Calcium in PDB 2vdn: Re-Refinement of Integrin ALPHAIIBBETA3 Headpiece Bound to Antagonist Eptifibatide

The structure of Re-Refinement of Integrin ALPHAIIBBETA3 Headpiece Bound to Antagonist Eptifibatide, PDB code: 2vdn 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)	47.19 / 2.90
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	149.593, 149.593, 175.683, 90.00, 90.00, 120.00
R / Rfree (%)	16.3 / 21.3

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

Magnesium

(Mg)

1 atom

The binding sites of Calcium atom in the Re-Refinement of Integrin ALPHAIIBBETA3 Headpiece Bound to Antagonist Eptifibatide (pdb code 2vdn). 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 Bound to Antagonist Eptifibatide, PDB code: 2vdn:
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 Bound to Antagonist Eptifibatide


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 Bound to Antagonist Eptifibatide within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2004 b:63.5 occ:1.00 O A:ASP247 2.3 67.5 1.0 OD2 A:ASP245 2.3 60.3 1.0 OE1 A:GLU243 2.5 45.9 1.0 O A:THR250 2.5 57.7 1.0 OG1 A:THR250 2.5 59.5 1.0 OE1 A:GLU252 2.6 52.7 1.0 OE2 A:GLU252 2.6 53.1 1.0 OE2 A:GLU243 2.8 49.8 1.0 CD A:GLU243 3.0 48.0 1.0 CD A:GLU252 3.0 52.6 1.0 C A:THR250 3.1 58.3 1.0 CG A:ASP245 3.2 59.6 1.0 C A:ASP247 3.4 67.2 1.0 OD1 A:ASP245 3.5 59.6 1.0 CB A:THR250 3.6 60.3 1.0 CA A:THR250 3.8 60.9 1.0 N A:THR250 4.0 65.1 1.0 N A:THR251 4.0 57.2 1.0 N A:ASP247 4.0 65.2 1.0 CA A:ASP247 4.1 66.9 1.0 CA A:THR251 4.3 57.0 1.0 CB A:ASP247 4.3 67.6 1.0 N A:LEU248 4.4 68.0 1.0 CG A:GLU243 4.4 47.7 1.0 CG A:GLU252 4.5 52.2 1.0 CB A:ASP245 4.5 58.9 1.0 C A:THR251 4.6 55.9 1.0 N A:ASP245 4.6 58.3 1.0 CA A:LEU248 4.6 69.3 1.0 N A:GLU252 4.7 53.6 1.0 C A:LEU248 4.8 69.6 1.0 N A:GLY246 4.8 62.0 1.0 CA A:GLU243 4.8 47.0 1.0 CG2 A:THR250 4.9 59.6 1.0 CA A:ASP245 5.0 58.7 1.0 N A:PHE244 5.0 51.3 1.0

Calcium binding site 2 out of 6 in the Re-Refinement of Integrin ALPHAIIBBETA3 Headpiece Bound to Antagonist Eptifibatide


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 Bound to Antagonist Eptifibatide within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2005 b:62.0 occ:1.00 OD1 A:ASN299 2.2 45.3 1.0 O A:ARG303 2.3 56.5 1.0 O A:HOH4124 2.3 43.9 1.0 OD1 A:ASP297 2.3 50.0 1.0 OD1 A:ASP301 2.4 47.1 1.0 OD1 A:ASP305 2.5 54.4 1.0 OD2 A:ASP305 2.7 55.1 1.0 CG A:ASP305 2.9 55.0 1.0 CG A:ASP297 3.3 49.1 1.0 CG A:ASN299 3.4 43.5 1.0 C A:ARG303 3.4 55.8 1.0 CG A:ASP301 3.5 47.1 1.0 CA A:ASP297 3.9 48.7 1.0 OD2 A:ASP301 4.0 47.2 1.0 ND2 A:ASN299 4.0 43.7 1.0 CB A:ASP297 4.0 48.8 1.0 N A:ARG303 4.1 53.4 1.0 N A:VAL298 4.1 47.6 1.0 CA A:ARG303 4.1 55.1 1.0 N A:ASN299 4.2 43.3 1.0 OD2 A:ASP297 4.2 48.6 1.0 CB A:ARG303 4.2 56.6 1.0 N A:ASP305 4.2 55.5 1.0 CB A:ASP305 4.3 54.4 1.0 C A:HIS304 4.4 56.4 1.0 C A:ASP297 4.4 48.0 1.0 N A:HIS304 4.5 56.9 1.0 CB A:ASN299 4.6 43.5 1.0 N A:ASP301 4.6 46.5 1.0 CA A:HIS304 4.7 57.9 1.0 O A:HIS304 4.7 54.5 1.0 CA A:ASP305 4.7 54.1 1.0 CD2 A:LEU332 4.8 45.4 1.0 CA A:ASN299 4.8 43.7 1.0 CB A:ASP301 4.8 48.0 1.0 N A:GLY300 4.8 45.6 1.0 N A:GLN333 4.9 46.7 1.0 N A:GLY302 5.0 50.8 1.0 C A:ASN299 5.0 44.2 1.0 O A:GLN333 5.0 47.0 1.0

Calcium binding site 3 out of 6 in the Re-Refinement of Integrin ALPHAIIBBETA3 Headpiece Bound to Antagonist Eptifibatide


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 Bound to Antagonist Eptifibatide within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2006 b:71.4 occ:1.00 O A:TYR371 2.4 50.8 1.0 OD2 A:ASP373 2.4 61.0 1.0 OD1 A:ASP367 2.4 48.9 1.0 OD1 A:ASP369 2.4 53.1 1.0 OD1 A:ASP373 2.7 59.3 1.0 OD2 A:ASP365 2.8 53.2 1.0 CG A:ASP373 2.9 59.1 1.0 CG A:ASP369 3.3 51.5 1.0 C A:TYR371 3.4 51.5 1.0 CG A:ASP367 3.5 49.4 1.0 OD2 A:ASP369 3.7 51.9 1.0 CG A:ASP365 3.9 52.3 1.0 OD2 A:ASP367 4.0 50.7 1.0 CB A:TYR371 4.1 51.9 1.0 CA A:TYR371 4.1 51.6 1.0 N A:TYR371 4.2 49.8 1.0 C A:ASN372 4.4 54.8 1.0 N A:ASP367 4.4 50.6 1.0 N A:LEU366 4.4 49.2 1.0 CB A:ASP373 4.4 57.1 1.0 CD2 A:LEU393 4.4 48.6 1.0 O A:ASN372 4.4 57.5 1.0 N A:ASN372 4.4 52.3 1.0 CA A:ASP365 4.5 50.5 1.0 N A:ASP369 4.5 51.5 1.0 CB A:ASP369 4.5 50.8 1.0 N A:GLY394 4.6 53.1 1.0 N A:ASP373 4.6 54.4 1.0 O A:GLY394 4.6 53.0 1.0 CA A:ASN372 4.6 53.6 1.0 OD1 A:ASP365 4.7 52.5 1.0 CB A:LEU393 4.7 50.2 1.0 C A:ASP365 4.7 49.8 1.0 CB A:ASP367 4.8 49.5 1.0 CB A:ASP365 4.8 51.3 1.0 N A:ARG368 4.8 52.8 1.0 CA A:ASP367 5.0 50.0 1.0 CA A:ASP373 5.0 55.5 1.0

Calcium binding site 4 out of 6 in the Re-Refinement of Integrin ALPHAIIBBETA3 Headpiece Bound to Antagonist Eptifibatide


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 Bound to Antagonist Eptifibatide within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2007 b:68.6 occ:1.00 O A:HOH4138 2.2 58.0 1.0 O A:TYR432 2.3 44.6 1.0 OD1 A:ASN430 2.3 42.2 1.0 OD1 A:ASP428 2.4 47.6 1.0 OD1 A:ASP426 2.5 49.2 1.0 OD2 A:ASP434 2.6 48.4 1.0 OD1 A:ASP434 2.7 49.8 1.0 CG A:ASP434 3.0 49.5 1.0 CG A:ASN430 3.4 42.2 1.0 C A:TYR432 3.4 44.7 1.0 CG A:ASP428 3.5 48.2 1.0 CG A:ASP426 3.6 48.3 1.0 OD2 A:ASP428 3.8 47.6 1.0 N A:TYR432 4.0 43.6 1.0 CA A:TYR432 4.0 43.5 1.0 ND2 A:ASN430 4.0 42.7 1.0 CB A:TYR432 4.1 43.5 1.0 O A:ALA450 4.2 53.3 1.0 CA A:ASP426 4.3 48.3 1.0 N A:ASN430 4.4 46.5 1.0 OD2 A:ASP426 4.4 47.7 1.0 CB A:ASP426 4.4 47.9 1.0 CB A:ASP434 4.4 48.9 1.0 CB A:ASN430 4.4 42.5 1.0 N A:PRO433 4.5 46.8 1.0 N A:ILE427 4.5 48.2 1.0 N A:ASP428 4.5 50.6 1.0 C A:PRO433 4.6 49.1 1.0 N A:ALA450 4.6 52.0 1.0 N A:ASP434 4.6 49.4 1.0 C A:ASP426 4.7 48.3 1.0 CA A:PRO433 4.7 47.7 1.0 N A:ASP429 4.7 52.2 1.0 CB A:ASP428 4.8 48.8 1.0 CA A:ASN430 4.8 43.8 1.0 N A:GLY431 4.9 43.0 1.0 CB A:ALA450 4.9 51.6 1.0 O A:PRO433 5.0 49.8 1.0 CA A:ASP434 5.0 48.8 1.0 C A:ASN430 5.0 43.0 1.0

Calcium binding site 5 out of 6 in the Re-Refinement of Integrin ALPHAIIBBETA3 Headpiece Bound to Antagonist Eptifibatide


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 Bound to Antagonist Eptifibatide within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2002 b:63.2 occ:1.00 O B:HOH4040 2.2 49.5 1.0 OD1 B:ASP127 2.3 64.0 1.0 OD2 B:ASP251 2.5 53.3 1.0 O B:SER123 2.7 58.1 1.0 OD1 B:ASP126 2.7 69.3 1.0 O1 B:GOL1462 3.0 0.2 1.0 CG B:ASP127 3.4 63.3 1.0 CG B:ASP126 3.5 67.3 1.0 OD2 B:ASP126 3.5 66.0 1.0 O B:HOH4071 3.5 72.9 1.0 CG B:ASP251 3.6 53.8 1.0 O2 B:GOL1462 3.7 0.4 1.0 C B:SER123 3.8 56.7 1.0 CB B:ASP251 3.9 53.7 1.0 OD2 B:ASP127 4.1 65.0 1.0 C1 B:GOL1462 4.3 0.1 1.0 CA C:PRO6 4.4 53.7 1.0 CB B:ASP127 4.5 61.4 1.0 C2 B:GOL1462 4.5 0.5 1.0 N B:MET124 4.6 56.7 1.0 CB C:PRO6 4.6 52.5 1.0 CA B:MET124 4.6 57.0 1.0 CB B:SER123 4.7 52.4 1.0 CA B:SER123 4.7 54.4 1.0 OD1 B:ASP251 4.7 53.9 1.0 N B:ASP127 4.8 60.0 1.0 CB B:ASP126 5.0 65.0 1.0 N C:CYS7 5.0 58.5 1.0

Calcium binding site 6 out of 6 in the Re-Refinement of Integrin ALPHAIIBBETA3 Headpiece Bound to Antagonist Eptifibatide


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 Bound to Antagonist Eptifibatide within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2003 b:46.4 occ:1.00 OD1 B:ASP217 2.2 52.7 1.0 OD1 B:ASN215 2.3 47.3 1.0 O B:PRO219 2.3 53.6 1.0 OE2 B:GLU220 2.4 51.8 1.0 OD2 B:ASP158 2.4 47.5 1.0 O B:ASP217 2.5 51.2 1.0 CG B:ASP217 3.2 50.9 1.0 CG B:ASN215 3.3 48.6 1.0 C B:PRO219 3.3 51.3 1.0 CG B:ASP158 3.4 47.8 1.0 CD B:GLU220 3.5 52.4 1.0 C B:ASP217 3.5 51.7 1.0 ND2 B:ASN215 3.7 48.4 1.0 CA B:GLU220 3.7 49.4 1.0 CB B:ASP158 3.7 48.5 1.0 OD2 B:ASP217 3.8 50.0 1.0 N B:GLU220 3.9 49.5 1.0 CA B:ASP217 4.1 51.0 1.0 N B:ASP217 4.1 49.4 1.0 NE2 B:HIS255 4.2 52.9 1.0 OE1 B:GLU220 4.2 51.6 1.0 CB B:ASP217 4.2 50.8 1.0 C B:ALA218 4.4 50.0 1.0 N B:PRO219 4.4 50.9 1.0 CG B:GLU220 4.4 51.8 1.0 CB B:GLU220 4.4 50.9 1.0 O B:ALA218 4.4 49.2 1.0 CA B:PRO219 4.5 51.5 1.0 OD1 B:ASP158 4.5 46.7 1.0 N B:ALA218 4.5 51.8 1.0 CD2 B:HIS255 4.5 52.7 1.0 CB B:ASN215 4.6 48.0 1.0 C B:GLU220 4.7 49.1 1.0 CA B:ALA218 4.9 50.1 1.0 CD B:PRO219 5.0 51.7 1.0 CD2 B:TYR164 5.0 50.7 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