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

The structure of Re-Refinement of Integrin ALPHAIIBBETA3 Headpiece, PDB code: 2vdk 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)	42.64 / 2.80
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	148.869, 148.869, 176.137, 90.00, 90.00, 120.00
R / Rfree (%)	16.1 / 20.5

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 2vdk). 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: 2vdk:
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:30.6 occ:1.00 OD2 A:ASP245 2.3 22.8 1.0 O A:ASP247 2.4 25.2 1.0 O A:THR250 2.4 17.4 1.0 OE1 A:GLU252 2.6 15.6 1.0 OG1 A:THR250 2.6 19.2 1.0 OE1 A:GLU243 2.6 5.7 1.0 OE2 A:GLU252 2.7 14.5 1.0 OE2 A:GLU243 2.7 8.9 1.0 CD A:GLU252 3.0 14.1 1.0 CD A:GLU243 3.0 7.3 1.0 C A:THR250 3.1 17.8 1.0 CG A:ASP245 3.2 22.4 1.0 C A:ASP247 3.5 25.7 1.0 OD1 A:ASP245 3.5 22.1 1.0 CB A:THR250 3.6 20.5 1.0 CA A:THR250 3.8 20.5 1.0 N A:THR250 4.0 23.9 1.0 N A:THR251 4.0 16.9 1.0 N A:ASP247 4.1 27.8 1.0 CA A:ASP247 4.1 26.9 1.0 CB A:ASP247 4.2 26.8 1.0 CA A:THR251 4.3 16.4 1.0 N A:ASP245 4.4 18.5 1.0 CB A:ASP245 4.5 21.3 1.0 CG A:GLU252 4.5 13.2 1.0 CG A:GLU243 4.5 6.9 1.0 N A:LEU248 4.5 26.4 1.0 N A:GLU252 4.7 12.6 1.0 C A:THR251 4.7 15.1 1.0 CA A:ASP245 4.8 20.2 1.0 N A:GLY246 4.8 23.8 1.0 C A:ASP245 4.8 21.4 1.0 N A:PHE244 4.8 11.8 1.0 CA A:LEU248 4.8 27.9 1.0 CG A:ASP247 4.9 26.5 1.0 CA A:GLU243 4.9 6.3 1.0 CG2 A:THR250 4.9 21.6 1.0 O A:HOH4150 5.0 19.8 1.0 C A:GLY246 5.0 28.1 1.0 C A:LEU248 5.0 27.4 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:26.8 occ:1.00 OD1 A:ASN299 2.2 16.2 1.0 O A:HOH4180 2.2 14.8 1.0 O A:ARG303 2.3 15.9 1.0 OD1 A:ASP297 2.3 15.6 1.0 OD1 A:ASP305 2.4 16.9 1.0 OD1 A:ASP301 2.4 8.4 1.0 OD2 A:ASP305 2.8 17.2 1.0 CG A:ASP305 2.9 17.7 1.0 CG A:ASN299 3.3 13.8 1.0 CG A:ASP297 3.4 15.0 1.0 C A:ARG303 3.4 16.3 1.0 CG A:ASP301 3.5 9.1 1.0 OD2 A:ASP301 3.9 8.4 1.0 ND2 A:ASN299 3.9 13.4 1.0 N A:ARG303 4.0 14.8 1.0 CB A:ARG303 4.1 17.0 1.0 CA A:ARG303 4.1 15.3 1.0 CA A:ASP297 4.1 15.5 1.0 CB A:ASP297 4.1 15.0 1.0 N A:ASN299 4.2 11.9 1.0 N A:VAL298 4.3 16.1 1.0 OD2 A:ASP297 4.3 14.0 1.0 N A:ASP305 4.3 18.9 1.0 CB A:ASP305 4.3 18.2 1.0 C A:HIS304 4.5 19.2 1.0 N A:HIS304 4.5 19.1 1.0 CB A:ASN299 4.6 12.9 1.0 C A:ASP297 4.6 16.2 1.0 N A:ASP301 4.6 8.9 1.0 CD2 A:LEU332 4.7 16.0 1.0 CA A:ASN299 4.7 12.1 1.0 CB A:ASP301 4.8 10.0 1.0 CA A:ASP305 4.8 18.8 1.0 N A:GLN333 4.8 15.0 1.0 CA A:HIS304 4.8 19.6 1.0 N A:GLY300 4.8 10.8 1.0 O A:HIS304 4.9 17.3 1.0 O A:GLN333 4.9 14.8 1.0 C A:ASN299 4.9 11.2 1.0 N A:GLY302 4.9 12.6 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:28.7 occ:1.00 O A:TYR371 2.3 20.1 1.0 O A:HOH4206 2.3 34.4 1.0 OD2 A:ASP365 2.5 17.7 1.0 OD1 A:ASP367 2.5 14.9 1.0 OD1 A:ASP369 2.6 23.6 1.0 OD2 A:ASP373 2.6 29.7 1.0 OD1 A:ASP373 2.8 29.4 1.0 CG A:ASP373 3.1 28.9 1.0 CG A:ASP369 3.4 22.1 1.0 C A:TYR371 3.5 20.2 1.0 CG A:ASP365 3.5 17.2 1.0 CG A:ASP367 3.6 16.5 1.0 OD2 A:ASP369 3.9 21.9 1.0 OD2 A:ASP367 4.0 18.4 1.0 N A:TYR371 4.1 18.7 1.0 CA A:TYR371 4.2 19.4 1.0 OD1 A:ASP365 4.2 16.4 1.0 CA A:ASP365 4.2 18.4 1.0 N A:LEU366 4.3 18.1 1.0 N A:ASP367 4.3 17.0 1.0 CB A:TYR371 4.3 18.7 1.0 N A:ASP369 4.3 20.4 1.0 CD2 A:LEU393 4.5 25.5 1.0 CB A:ASP369 4.5 21.8 1.0 CB A:ASP365 4.5 17.9 1.0 C A:ASP365 4.5 18.6 1.0 N A:ASN372 4.5 20.2 1.0 C A:ASN372 4.6 23.1 1.0 CB A:ASP373 4.6 26.5 1.0 N A:ARG368 4.7 20.0 1.0 CA A:ASN372 4.7 21.3 1.0 N A:GLY394 4.7 26.3 1.0 O A:ASN372 4.8 24.8 1.0 N A:ASP373 4.8 23.4 1.0 CB A:ASP367 4.8 16.5 1.0 CA A:ASP369 4.9 21.4 1.0 CA A:ASP367 4.9 17.0 1.0 CB A:LEU393 4.9 25.2 1.0 N A:GLY370 4.9 21.2 1.0 O A:GLY394 4.9 23.0 1.0 C A:ASP367 5.0 17.6 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:32.0 occ:1.00 OD1 A:ASN430 2.2 21.9 1.0 O A:HOH4217 2.3 15.7 1.0 O A:TYR432 2.4 17.9 1.0 OD1 A:ASP426 2.4 31.4 1.0 OD1 A:ASP428 2.5 20.8 1.0 OD2 A:ASP434 2.5 16.2 1.0 OD1 A:ASP434 2.8 21.2 1.0 CG A:ASP434 3.0 18.9 1.0 CG A:ASN430 3.2 20.6 1.0 C A:TYR432 3.5 19.8 1.0 CG A:ASP426 3.5 30.3 1.0 CG A:ASP428 3.6 21.2 1.0 ND2 A:ASN430 3.9 20.9 1.0 N A:TYR432 4.0 21.5 1.0 OD2 A:ASP428 4.1 19.7 1.0 CA A:TYR432 4.1 21.0 1.0 O A:ALA450 4.1 30.6 1.0 CB A:TYR432 4.2 20.9 1.0 CA A:ASP426 4.3 28.1 1.0 N A:ASN430 4.3 20.3 1.0 OD2 A:ASP426 4.3 30.3 1.0 CB A:ASN430 4.3 19.4 1.0 CB A:ASP426 4.3 29.1 1.0 CB A:ASP434 4.4 18.9 1.0 N A:ALA450 4.5 26.8 1.0 N A:PRO433 4.5 20.5 1.0 N A:ASP428 4.5 25.7 1.0 C A:PRO433 4.5 22.5 1.0 N A:ILE427 4.5 27.1 1.0 N A:ASP434 4.6 22.0 1.0 C A:ASP426 4.7 28.4 1.0 CA A:ASN430 4.7 19.7 1.0 CA A:PRO433 4.7 21.4 1.0 N A:ASP429 4.8 23.2 1.0 N A:GLY431 4.8 19.5 1.0 O A:PRO433 4.8 23.7 1.0 CB A:ASP428 4.8 21.8 1.0 C A:ASN430 4.9 19.9 1.0 CB A:ALA450 4.9 27.2 1.0 CA A:ASP434 5.0 20.3 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:6.9 occ:1.00 OD1 B:ASP127 2.2 13.5 1.0 OD2 B:ASP251 2.3 16.3 1.0 O B:SER123 2.3 16.9 1.0 O B:HOH4125 2.4 4.1 1.0 OD1 B:ASP126 2.4 21.4 1.0 O2 B:GOL1463 2.4 38.3 1.0 O1 B:GOL1463 3.0 36.9 1.0 C2 B:GOL1463 3.2 38.4 1.0 CG B:ASP127 3.4 14.9 1.0 CG B:ASP126 3.4 20.4 1.0 CG B:ASP251 3.4 16.4 1.0 C B:SER123 3.4 14.4 1.0 OD2 B:ASP126 3.6 19.8 1.0 C1 B:GOL1463 3.6 37.8 1.0 OD2 B:ASP127 4.0 14.5 1.0 CB B:ASP251 4.0 16.4 1.0 O B:HOH4017 4.1 22.7 1.0 CA B:SER123 4.3 15.2 1.0 N B:MET124 4.3 13.2 1.0 OD1 B:ASP251 4.4 16.4 1.0 CB B:SER123 4.4 15.8 1.0 CA B:MET124 4.4 12.6 1.0 CB B:ASP127 4.5 14.5 1.0 C3 B:GOL1463 4.6 39.4 1.0 O B:HOH4124 4.6 9.8 1.0 N B:ASP127 4.7 14.6 1.0 O3 B:GOL1463 4.8 39.8 1.0 CB B:ASP126 4.8 19.1 1.0 OG B:SER123 5.0 14.5 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:4.8 occ:1.00 OD1 B:ASN215 2.2 7.4 1.0 OD1 B:ASP217 2.3 7.0 1.0 O B:PRO219 2.3 15.0 1.0 OD2 B:ASP158 2.3 6.6 1.0 OE2 B:GLU220 2.4 15.4 1.0 O B:ASP217 2.4 9.2 1.0 CG B:ASP217 3.3 9.0 1.0 CG B:ASN215 3.3 8.7 1.0 C B:PRO219 3.4 11.5 1.0 CG B:ASP158 3.4 8.4 1.0 CD B:GLU220 3.4 15.8 1.0 C B:ASP217 3.5 10.1 1.0 ND2 B:ASN215 3.7 9.8 1.0 CA B:GLU220 3.7 10.9 1.0 CB B:ASP158 3.7 8.9 1.0 OD2 B:ASP217 4.0 9.9 1.0 N B:GLU220 4.0 11.6 1.0 N B:ASP217 4.1 9.0 1.0 CA B:ASP217 4.1 9.3 1.0 OE1 B:GLU220 4.1 14.4 1.0 NE2 B:HIS255 4.1 14.3 1.0 CB B:ASP217 4.3 8.4 1.0 C B:ALA218 4.3 9.6 1.0 N B:PRO219 4.4 10.4 1.0 O B:ALA218 4.4 10.0 1.0 CG B:GLU220 4.4 13.4 1.0 C2 B:CAC1462 4.4 2.2 1.0 CA B:PRO219 4.5 11.3 1.0 CD2 B:HIS255 4.5 14.1 1.0 CB B:GLU220 4.5 12.3 1.0 OD1 B:ASP158 4.5 9.8 1.0 N B:ALA218 4.5 10.7 1.0 CB B:ASN215 4.6 7.8 1.0 C B:GLU220 4.8 9.9 1.0 CA B:ALA218 4.9 9.0 1.0 CD B:PRO219 5.0 10.1 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