 40.7 1.0 CA A:THR251 4.4 42.4 1.0 CB A:ASP245 4.4 49.5 1.0 CG A:GLU243 4.4 34.7 1.0 N A:LEU248 4.5 56.2 1.0 N A:ASP245 4.5 47.4 1.0 C A:THR251 4.7 40.7 1.0 N A:GLU252 4.7 38.0 1.0 CA A:LEU248 4.7 57.0 1.0 C A:ASP245 4.8 49.2 1.0 CA A:ASP245 4.8 48.3 1.0 N A:GLY246 4.8 51.9 1.0 CG2 A:THR250 4.9 47.0 1.0 CG A:ASP247 4.9 56.5 1.0 N A:PHE244 4.9 39.9 1.0 O A:HOH4264 4.9 55.9 1.0 C A:LEU248 4.9 56.1 1.0 CA A:GLU243 4.9 33.9 1.0 OD1 A:ASP247 4.9 56.2 1.0 C A:GLY246 5.0 57.3 1.0

Calcium binding site 2 out of 6 in the Re-Refinement of Integrin ALPHAIIBBETA3 Headpiece


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Re-Refinement of Integrin ALPHAIIBBETA3 Headpiece within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2005 b:41.9 occ:1.00 OD1 A:ASN299 2.1 41.0 1.0 O A:HOH4332 2.3 29.3 1.0 OD1 A:ASP297 2.3 44.5 1.0 OD1 A:ASP301 2.4 35.5 1.0 O A:ARG303 2.4 40.4 1.0 OD1 A:ASP305 2.5 39.8 1.0 OD2 A:ASP305 2.8 42.5 1.0 CG A:ASP305 2.9 42.3 1.0 CG A:ASN299 3.3 37.2 1.0 CG A:ASP297 3.4 42.8 1.0 CG A:ASP301 3.4 35.5 1.0 C A:ARG303 3.5 41.4 1.0 OD2 A:ASP301 3.8 35.8 1.0 ND2 A:ASN299 3.9 36.4 1.0 N A:ARG303 4.0 41.0 1.0 CB A:ARG303 4.0 45.8 1.0 CA A:ARG303 4.1 42.7 1.0 CB A:ASP297 4.1 41.7 1.0 CA A:ASP297 4.2 41.9 1.0 N A:ASN299 4.2 36.4 1.0 OD2 A:ASP297 4.2 42.5 1.0 N A:VAL298 4.4 40.1 1.0 CB A:ASP305 4.4 42.3 1.0 N A:ASP305 4.4 43.7 1.0 CB A:ASN299 4.5 36.5 1.0 N A:ASP301 4.5 34.2 1.0 C A:HIS304 4.6 43.3 1.0 N A:HIS304 4.6 42.5 1.0 C A:ASP297 4.6 42.2 1.0 CA A:ASN299 4.7 35.8 1.0 CB A:ASP301 4.7 36.0 1.0 N A:GLY300 4.8 37.2 1.0 CD2 A:LEU332 4.8 43.3 1.0 C A:ASN299 4.8 35.6 1.0 CA A:ASP305 4.9 43.2 1.0 N A:GLN333 4.9 44.4 1.0 N A:GLY302 4.9 39.7 1.0 O A:GLN333 4.9 41.9 1.0 O A:HIS304 4.9 40.5 1.0 CA A:HIS304 4.9 44.4 1.0

Calcium binding site 3 out of 6 in the Re-Refinement of Integrin ALPHAIIBBETA3 Headpiece


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Re-Refinement of Integrin ALPHAIIBBETA3 Headpiece within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2006 b:57.5 occ:1.00 O A:HOH4362 2.3 56.0 1.0 OD1 A:ASP367 2.3 45.3 1.0 O A:TYR371 2.4 45.8 1.0 OD2 A:ASP365 2.4 48.0 1.0 OD1 A:ASP373 2.6 56.4 1.0 OD2 A:ASP373 2.7 56.2 1.0 OD1 A:ASP369 2.7 49.7 1.0 CG A:ASP373 3.0 55.1 1.0 CG A:ASP369 3.4 47.8 1.0 CG A:ASP367 3.5 45.6 1.0 CG A:ASP365 3.5 48.5 1.0 C A:TYR371 3.6 45.9 1.0 OD2 A:ASP369 3.7 47.5 1.0 N A:ASP367 4.1 45.4 1.0 OD2 A:ASP367 4.1 48.5 1.0 N A:LEU366 4.2 47.0 1.0 N A:ASP369 4.2 46.5 1.0 CA A:ASP365 4.2 47.6 1.0 OD1 A:ASP365 4.3 49.8 1.0 N A:TYR371 4.3 42.6 1.0 CA A:TYR371 4.3 44.5 1.0 N A:ARG368 4.4 46.2 1.0 C A:ASP365 4.4 47.4 1.0 CB A:ASP369 4.5 46.5 1.0 CB A:ASP365 4.5 47.7 1.0 CB A:ASP373 4.5 52.2 1.0 CB A:TYR371 4.6 44.0 1.0 N A:ASN372 4.6 45.5 1.0 C A:ASN372 4.7 48.3 1.0 CB A:ASP367 4.7 45.4 1.0 CA A:ASP367 4.7 45.0 1.0 C A:ASP367 4.7 44.3 1.0 CA A:ASN372 4.8 46.1 1.0 CD2 A:LEU393 4.8 47.5 1.0 N A:ASP373 4.8 49.5 1.0 CA A:ASP369 4.8 45.8 1.0 N A:GLY394 4.8 51.0 1.0 N A:GLY370 4.9 44.7 1.0 CB A:LEU393 4.9 48.9 1.0 O A:ASN372 4.9 50.8 1.0 O A:GLY394 4.9 45.4 1.0

Calcium binding site 4 out of 6 in the Re-Refinement of Integrin ALPHAIIBBETA3 Headpiece


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Re-Refinement of Integrin ALPHAIIBBETA3 Headpiece within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2007 b:53.9 occ:1.00 OD1 A:ASN430 2.1 50.5 1.0 O A:HOH4402 2.2 33.8 1.0 O A:TYR432 2.3 44.7 1.0 OD1 A:ASP426 2.3 52.4 1.0 OD1 A:ASP428 2.4 46.7 1.0 OD2 A:ASP434 2.5 41.3 1.0 OD1 A:ASP434 2.7 48.8 1.0 CG A:ASP434 3.0 45.3 1.0 CG A:ASN430 3.2 48.9 1.0 C A:TYR432 3.4 45.5 1.0 CG A:ASP426 3.4 51.5 1.0 CG A:ASP428 3.5 46.6 1.0 ND2 A:ASN430 3.9 49.0 1.0 OD2 A:ASP428 4.0 46.6 1.0 N A:TYR432 4.0 46.4 1.0 CA A:TYR432 4.2 46.3 1.0 CB A:ASN430 4.2 48.0 1.0 N A:ASN430 4.2 49.0 1.0 CA A:ASP426 4.3 49.6 1.0 OD2 A:ASP426 4.3 50.1 1.0 O A:ALA450 4.3 53.6 1.0 CB A:ASP426 4.3 50.4 1.0 CB A:TYR432 4.3 47.1 1.0 CB A:ASP434 4.4 45.0 1.0 N A:PRO433 4.5 45.7 1.0 N A:ASP428 4.5 48.0 1.0 N A:ILE427 4.5 47.6 1.0 N A:ALA450 4.6 50.9 1.0 C A:PRO433 4.6 48.8 1.0 N A:ASP434 4.6 48.0 1.0 CA A:ASN430 4.6 47.5 1.0 CA A:PRO433 4.7 47.4 1.0 N A:ASP429 4.7 48.5 1.0 C A:ASP426 4.7 49.4 1.0 N A:GLY431 4.7 45.4 1.0 CB A:ASP428 4.8 46.4 1.0 C A:ASN430 4.9 46.8 1.0 CB A:ALA450 4.9 50.7 1.0 CA A:ASP428 5.0 47.3 1.0 C A:ASP428 5.0 47.0 1.0 CA A:ASP434 5.0 45.8 1.0

Calcium binding site 5 out of 6 in the Re-Refinement of Integrin ALPHAIIBBETA3 Headpiece


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Re-Refinement of Integrin ALPHAIIBBETA3 Headpiece within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2002 b:32.7 occ:1.00 OD1 B:ASP127 2.1 36.3 1.0 OD2 B:ASP251 2.3 42.2 1.0 O B:SER123 2.4 44.7 1.0 OD1 B:ASP126 2.4 54.5 1.0 O B:HOH4231 2.5 37.4 1.0 O2 B:GOL1463 2.7 58.4 1.0 O1 B:GOL1463 2.8 57.6 1.0 C2 B:GOL1463 3.1 58.5 1.0 CG B:ASP127 3.4 40.3 1.0 C B:SER123 3.4 41.6 1.0 CG B:ASP126 3.4 53.1 1.0 CG B:ASP251 3.5 42.5 1.0 C1 B:GOL1463 3.5 58.3 1.0 OD2 B:ASP126 3.7 56.5 1.0 O B:HOH4036 4.0 44.0 1.0 OD2 B:ASP127 4.0 40.1 1.0 CB B:ASP251 4.0 40.6 1.0 N B:MET124 4.3 40.2 1.0 CA B:MET124 4.3 38.8 1.0 CA B:SER123 4.3 40.6 1.0 CB B:SER123 4.4 40.4 1.0 OD1 B:ASP251 4.5 44.1 1.0 CB B:ASP127 4.5 40.2 1.0 C3 B:GOL1463 4.6 60.5 1.0 N B:ASP127 4.7 40.9 1.0 CB B:ASP126 4.8 49.3 1.0 O3 B:GOL1463 4.8 61.4 1.0 O B:HOH4112 4.9 46.3 1.0 OG B:SER123 4.9 40.8 1.0 C B:MET124 5.0 38.2 1.0

Calcium binding site 6 out of 6 in the Re-Refinement of Integrin ALPHAIIBBETA3 Headpiece


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Re-Refinement of Integrin ALPHAIIBBETA3 Headpiece within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2003 b:25.8 occ:1.00 OD1 B:ASN215 2.3 35.9 1.0 O B:PRO219 2.3 40.6 1.0 OD1 B:ASP217 2.3 35.3 1.0 O B:ASP217 2.3 37.8 1.0 OD2 B:ASP158 2.3 34.3 1.0 OE2 B:GLU220 2.4 37.1 1.0 CG B:ASP217 3.2 37.3 1.0 C B:PRO219 3.3 36.1 1.0 CG B:ASN215 3.3 35.9 1.0 C B:ASP217 3.4 38.3 1.0 CG B:ASP158 3.4 33.4 1.0 CD B:GLU220 3.5 39.5 1.0 ND2 B:ASN215 3.7 36.0 1.0 CB B:ASP158 3.8 33.1 1.0 CA B:GLU220 3.8 37.2 1.0 OD2 B:ASP217 3.9 37.5 1.0 N B:GLU220 4.0 37.3 1.0 CA B:ASP217 4.0 36.3 1.0 N B:ASP217 4.1 36.6 1.0 NE2 B:HIS255 4.1 39.3 1.0 OE1 B:GLU220 4.2 39.4 1.0 CB B:ASP217 4.2 36.3 1.0 C B:ALA218 4.2 34.8 1.0 N B:PRO219 4.3 34.7 1.0 O B:ALA218 4.3 36.7 1.0 CA B:PRO219 4.4 34.9 1.0 CG B:GLU220 4.4 39.0 1.0 N B:ALA218 4.5 39.1 1.0 CD2 B:HIS255 4.5 39.7 1.0 OD1 B:ASP158 4.5 32.2 1.0 CB B:GLU220 4.5 37.9 1.0 C2 B:CAC1462 4.6 53.5 1.0 CB B:ASN215 4.6 35.5 1.0 CA B:ALA218 4.8 35.8 1.0 C B:GLU220 4.8 38.0 1.0 CD B:PRO219 4.9 35.9 1.0

T.A.Springer, J.Zhu, T.Xiao. Structural Basis For Distinctive Recognition of Fibrinogen Gammac Peptide By the Platelet Integrin ALPHAIIBBETA3. J.Cell Biol. V. 182 791 2008.
ISSN: ISSN 0021-9525
PubMed: 18710925
DOI: 10.1083/JCB.200801146