Calcium in PDB 2vdm: Re-Refinement of Integrin ALPHAIIBBETA3 Headpiece Bound to Antagonist Tirofiban

The structure of Re-Refinement of Integrin ALPHAIIBBETA3 Headpiece Bound to Antagonist Tirofiban, PDB code: 2vdm 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)	46.23 / 2.90
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	148.577, 148.577, 177.239, 90.00, 90.00, 120.00
R / Rfree (%)	16.7 / 20.6

The structure of Re-Refinement of Integrin ALPHAIIBBETA3 Headpiece Bound to Antagonist Tirofiban 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 Tirofiban (pdb code 2vdm). 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 Tirofiban, PDB code: 2vdm:
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 Tirofiban


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 Tirofiban within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2004 b:60.0 occ:1.00 OE1 A:GLU252 2.4 47.4 1.0 O A:ASP247 2.4 59.2 1.0 OD2 A:ASP245 2.4 56.6 1.0 O A:THR250 2.4 51.2 1.0 OE2 A:GLU252 2.7 48.5 1.0 OG1 A:THR250 2.7 52.6 1.0 OE1 A:GLU243 2.7 50.9 1.0 OE2 A:GLU243 2.8 50.9 1.0 CD A:GLU252 2.9 48.0 1.0 CD A:GLU243 3.1 50.0 1.0 C A:THR250 3.1 51.2 1.0 CG A:ASP245 3.2 57.0 1.0 OD1 A:ASP245 3.4 58.0 1.0 C A:ASP247 3.5 58.6 1.0 CB A:THR250 3.7 53.9 1.0 CA A:THR250 3.8 53.9 1.0 N A:THR251 4.0 50.4 1.0 N A:THR250 4.0 56.2 1.0 N A:ASP247 4.2 57.1 1.0 CA A:ASP247 4.2 57.9 1.0 CB A:ASP247 4.3 57.7 1.0 CA A:THR251 4.3 50.7 1.0 CG A:GLU252 4.4 47.4 1.0 N A:LEU248 4.5 59.5 1.0 CB A:ASP245 4.6 56.4 1.0 CG A:GLU243 4.6 48.9 1.0 N A:ASP245 4.6 55.2 1.0 C A:THR251 4.6 50.3 1.0 N A:GLU252 4.7 49.1 1.0 CA A:LEU248 4.8 60.4 1.0 CG A:ASP247 4.9 57.5 1.0 C A:LEU248 4.9 60.7 1.0 CA A:ASP245 4.9 55.6 1.0 N A:PHE244 4.9 51.4 1.0 N A:GLY246 5.0 54.2 1.0 CA A:GLU243 5.0 48.8 1.0

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


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 Tirofiban within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2005 b:58.4 occ:1.00 O A:HOH4120 2.1 46.6 1.0 OD1 A:ASN299 2.2 45.8 1.0 OD1 A:ASP297 2.3 54.4 1.0 O A:ARG303 2.3 54.0 1.0 OD1 A:ASP305 2.4 49.4 1.0 OD1 A:ASP301 2.5 42.0 1.0 OD2 A:ASP305 2.9 49.7 1.0 CG A:ASP305 3.0 50.2 1.0 CG A:ASN299 3.3 44.6 1.0 CG A:ASP297 3.4 53.0 1.0 C A:ARG303 3.5 54.2 1.0 CG A:ASP301 3.6 44.0 1.0 ND2 A:ASN299 3.9 44.6 1.0 OD2 A:ASP301 4.0 43.4 1.0 CA A:ASP297 4.0 51.1 1.0 CB A:ASP297 4.0 51.7 1.0 N A:ARG303 4.2 53.5 1.0 CA A:ARG303 4.2 54.4 1.0 CB A:ARG303 4.2 55.7 1.0 N A:ASN299 4.2 43.5 1.0 OD2 A:ASP297 4.3 52.6 1.0 N A:VAL298 4.4 50.0 1.0 N A:ASP305 4.4 51.6 1.0 CB A:ASP305 4.4 50.7 1.0 C A:HIS304 4.4 52.2 1.0 CB A:ASN299 4.5 44.5 1.0 C A:ASP297 4.5 50.6 1.0 N A:HIS304 4.6 54.1 1.0 N A:ASP301 4.7 45.0 1.0 CA A:ASN299 4.7 44.3 1.0 O A:HIS304 4.7 50.5 1.0 CD2 A:LEU332 4.8 40.1 1.0 CA A:HIS304 4.8 53.0 1.0 CB A:ASP301 4.8 45.0 1.0 CA A:ASP305 4.8 50.1 1.0 N A:GLN333 4.8 39.8 1.0 C A:ASN299 4.9 43.1 1.0 O A:GLN333 4.9 37.6 1.0 N A:GLY300 4.9 44.3 1.0 N A:GLY302 5.0 48.7 1.0

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


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 Tirofiban within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2006 b:68.1 occ:1.00 O A:TYR371 2.3 51.4 1.0 OD1 A:ASP367 2.4 46.3 1.0 OD2 A:ASP373 2.5 62.2 1.0 OD1 A:ASP369 2.6 57.0 1.0 OD2 A:ASP365 2.7 52.6 1.0 OD1 A:ASP373 2.9 61.2 1.0 CG A:ASP373 3.1 60.1 1.0 CG A:ASP369 3.2 54.7 1.0 C A:TYR371 3.4 51.7 1.0 OD2 A:ASP369 3.4 54.2 1.0 CG A:ASP367 3.5 48.2 1.0 CG A:ASP365 3.7 52.3 1.0 OD2 A:ASP367 3.8 48.1 1.0 CA A:TYR371 4.1 52.1 1.0 N A:TYR371 4.1 51.6 1.0 CD2 A:LEU393 4.2 46.2 1.0 CB A:TYR371 4.2 52.0 1.0 OD1 A:ASP365 4.4 53.8 1.0 N A:ASP369 4.4 54.6 1.0 N A:GLY394 4.4 45.9 1.0 CB A:ASP369 4.4 54.3 1.0 N A:ASN372 4.5 50.9 1.0 C A:ASN372 4.5 52.6 1.0 N A:ASP367 4.5 49.9 1.0 CA A:ASP365 4.6 50.2 1.0 CB A:ASP373 4.6 57.1 1.0 O A:GLY394 4.6 47.3 1.0 O A:ASN372 4.6 54.4 1.0 N A:LEU366 4.6 49.2 1.0 CA A:ASN372 4.7 51.2 1.0 N A:ASP373 4.7 53.2 1.0 CB A:ASP365 4.8 50.9 1.0 CB A:ASP367 4.8 48.4 1.0 CB A:LEU393 4.8 46.6 1.0 N A:ARG368 4.8 52.1 1.0 N A:GLY370 4.9 53.2 1.0 CA A:ASP369 4.9 54.2 1.0 C A:ASP365 4.9 49.6 1.0

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


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 Tirofiban within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2007 b:59.0 occ:1.00 O A:HOH4134 2.2 34.6 1.0 OD1 A:ASN430 2.2 44.0 1.0 O A:TYR432 2.3 48.0 1.0 OD1 A:ASP426 2.3 55.0 1.0 OD1 A:ASP428 2.5 45.5 1.0 OD2 A:ASP434 2.5 49.8 1.0 OD1 A:ASP434 2.8 53.4 1.0 CG A:ASP434 3.0 51.1 1.0 CG A:ASN430 3.2 43.4 1.0 CG A:ASP426 3.4 53.6 1.0 C A:TYR432 3.5 47.0 1.0 CG A:ASP428 3.6 45.9 1.0 ND2 A:ASN430 3.8 42.7 1.0 OD2 A:ASP428 4.1 45.9 1.0 N A:TYR432 4.1 45.7 1.0 O A:ALA450 4.1 53.7 1.0 CA A:TYR432 4.2 46.2 1.0 CA A:ASP426 4.2 51.5 1.0 OD2 A:ASP426 4.2 54.0 1.0 CB A:ASP426 4.2 52.2 1.0 CB A:TYR432 4.3 45.6 1.0 CB A:ASN430 4.3 43.1 1.0 N A:ASN430 4.4 44.9 1.0 N A:ALA450 4.4 52.1 1.0 CB A:ASP434 4.4 50.4 1.0 N A:ILE427 4.5 51.2 1.0 N A:PRO433 4.5 47.6 1.0 N A:ASP428 4.5 48.1 1.0 N A:ASP434 4.5 50.2 1.0 C A:PRO433 4.5 49.1 1.0 C A:ASP426 4.6 52.4 1.0 CA A:PRO433 4.7 48.1 1.0 CB A:ALA450 4.7 52.6 1.0 CA A:ASN430 4.8 43.7 1.0 N A:ASP429 4.8 46.2 1.0 N A:GLY431 4.8 45.1 1.0 CB A:ASP428 4.9 46.0 1.0 CA A:ASP434 4.9 50.5 1.0 C A:ALA450 4.9 54.1 1.0 CA A:ALA450 4.9 52.9 1.0 O A:PRO433 5.0 50.3 1.0 C A:ASN430 5.0 44.0 1.0

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


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 Tirofiban within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2002 b:38.5 occ:1.00 O B:SER123 2.3 53.5 1.0 OD1 B:ASP127 2.4 50.4 1.0 O B:HOH4009 2.4 28.6 1.0 OD1 B:ASP126 2.4 58.7 1.0 O2 B:GOL1463 2.4 58.6 1.0 OD2 B:ASP251 2.5 51.4 1.0 O1 B:GOL1463 2.9 53.7 1.0 C2 B:GOL1463 3.3 57.6 1.0 CG B:ASP126 3.3 58.6 1.0 C B:SER123 3.4 52.0 1.0 CG B:ASP127 3.5 51.3 1.0 OD2 B:ASP126 3.5 57.9 1.0 CG B:ASP251 3.6 52.3 1.0 C1 B:GOL1463 3.6 55.8 1.0 O B:HOH4010 3.9 37.9 1.0 CB B:ASP251 4.1 52.5 1.0 OD2 B:ASP127 4.2 50.1 1.0 N B:MET124 4.3 51.7 1.0 CA B:MET124 4.3 51.6 1.0 CA B:SER123 4.3 53.0 1.0 CB B:ASP127 4.4 51.7 1.0 CB B:SER123 4.5 53.6 1.0 OD1 B:ASP251 4.6 52.9 1.0 N B:ASP127 4.6 51.9 1.0 C3 B:GOL1463 4.7 59.4 1.0 CB B:ASP126 4.8 57.7 1.0 O B:HOH4031 4.9 37.1 1.0 C B:MET124 5.0 51.4 1.0

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


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 Tirofiban within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2003 b:38.3 occ:1.00 OD1 B:ASN215 2.2 41.8 1.0 O B:PRO219 2.3 54.1 1.0 OD1 B:ASP217 2.3 47.5 1.0 OE2 B:GLU220 2.3 50.8 1.0 OD2 B:ASP158 2.4 45.1 1.0 O B:ASP217 2.4 44.8 1.0 CG B:ASP217 3.2 46.9 1.0 CG B:ASN215 3.3 44.8 1.0 C B:PRO219 3.3 51.7 1.0 CG B:ASP158 3.4 45.7 1.0 C B:ASP217 3.4 47.7 1.0 CD B:GLU220 3.4 52.2 1.0 CA B:GLU220 3.7 49.2 1.0 ND2 B:ASN215 3.7 43.4 1.0 CB B:ASP158 3.7 46.9 1.0 OD2 B:ASP217 3.9 44.2 1.0 N B:GLU220 3.9 50.3 1.0 NE2 B:HIS255 4.0 54.2 1.0 CA B:ASP217 4.1 47.9 1.0 N B:ASP217 4.1 48.3 1.0 OE1 B:GLU220 4.1 53.1 1.0 CB B:ASP217 4.2 47.1 1.0 N B:PRO219 4.3 49.6 1.0 C B:ALA218 4.3 50.1 1.0 CG B:GLU220 4.4 50.3 1.0 CD2 B:HIS255 4.4 54.5 1.0 CA B:PRO219 4.4 49.8 1.0 N B:ALA218 4.4 50.2 1.0 CB B:GLU220 4.5 49.6 1.0 O B:ALA218 4.5 50.5 1.0 OD1 B:ASP158 4.5 45.8 1.0 CB B:ASN215 4.6 47.1 1.0 C B:GLU220 4.7 50.3 1.0 CA B:ALA218 4.9 50.1 1.0 CD B:PRO219 4.9 49.7 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