Calcium in PDB 2vdr: Integrin ALPHAIIBBETA3 Headpiece Bound to A Chimeric Fibrinogen Gamma Chain Peptide, Lggakqrgdv

The structure of Integrin ALPHAIIBBETA3 Headpiece Bound to A Chimeric Fibrinogen Gamma Chain Peptide, Lggakqrgdv, PDB code: 2vdr 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)	43.44 / 2.40
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	148.328, 148.328, 176.793, 90.00, 90.00, 120.00
R / Rfree (%)	14.8 / 19.3

The structure of Integrin ALPHAIIBBETA3 Headpiece Bound to A Chimeric Fibrinogen Gamma Chain Peptide, Lggakqrgdv also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Calcium atom in the Integrin ALPHAIIBBETA3 Headpiece Bound to A Chimeric Fibrinogen Gamma Chain Peptide, Lggakqrgdv (pdb code 2vdr). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Integrin ALPHAIIBBETA3 Headpiece Bound to A Chimeric Fibrinogen Gamma Chain Peptide, Lggakqrgdv, PDB code: 2vdr:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Integrin ALPHAIIBBETA3 Headpiece Bound to A Chimeric Fibrinogen Gamma Chain Peptide, Lggakqrgdv


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Integrin ALPHAIIBBETA3 Headpiece Bound to A Chimeric Fibrinogen Gamma Chain Peptide, Lggakqrgdv within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2004 b:55.7 occ:1.00 OE1 A:GLU243 2.3 39.6 1.0 OD2 A:ASP245 2.3 59.0 1.0 O A:ASP247 2.4 63.0 1.0 O A:THR250 2.4 51.0 1.0 OG1 A:THR250 2.4 49.0 1.0 OE1 A:GLU252 2.4 52.9 1.0 OE2 A:GLU252 2.6 55.2 1.0 OE2 A:GLU243 2.7 46.2 1.0 CD A:GLU252 2.8 52.1 1.0 CD A:GLU243 2.8 42.8 1.0 CG A:ASP245 3.1 59.0 1.0 C A:THR250 3.2 53.0 1.0 OD1 A:ASP245 3.3 60.6 1.0 C A:ASP247 3.5 65.8 1.0 CB A:THR250 3.6 53.8 1.0 CA A:THR250 3.8 54.0 1.0 N A:THR250 4.0 58.3 1.0 N A:ASP247 4.1 65.5 1.0 N A:THR251 4.2 54.1 1.0 CA A:ASP247 4.2 66.6 1.0 N A:ASP245 4.3 56.6 1.0 CB A:ASP247 4.3 68.1 1.0 CB A:ASP245 4.3 58.8 1.0 CG A:GLU243 4.3 41.6 1.0 CG A:GLU252 4.3 51.0 1.0 CA A:THR251 4.5 54.9 1.0 N A:LEU248 4.5 67.6 1.0 N A:PHE244 4.6 45.8 1.0 CA A:ASP245 4.7 57.7 1.0 N A:GLU252 4.7 50.1 1.0 CA A:GLU243 4.7 40.5 1.0 C A:THR251 4.7 52.3 1.0 CA A:LEU248 4.8 69.1 1.0 N A:GLY246 4.8 60.1 1.0 CG2 A:THR250 4.8 55.3 1.0 C A:ASP245 4.8 58.6 1.0 CB A:GLU243 4.9 41.3 1.0 C A:LEU248 5.0 66.8 1.0

Calcium binding site 2 out of 6 in the Integrin ALPHAIIBBETA3 Headpiece Bound to A Chimeric Fibrinogen Gamma Chain Peptide, Lggakqrgdv


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Integrin ALPHAIIBBETA3 Headpiece Bound to A Chimeric Fibrinogen Gamma Chain Peptide, Lggakqrgdv within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2005 b:52.0 occ:1.00 O A:HOH4317 2.3 47.6 1.0 OD1 A:ASN299 2.3 50.5 1.0 OD1 A:ASP297 2.3 47.5 1.0 O A:ARG303 2.4 52.8 1.0 OD1 A:ASP305 2.5 41.3 1.0 OD1 A:ASP301 2.6 47.0 1.0 OD2 A:ASP305 2.6 45.6 1.0 CG A:ASP305 2.9 43.4 1.0 CG A:ASN299 3.3 45.4 1.0 CG A:ASP297 3.4 48.7 1.0 CG A:ASP301 3.4 49.1 1.0 C A:ARG303 3.6 52.8 1.0 OD2 A:ASP301 3.7 48.7 1.0 ND2 A:ASN299 3.9 42.3 1.0 N A:ARG303 4.1 50.5 1.0 N A:ASN299 4.2 45.7 1.0 CA A:ASP297 4.2 49.0 1.0 CB A:ASP297 4.2 48.1 1.0 CA A:ARG303 4.2 52.5 1.0 OD2 A:ASP297 4.3 49.7 1.0 N A:VAL298 4.3 47.2 1.0 CB A:ARG303 4.3 54.8 1.0 CB A:ASP305 4.4 46.2 1.0 CB A:ASN299 4.5 43.5 1.0 N A:ASP301 4.5 48.0 1.0 N A:ASP305 4.6 49.4 1.0 C A:ASP297 4.6 48.5 1.0 C A:HIS304 4.6 51.3 1.0 N A:HIS304 4.7 52.0 1.0 CB A:ASP301 4.7 49.3 1.0 CA A:ASN299 4.7 44.6 1.0 CD2 A:LEU332 4.7 48.1 1.0 N A:GLY300 4.8 46.9 1.0 C A:ASN299 4.8 43.8 1.0 O A:GLN333 4.9 46.6 1.0 N A:GLN333 4.9 52.2 1.0 O A:HIS304 4.9 48.5 1.0 N A:GLY302 4.9 50.9 1.0 CA A:HIS304 5.0 52.8 1.0 CA A:ASP305 5.0 46.5 1.0

Calcium binding site 3 out of 6 in the Integrin ALPHAIIBBETA3 Headpiece Bound to A Chimeric Fibrinogen Gamma Chain Peptide, Lggakqrgdv


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Integrin ALPHAIIBBETA3 Headpiece Bound to A Chimeric Fibrinogen Gamma Chain Peptide, Lggakqrgdv within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2006 b:61.2 occ:1.00 O A:TYR371 2.2 52.0 1.0 OD1 A:ASP367 2.3 49.2 1.0 O A:HOH4361 2.4 50.9 1.0 OD1 A:ASP369 2.5 59.5 1.0 OD2 A:ASP365 2.5 51.4 1.0 OD2 A:ASP373 2.7 57.7 1.0 OD1 A:ASP373 2.7 63.0 1.0 CG A:ASP373 3.0 60.0 1.0 CG A:ASP367 3.4 50.2 1.0 C A:TYR371 3.4 53.3 1.0 CG A:ASP369 3.4 56.1 1.0 CG A:ASP365 3.6 51.7 1.0 OD2 A:ASP367 3.8 52.5 1.0 OD2 A:ASP369 3.8 57.5 1.0 CA A:TYR371 4.1 53.4 1.0 N A:TYR371 4.1 53.0 1.0 CB A:TYR371 4.2 52.0 1.0 N A:ASP367 4.3 51.5 1.0 CA A:ASP365 4.3 52.8 1.0 N A:LEU366 4.3 52.5 1.0 OD1 A:ASP365 4.3 53.1 1.0 N A:ASN372 4.4 52.8 1.0 C A:ASN372 4.4 53.3 1.0 N A:ASP369 4.5 54.0 1.0 CB A:ASP373 4.5 56.2 1.0 CB A:ASP365 4.5 52.3 1.0 CD2 A:LEU393 4.6 54.0 1.0 CA A:ASN372 4.6 54.5 1.0 C A:ASP365 4.6 53.1 1.0 CB A:ASP369 4.6 54.9 1.0 CB A:ASP367 4.6 50.5 1.0 O A:ASN372 4.7 55.1 1.0 N A:ASP373 4.7 53.0 1.0 O A:GLY394 4.7 57.3 1.0 N A:ARG368 4.7 54.1 1.0 N A:GLY394 4.7 60.8 1.0 CA A:ASP367 4.8 51.5 1.0 CB A:LEU393 4.9 54.9 1.0 N A:GLY370 5.0 52.8 1.0

Calcium binding site 4 out of 6 in the Integrin ALPHAIIBBETA3 Headpiece Bound to A Chimeric Fibrinogen Gamma Chain Peptide, Lggakqrgdv


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Integrin ALPHAIIBBETA3 Headpiece Bound to A Chimeric Fibrinogen Gamma Chain Peptide, Lggakqrgdv within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2007 b:57.9 occ:1.00 OD1 A:ASN430 2.2 53.8 1.0 O A:TYR432 2.3 57.7 1.0 O A:HOH4399 2.3 53.1 1.0 OD1 A:ASP426 2.4 48.5 1.0 OD1 A:ASP428 2.4 56.1 1.0 OD2 A:ASP434 2.4 50.7 1.0 OD1 A:ASP434 2.6 55.9 1.0 CG A:ASP434 2.9 53.6 1.0 CG A:ASN430 3.3 53.6 1.0 CG A:ASP426 3.4 53.3 1.0 C A:TYR432 3.5 58.4 1.0 CG A:ASP428 3.5 55.9 1.0 ND2 A:ASN430 4.0 54.3 1.0 OD2 A:ASP428 4.0 55.8 1.0 N A:TYR432 4.1 58.2 1.0 CA A:ASP426 4.2 55.8 1.0 CA A:TYR432 4.2 58.2 1.0 N A:ASN430 4.2 56.2 1.0 O A:ALA450 4.2 57.8 1.0 CB A:ASP426 4.2 54.1 1.0 CB A:ASN430 4.3 53.4 1.0 OD2 A:ASP426 4.3 54.5 1.0 N A:ASP428 4.3 58.9 1.0 CB A:ASP434 4.4 53.4 1.0 CB A:TYR432 4.4 57.5 1.0 N A:ILE427 4.4 58.3 1.0 N A:PRO433 4.5 59.3 1.0 C A:ASP426 4.6 58.0 1.0 N A:ASP434 4.6 59.7 1.0 N A:ALA450 4.6 54.1 1.0 C A:PRO433 4.6 61.3 1.0 N A:ASP429 4.6 58.6 1.0 CA A:ASN430 4.7 54.7 1.0 CA A:PRO433 4.7 61.0 1.0 CB A:ASP428 4.7 55.2 1.0 N A:GLY431 4.8 56.2 1.0 CA A:ASP428 4.9 57.0 1.0 CA A:ASP434 4.9 56.1 1.0 CG A:ARG449 5.0 55.6 1.0 CB A:ALA450 5.0 55.9 1.0 C A:ASP428 5.0 57.3 1.0 C A:ASN430 5.0 55.6 1.0

Calcium binding site 5 out of 6 in the Integrin ALPHAIIBBETA3 Headpiece Bound to A Chimeric Fibrinogen Gamma Chain Peptide, Lggakqrgdv


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Integrin ALPHAIIBBETA3 Headpiece Bound to A Chimeric Fibrinogen Gamma Chain Peptide, Lggakqrgdv within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2002 b:40.9 occ:1.00 OD1 B:ASP127 2.3 52.0 1.0 O C:HOH4011 2.3 47.5 1.0 OD2 B:ASP251 2.3 46.0 1.0 OD1 B:ASP126 2.4 56.0 1.0 O B:SER123 2.4 45.9 1.0 O2 B:GOL1462 2.6 62.9 1.0 C2 B:GOL1462 3.0 62.8 1.0 O1 B:GOL1462 3.0 65.9 1.0 CG B:ASP126 3.4 58.7 1.0 CG B:ASP127 3.4 50.5 1.0 C B:SER123 3.5 46.4 1.0 CG B:ASP251 3.5 48.4 1.0 C1 B:GOL1462 3.5 64.0 1.0 OD2 B:ASP126 3.6 64.5 1.0 CB B:ASP251 4.0 47.1 1.0 OD2 B:ASP127 4.0 53.0 1.0 O B:HOH4044 4.1 57.5 1.0 CA B:SER123 4.3 45.9 1.0 N B:MET124 4.3 47.0 1.0 C3 B:GOL1462 4.4 63.4 1.0 CA B:MET124 4.4 50.1 1.0 CB B:SER123 4.4 45.5 1.0 O B:HOH4234 4.4 76.3 1.0 OD1 B:ASP251 4.5 49.2 1.0 CB B:ASP127 4.6 48.7 1.0 O3 B:GOL1462 4.6 62.6 1.0 OXT C:VAL411 4.7 52.9 1.0 N B:ASP127 4.7 51.7 1.0 O B:HOH4235 4.7 50.8 1.0 CB B:ASP126 4.7 53.4 1.0 OG B:SER123 4.9 44.1 1.0 C B:MET124 4.9 50.3 1.0 N B:ASP126 5.0 49.2 1.0

Calcium binding site 6 out of 6 in the Integrin ALPHAIIBBETA3 Headpiece Bound to A Chimeric Fibrinogen Gamma Chain Peptide, Lggakqrgdv


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Integrin ALPHAIIBBETA3 Headpiece Bound to A Chimeric Fibrinogen Gamma Chain Peptide, Lggakqrgdv within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2003 b:35.9 occ:1.00 OD1 B:ASP217 2.2 47.1 1.0 O B:PRO219 2.3 48.2 1.0 OD1 B:ASN215 2.3 46.6 1.0 OD2 B:ASP158 2.4 41.7 1.0 OE2 B:GLU220 2.4 44.7 1.0 O B:ASP217 2.4 41.1 1.0 CG B:ASP217 3.2 44.9 1.0 CG B:ASN215 3.4 45.8 1.0 C B:ASP217 3.4 44.8 1.0 CG B:ASP158 3.4 44.0 1.0 C B:PRO219 3.4 45.8 1.0 CD B:GLU220 3.5 48.9 1.0 CB B:ASP158 3.7 41.9 1.0 ND2 B:ASN215 3.7 46.2 1.0 CA B:GLU220 3.9 44.2 1.0 OD2 B:ASP217 4.0 47.8 1.0 CA B:ASP217 4.0 43.4 1.0 N B:ASP217 4.1 42.9 1.0 N B:GLU220 4.1 47.3 1.0 NE2 B:HIS255 4.1 42.6 1.0 OE1 B:GLU220 4.2 44.6 1.0 CB B:ASP217 4.2 43.6 1.0 C B:ALA218 4.3 44.9 1.0 N B:PRO219 4.3 44.0 1.0 CD2 B:HIS255 4.4 43.0 1.0 N B:ALA218 4.4 44.4 1.0 CG B:GLU220 4.4 46.0 1.0 O B:ALA218 4.5 45.8 1.0 CA B:PRO219 4.5 44.0 1.0 OD1 B:ASP158 4.5 43.6 1.0 CB B:GLU220 4.6 44.0 1.0 CB B:ASN215 4.7 46.2 1.0 CD B:PRO219 4.8 45.0 1.0 CA B:ALA218 4.8 44.7 1.0 C B:GLU220 4.9 42.5 1.0 CB B:TYR164 4.9 45.5 1.0 CD2 B:TYR164 5.0 44.7 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