Calcium in PDB 2vdo: Integrin ALPHAIIBBETA3 Headpiece Bound to Fibrinogen Gamma Chain Peptide, Hhlggakqagdv

The structure of Integrin ALPHAIIBBETA3 Headpiece Bound to Fibrinogen Gamma Chain Peptide, Hhlggakqagdv, PDB code: 2vdo 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)	46.13 / 2.51
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	148.331, 148.331, 176.567, 90.00, 90.00, 120.00
R / Rfree (%)	14.8 / 19

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

Magnesium

(Mg)

1 atom

The binding sites of Calcium atom in the Integrin ALPHAIIBBETA3 Headpiece Bound to Fibrinogen Gamma Chain Peptide, Hhlggakqagdv (pdb code 2vdo). 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 Fibrinogen Gamma Chain Peptide, Hhlggakqagdv, PDB code: 2vdo:
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 Fibrinogen Gamma Chain Peptide, Hhlggakqagdv


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 Fibrinogen Gamma Chain Peptide, Hhlggakqagdv within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2004 b:67.8 occ:1.00 OE1 A:GLU243 2.3 52.4 1.0 OD2 A:ASP245 2.3 71.9 1.0 O A:ASP247 2.4 72.0 1.0 OG1 A:THR250 2.4 60.2 1.0 OE1 A:GLU252 2.5 61.5 1.0 O A:THR250 2.5 62.6 1.0 OE2 A:GLU243 2.7 57.8 1.0 OE2 A:GLU252 2.7 64.6 1.0 CD A:GLU243 2.8 54.6 1.0 CD A:GLU252 2.9 62.4 1.0 C A:THR250 3.2 62.2 1.0 CG A:ASP245 3.3 71.4 1.0 C A:ASP247 3.5 73.1 1.0 CB A:THR250 3.5 63.3 1.0 OD1 A:ASP245 3.7 71.7 1.0 CA A:THR250 3.8 64.7 1.0 N A:THR251 4.0 62.5 1.0 N A:THR250 4.0 70.1 1.0 N A:ASP247 4.1 73.7 1.0 CA A:ASP247 4.2 74.5 1.0 CG A:GLU243 4.3 53.5 1.0 CB A:ASP247 4.3 75.6 1.0 CA A:THR251 4.3 62.7 1.0 N A:ASP245 4.4 66.7 1.0 CG A:GLU252 4.5 61.0 1.0 CB A:ASP245 4.5 70.6 1.0 N A:LEU248 4.5 74.2 1.0 CA A:GLU243 4.6 53.4 1.0 N A:PHE244 4.7 56.8 1.0 C A:THR251 4.7 60.1 1.0 N A:GLU252 4.7 56.9 1.0 N A:GLY246 4.7 71.7 1.0 CA A:LEU248 4.8 76.7 1.0 CA A:ASP245 4.8 68.2 1.0 CG2 A:THR250 4.8 64.4 1.0 C A:ASP245 4.8 70.0 1.0 CB A:GLU243 4.8 53.0 1.0 C A:LEU248 5.0 76.2 1.0

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


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 Fibrinogen Gamma Chain Peptide, Hhlggakqagdv within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2005 b:61.3 occ:1.00 O A:HOH4304 2.2 62.8 1.0 OD1 A:ASN299 2.3 56.6 1.0 OD1 A:ASP297 2.3 56.1 1.0 O A:ARG303 2.4 53.9 1.0 OD1 A:ASP301 2.5 45.6 1.0 OD1 A:ASP305 2.6 53.0 1.0 OD2 A:ASP305 2.6 55.3 1.0 CG A:ASP305 2.9 53.9 1.0 CG A:ASP301 3.3 48.9 1.0 CG A:ASN299 3.4 52.6 1.0 CG A:ASP297 3.4 56.1 1.0 C A:ARG303 3.6 57.3 1.0 OD2 A:ASP301 3.6 47.3 1.0 ND2 A:ASN299 3.9 51.0 1.0 N A:ARG303 4.1 58.6 1.0 CB A:ASP297 4.2 55.0 1.0 CA A:ARG303 4.2 58.3 1.0 CA A:ASP297 4.2 56.4 1.0 OD2 A:ASP297 4.2 56.6 1.0 N A:ASN299 4.3 50.6 1.0 CB A:ARG303 4.3 59.0 1.0 CB A:ASP305 4.4 54.0 1.0 N A:VAL298 4.4 54.8 1.0 C A:HIS304 4.6 57.6 1.0 N A:ASP305 4.6 56.6 1.0 N A:ASP301 4.6 50.3 1.0 CB A:ASN299 4.6 50.4 1.0 CB A:ASP301 4.6 50.4 1.0 N A:HIS304 4.6 57.2 1.0 C A:ASP297 4.7 56.9 1.0 CA A:ASN299 4.8 50.0 1.0 O A:HIS304 4.8 55.5 1.0 CD2 A:LEU332 4.8 58.5 1.0 O A:GLN333 4.8 60.4 1.0 N A:GLN333 4.8 61.0 1.0 C A:ASN299 4.9 48.9 1.0 N A:GLY302 4.9 55.5 1.0 CA A:HIS304 4.9 58.1 1.0 N A:GLY300 4.9 49.3 1.0 CA A:ASP305 4.9 54.7 1.0 CA A:ASP301 5.0 51.8 1.0

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


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 Fibrinogen Gamma Chain Peptide, Hhlggakqagdv within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2006 b:70.5 occ:1.00 OD1 A:ASP367 2.3 57.5 1.0 O A:TYR371 2.3 58.2 1.0 O A:HOH4342 2.3 62.9 1.0 OD2 A:ASP365 2.5 63.6 1.0 OD1 A:ASP369 2.6 62.2 1.0 OD1 A:ASP373 2.7 67.6 1.0 OD2 A:ASP373 2.7 63.9 1.0 CG A:ASP373 3.0 65.0 1.0 CG A:ASP367 3.3 57.9 1.0 CG A:ASP369 3.4 60.3 1.0 C A:TYR371 3.5 58.8 1.0 CG A:ASP365 3.6 62.6 1.0 OD2 A:ASP369 3.7 60.0 1.0 OD2 A:ASP367 3.8 60.8 1.0 N A:ASP367 4.2 59.2 1.0 CA A:TYR371 4.2 58.0 1.0 N A:TYR371 4.2 58.4 1.0 OD1 A:ASP365 4.3 64.3 1.0 N A:LEU366 4.3 60.1 1.0 CB A:TYR371 4.3 56.5 1.0 CA A:ASP365 4.4 60.9 1.0 N A:ASP369 4.5 59.8 1.0 N A:ASN372 4.5 58.1 1.0 CD2 A:LEU393 4.5 52.5 1.0 C A:ASN372 4.5 58.6 1.0 CB A:ASP373 4.5 61.4 1.0 CB A:ASP365 4.6 61.4 1.0 C A:ASP365 4.6 60.0 1.0 CB A:ASP367 4.6 57.4 1.0 CB A:ASP369 4.7 60.1 1.0 N A:ARG368 4.7 61.0 1.0 CA A:ASN372 4.7 59.1 1.0 O A:ASN372 4.7 61.0 1.0 O A:GLY394 4.8 57.4 1.0 N A:GLY394 4.8 62.2 1.0 CA A:ASP367 4.8 58.4 1.0 N A:ASP373 4.8 58.6 1.0 CB A:LEU393 4.8 57.2 1.0 C A:ASP367 4.9 58.7 1.0

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


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 Fibrinogen Gamma Chain Peptide, Hhlggakqagdv within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2007 b:65.3 occ:1.00 OD1 A:ASN430 2.2 58.2 1.0 O A:HOH4381 2.3 62.9 1.0 O A:TYR432 2.3 59.6 1.0 OD1 A:ASP426 2.3 66.3 1.0 OD1 A:ASP428 2.4 60.7 1.0 OD2 A:ASP434 2.5 59.4 1.0 OD1 A:ASP434 2.6 62.9 1.0 CG A:ASP434 2.9 59.9 1.0 CG A:ASN430 3.2 54.8 1.0 CG A:ASP426 3.5 66.0 1.0 C A:TYR432 3.5 60.4 1.0 CG A:ASP428 3.6 61.0 1.0 ND2 A:ASN430 3.8 53.7 1.0 OD2 A:ASP428 4.0 60.2 1.0 N A:TYR432 4.0 61.9 1.0 CA A:TYR432 4.1 60.8 1.0 CB A:ASN430 4.2 55.3 1.0 CA A:ASP426 4.2 63.9 1.0 O A:ALA450 4.2 63.6 1.0 N A:ASN430 4.2 58.5 1.0 CB A:TYR432 4.3 60.6 1.0 OD2 A:ASP426 4.3 65.5 1.0 CB A:ASP426 4.3 64.2 1.0 N A:ASP428 4.4 64.3 1.0 CB A:ASP434 4.4 59.7 1.0 N A:ILE427 4.5 65.0 1.0 N A:PRO433 4.5 62.0 1.0 C A:ASP426 4.6 65.0 1.0 C A:PRO433 4.6 64.6 1.0 N A:ALA450 4.6 61.3 1.0 CA A:ASN430 4.7 56.7 1.0 N A:ASP434 4.7 63.2 1.0 N A:ASP429 4.7 63.5 1.0 CA A:PRO433 4.7 63.6 1.0 CB A:ASP428 4.8 60.9 1.0 N A:GLY431 4.8 58.8 1.0 CA A:ASP428 4.9 62.9 1.0 C A:ASN430 5.0 57.7 1.0 C A:ASP428 5.0 62.2 1.0 CA A:ASP434 5.0 60.2 1.0

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


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 Fibrinogen Gamma Chain Peptide, Hhlggakqagdv within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2002 b:50.4 occ:1.00 OD2 B:ASP251 2.2 61.1 1.0 OD1 B:ASP127 2.2 58.7 1.0 OD1 B:ASP126 2.3 72.4 1.0 O B:SER123 2.4 57.3 1.0 O C:HOH4014 2.4 45.3 1.0 O2 B:GOL1462 2.5 72.5 1.0 O1 B:GOL1462 3.0 74.5 1.0 C2 B:GOL1462 3.0 72.3 1.0 CG B:ASP126 3.4 72.6 1.0 CG B:ASP127 3.4 57.4 1.0 CG B:ASP251 3.4 61.4 1.0 C B:SER123 3.5 57.2 1.0 C1 B:GOL1462 3.6 73.0 1.0 OD2 B:ASP126 3.6 75.6 1.0 OD2 B:ASP127 4.0 56.0 1.0 CB B:ASP251 4.0 58.6 1.0 O B:HOH4028 4.1 61.4 1.0 C3 B:GOL1462 4.4 73.3 1.0 N B:MET124 4.4 56.8 1.0 CA B:SER123 4.4 57.0 1.0 OD1 B:ASP251 4.4 60.6 1.0 CA B:MET124 4.4 57.4 1.0 CB B:SER123 4.5 56.7 1.0 CB B:ASP127 4.5 57.0 1.0 O3 B:GOL1462 4.5 72.5 1.0 N B:ASP127 4.7 61.6 1.0 CB B:ASP126 4.7 67.9 1.0 OXT C:VAL411 4.8 64.6 1.0 N B:ASP126 5.0 63.1 1.0

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


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 Fibrinogen Gamma Chain Peptide, Hhlggakqagdv within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2003 b:41.3 occ:1.00 OD1 B:ASP217 2.2 57.0 1.0 O B:PRO219 2.3 62.2 1.0 OD1 B:ASN215 2.3 55.2 1.0 O B:ASP217 2.3 50.6 1.0 OE2 B:GLU220 2.3 54.7 1.0 OD2 B:ASP158 2.4 49.9 1.0 CG B:ASP217 3.2 57.2 1.0 C B:ASP217 3.3 52.5 1.0 C B:PRO219 3.4 54.5 1.0 CG B:ASN215 3.4 56.6 1.0 CG B:ASP158 3.4 52.2 1.0 CD B:GLU220 3.4 57.4 1.0 CB B:ASP158 3.8 52.2 1.0 ND2 B:ASN215 3.8 57.5 1.0 OD2 B:ASP217 3.9 60.2 1.0 CA B:GLU220 3.9 54.1 1.0 CA B:ASP217 4.0 52.1 1.0 N B:ASP217 4.0 53.1 1.0 N B:GLU220 4.1 54.3 1.0 NE2 B:HIS255 4.1 57.9 1.0 OE1 B:GLU220 4.1 55.4 1.0 CB B:ASP217 4.2 53.4 1.0 C B:ALA218 4.3 53.9 1.0 N B:PRO219 4.3 55.2 1.0 O B:ALA218 4.4 54.9 1.0 N B:ALA218 4.4 52.6 1.0 CD2 B:HIS255 4.4 58.7 1.0 CA B:PRO219 4.4 57.0 1.0 CG B:GLU220 4.4 55.6 1.0 OD1 B:ASP158 4.5 51.2 1.0 CB B:GLU220 4.6 53.8 1.0 CB B:ASN215 4.7 56.1 1.0 CD B:PRO219 4.8 56.8 1.0 CA B:ALA218 4.8 54.0 1.0 C B:GLU220 5.0 55.5 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