Calcium in PDB 2vc2: Re-Refinement of Integrin ALPHAIIBBETA3 Headpiece Bound to Antagonist L-739758

The structure of Re-Refinement of Integrin ALPHAIIBBETA3 Headpiece Bound to Antagonist L-739758, PDB code: 2vc2 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)	42.72 / 3.10
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	149.151, 149.151, 176.217, 90.00, 90.00, 120.00
R / Rfree (%)	17.7 / 21.7

The structure of Re-Refinement of Integrin ALPHAIIBBETA3 Headpiece Bound to Antagonist L-739758 also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Calcium atom in the Re-Refinement of Integrin ALPHAIIBBETA3 Headpiece Bound to Antagonist L-739758 (pdb code 2vc2). 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 L-739758, PDB code: 2vc2:
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 L-739758


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 L-739758 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2004 b:7.8 occ:1.00 OE1 A:GLU252 2.3 2.0 1.0 OD2 A:ASP245 2.3 6.9 1.0 O A:ASP247 2.4 10.2 1.0 O A:THR250 2.5 2.0 1.0 OG1 A:THR250 2.5 2.0 1.0 OE2 A:GLU252 2.6 2.6 1.0 OE1 A:GLU243 2.6 2.0 1.0 CD A:GLU252 2.8 2.0 1.0 OE2 A:GLU243 2.9 3.2 1.0 C A:THR250 3.1 2.0 1.0 CG A:ASP245 3.1 6.4 1.0 CD A:GLU243 3.1 2.1 1.0 OD1 A:ASP245 3.3 5.3 1.0 C A:ASP247 3.5 9.1 1.0 CB A:THR250 3.5 2.1 1.0 CA A:THR250 3.7 2.0 1.0 N A:THR250 3.9 3.6 1.0 N A:THR251 3.9 2.0 1.0 CA A:ASP247 4.2 10.3 1.0 N A:ASP247 4.2 10.2 1.0 CB A:ASP247 4.2 10.9 1.0 CA A:THR251 4.3 2.0 1.0 CG A:GLU252 4.3 2.0 1.0 CB A:ASP245 4.4 6.5 1.0 N A:LEU248 4.5 6.5 1.0 N A:ASP245 4.5 7.1 1.0 C A:THR251 4.6 2.0 1.0 CG A:GLU243 4.6 2.5 1.0 N A:GLU252 4.6 2.0 1.0 CA A:LEU248 4.7 4.6 1.0 C A:LEU248 4.8 3.3 1.0 N A:PHE244 4.8 3.7 1.0 CG2 A:THR250 4.8 3.9 1.0 CA A:ASP245 4.9 6.7 1.0 CG A:ASP247 4.9 10.5 1.0 CA A:GLU243 4.9 2.0 1.0

Calcium binding site 2 out of 6 in the Re-Refinement of Integrin ALPHAIIBBETA3 Headpiece Bound to Antagonist L-739758


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 L-739758 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2005 b:5.0 occ:1.00 O A:ARG303 2.3 2.0 1.0 OD1 A:ASN299 2.4 2.0 1.0 OD1 A:ASP305 2.4 2.0 1.0 OD1 A:ASP301 2.4 2.0 1.0 OD1 A:ASP297 2.5 4.2 1.0 OD2 A:ASP305 2.9 2.0 1.0 CG A:ASP305 3.0 2.0 1.0 CG A:ASP301 3.3 2.0 1.0 CG A:ASN299 3.4 2.0 1.0 C A:ARG303 3.5 2.1 1.0 OD2 A:ASP301 3.5 2.0 1.0 CG A:ASP297 3.6 3.1 1.0 ND2 A:ASN299 3.9 2.0 1.0 CA A:ARG303 4.1 3.4 1.0 N A:ARG303 4.2 2.0 1.0 CB A:ARG303 4.2 4.2 1.0 C A:HIS304 4.3 2.9 1.0 CB A:ASP297 4.4 2.9 1.0 O A:HIS304 4.4 2.0 1.0 N A:ASP305 4.4 2.4 1.0 CA A:ASP297 4.4 2.5 1.0 CB A:ASP305 4.4 2.0 1.0 OD2 A:ASP297 4.4 2.0 1.0 N A:ASN299 4.5 2.0 1.0 N A:HIS304 4.5 2.6 1.0 O A:GLN333 4.6 2.0 1.0 CB A:ASP301 4.6 2.0 1.0 N A:GLN333 4.6 2.0 1.0 N A:VAL298 4.6 3.9 1.0 N A:ASP301 4.7 2.0 1.0 CB A:ASN299 4.7 2.0 1.0 CA A:HIS304 4.7 4.2 1.0 CD2 A:LEU332 4.7 2.0 1.0 CA A:ASP305 4.8 2.0 1.0 C A:ASP297 4.9 3.3 1.0 CA A:ASN299 4.9 2.0 1.0

Calcium binding site 3 out of 6 in the Re-Refinement of Integrin ALPHAIIBBETA3 Headpiece Bound to Antagonist L-739758


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 L-739758 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2006 b:12.1 occ:1.00 O A:TYR371 2.3 5.7 1.0 OD1 A:ASP367 2.4 2.0 1.0 OD1 A:ASP369 2.4 7.6 1.0 OD2 A:ASP373 2.5 9.0 1.0 OD2 A:ASP365 2.6 2.0 1.0 OD1 A:ASP373 2.8 7.5 1.0 CG A:ASP373 3.0 7.2 1.0 CG A:ASP369 3.2 6.3 1.0 CG A:ASP367 3.4 2.0 1.0 C A:TYR371 3.5 3.8 1.0 OD2 A:ASP369 3.6 5.1 1.0 CG A:ASP365 3.8 2.0 1.0 OD2 A:ASP367 3.8 2.0 1.0 CA A:TYR371 4.1 3.1 1.0 N A:TYR371 4.1 2.3 1.0 CB A:TYR371 4.2 2.4 1.0 CB A:ASP369 4.3 5.7 1.0 N A:ASP369 4.4 4.7 1.0 CD2 A:LEU393 4.4 2.0 1.0 N A:ASP367 4.4 2.0 1.0 OD1 A:ASP365 4.4 2.0 1.0 CB A:ASP373 4.5 4.5 1.0 N A:ASN372 4.5 2.5 1.0 C A:ASN372 4.5 3.6 1.0 N A:GLY394 4.5 2.0 1.0 CA A:ASP365 4.6 2.0 1.0 N A:LEU366 4.6 2.0 1.0 O A:GLY394 4.7 2.0 1.0 CB A:LEU393 4.7 2.0 1.0 O A:ASN372 4.7 4.3 1.0 N A:ASP373 4.7 3.7 1.0 CA A:ASN372 4.7 2.4 1.0 CB A:ASP367 4.7 2.0 1.0 CB A:ASP365 4.8 2.0 1.0 C A:ASP365 4.8 2.0 1.0 CA A:ASP369 4.8 5.2 1.0 N A:ARG368 4.9 2.4 1.0 N A:GLY370 4.9 5.2 1.0 CG A:LEU393 4.9 2.0 1.0 CA A:ASP367 5.0 2.0 1.0

Calcium binding site 4 out of 6 in the Re-Refinement of Integrin ALPHAIIBBETA3 Headpiece Bound to Antagonist L-739758


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 L-739758 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2007 b:3.6 occ:1.00 O A:HOH4029 2.4 2.0 1.0 O A:TYR432 2.4 2.0 1.0 OD1 A:ASN430 2.4 2.0 1.0 OD1 A:ASP428 2.5 2.0 1.0 OD2 A:ASP434 2.6 2.0 1.0 OD1 A:ASP426 2.6 2.4 1.0 OD1 A:ASP434 2.8 2.0 1.0 CG A:ASP434 3.0 2.0 1.0 CG A:ASN430 3.3 2.0 1.0 CG A:ASP428 3.5 2.0 1.0 C A:TYR432 3.5 2.0 1.0 CG A:ASP426 3.6 2.0 1.0 OD2 A:ASP428 3.8 2.0 1.0 ND2 A:ASN430 3.9 2.0 1.0 N A:TYR432 4.2 2.0 1.0 O A:ALA450 4.2 3.1 1.0 CA A:TYR432 4.2 2.0 1.0 N A:ASN430 4.3 2.0 1.0 OD2 A:ASP426 4.3 2.3 1.0 CA A:ASP426 4.3 2.0 1.0 C A:PRO433 4.3 2.2 1.0 CB A:ASN430 4.4 2.0 1.0 CB A:TYR432 4.4 2.0 1.0 CB A:ASP434 4.4 2.0 1.0 N A:ASP428 4.4 2.0 1.0 N A:PRO433 4.4 2.0 1.0 CB A:ASP426 4.5 2.0 1.0 N A:ILE427 4.5 2.0 1.0 N A:ALA450 4.5 3.6 1.0 O A:PRO433 4.5 4.0 1.0 N A:ASP434 4.5 2.0 1.0 CA A:PRO433 4.6 2.0 1.0 C A:ASP426 4.7 2.0 1.0 N A:ASP429 4.7 2.0 1.0 CB A:ASP428 4.7 2.0 1.0 CA A:ASN430 4.8 2.0 1.0 CB A:ALA450 4.8 3.4 1.0 CA A:ASP434 4.9 2.0 1.0 CG A:ARG449 4.9 2.3 1.0 N A:GLY431 5.0 2.0 1.0 CA A:ASP428 5.0 2.0 1.0

Calcium binding site 5 out of 6 in the Re-Refinement of Integrin ALPHAIIBBETA3 Headpiece Bound to Antagonist L-739758


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 L-739758 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2002 b:2.0 occ:1.00 OD2 B:ASP251 2.3 6.5 1.0 OD1 B:ASP127 2.3 3.0 1.0 O2 B:GOL1478 2.3 29.8 1.0 O B:HOH4025 2.3 2.0 1.0 O B:SER123 2.4 2.8 1.0 OD1 B:ASP126 2.7 11.7 1.0 O1 B:GOL1478 3.0 29.9 1.0 C2 B:GOL1478 3.3 29.8 1.0 CG B:ASP251 3.4 6.3 1.0 C B:SER123 3.4 2.0 1.0 CG B:ASP127 3.4 5.0 1.0 CG B:ASP126 3.5 10.9 1.0 OD2 B:ASP126 3.6 10.4 1.0 C1 B:GOL1478 3.7 29.6 1.0 CB B:ASP251 3.9 6.0 1.0 OD2 B:ASP127 3.9 5.8 1.0 CA B:SER123 4.2 2.0 1.0 CB B:SER123 4.3 2.0 1.0 N B:MET124 4.4 2.0 1.0 OD1 B:ASP251 4.4 6.5 1.0 CA B:MET124 4.5 2.0 1.0 C3 B:GOL1478 4.6 30.0 1.0 CB B:ASP127 4.7 4.9 1.0 N B:ASP127 4.9 4.8 1.0 CB B:ASP126 5.0 9.6 1.0 O3 B:GOL1478 5.0 29.8 1.0

Calcium binding site 6 out of 6 in the Re-Refinement of Integrin ALPHAIIBBETA3 Headpiece Bound to Antagonist L-739758


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 L-739758 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2003 b:2.0 occ:1.00 OD1 B:ASN215 2.2 2.0 1.0 OD1 B:ASP217 2.2 2.0 1.0 OE2 B:GLU220 2.2 2.4 1.0 O B:PRO219 2.3 3.6 1.0 OD2 B:ASP158 2.3 2.0 1.0 O B:ASP217 2.5 2.0 1.0 CG B:ASN215 3.3 2.0 1.0 CG B:ASP217 3.3 2.0 1.0 CG B:ASP158 3.3 2.1 1.0 C B:PRO219 3.3 2.1 1.0 CD B:GLU220 3.4 2.5 1.0 C B:ASP217 3.5 2.0 1.0 CB B:ASP158 3.6 2.0 1.0 CA B:GLU220 3.8 2.0 1.0 ND2 B:ASN215 3.8 2.0 1.0 N B:GLU220 4.0 2.0 1.0 OD2 B:ASP217 4.0 2.0 1.0 OE1 B:GLU220 4.1 3.6 1.0 CA B:ASP217 4.2 2.0 1.0 N B:ASP217 4.2 2.0 1.0 NE2 B:HIS255 4.2 2.0 1.0 CB B:ASP217 4.3 2.0 1.0 C B:ALA218 4.4 2.0 1.0 N B:PRO219 4.4 2.0 1.0 CG B:GLU220 4.4 2.0 1.0 O B:ALA218 4.4 2.0 1.0 CA B:PRO219 4.5 2.0 1.0 CB B:GLU220 4.5 2.0 1.0 OD1 B:ASP158 4.5 2.1 1.0 CD2 B:HIS255 4.5 2.0 1.0 CB B:ASN215 4.6 2.0 1.0 N B:ALA218 4.6 2.0 1.0 C B:GLU220 4.8 2.0 1.0 CA B:ALA218 4.9 2.0 1.0 CB B:TYR164 5.0 2.0 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