Calcium in PDB 2ffd: Fibrinogen Fragment D with "A" Knob Peptide Mimic Gprvve

The structure of Fibrinogen Fragment D with "A" Knob Peptide Mimic Gprvve, PDB code: 2ffd was solved by L.Betts, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.89
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	89.521, 94.652, 227.490, 90.00, 90.00, 90.00
R / Rfree (%)	21.1 / 26.8

The binding sites of Calcium atom in the Fibrinogen Fragment D with "A" Knob Peptide Mimic Gprvve (pdb code 2ffd). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Fibrinogen Fragment D with "A" Knob Peptide Mimic Gprvve, PDB code: 2ffd:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Fibrinogen Fragment D with "A" Knob Peptide Mimic Gprvve


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Fibrinogen Fragment D with "A" Knob Peptide Mimic Gprvve within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca600 b:44.7 occ:1.00 OD1 B:ASP383 2.3 40.1 1.0 O B:TRP385 2.4 48.9 1.0 OD2 B:ASP381 2.5 34.0 1.0 OD1 B:ASP381 2.6 34.2 1.0 CG B:ASP381 2.9 34.7 1.0 CG B:ASP383 3.4 40.8 1.0 C B:TRP385 3.4 49.0 1.0 OD2 B:ASP383 3.8 41.5 1.0 O B:ASP383 3.8 41.7 1.0 N B:TRP385 4.2 47.1 1.0 CA B:TRP385 4.2 48.4 1.0 N B:LEU386 4.3 49.9 1.0 CB B:ASP381 4.4 34.8 1.0 CB B:TRP385 4.4 48.7 1.0 CA B:LEU386 4.5 50.9 1.0 C B:ASP383 4.5 41.8 1.0 N B:ASP383 4.5 39.6 1.0 CB B:ASP383 4.6 40.8 1.0 N B:THR387 4.8 52.4 1.0 CA B:ASP383 4.8 40.9 1.0

Calcium binding site 2 out of 4 in the Fibrinogen Fragment D with "A" Knob Peptide Mimic Gprvve


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Fibrinogen Fragment D with "A" Knob Peptide Mimic Gprvve within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca601 b:33.4 occ:1.00 O C:PHE322 2.3 44.8 1.0 OD1 C:ASP320 2.4 43.4 1.0 O C:GLY324 2.6 43.3 1.0 OD1 C:ASP318 2.6 42.8 1.0 OD2 C:ASP318 2.8 43.1 1.0 CG C:ASP318 2.9 42.5 1.0 CG C:ASP320 3.4 43.9 1.0 C C:PHE322 3.5 44.8 1.0 O C:ASP320 3.6 43.9 1.0 O C:HOH627 3.6 34.4 1.0 OD2 C:ASP320 3.8 44.3 1.0 C C:GLY324 3.8 43.4 1.0 C C:GLU323 4.1 44.3 1.0 CB C:ASP318 4.2 42.0 1.0 CA C:GLU323 4.3 44.8 1.0 O C:GLU323 4.3 44.4 1.0 N C:GLU323 4.3 44.8 1.0 N C:PHE322 4.3 44.6 1.0 N C:GLY324 4.3 44.0 1.0 C C:ASP320 4.4 43.9 1.0 CA C:PHE322 4.5 44.7 1.0 N C:ASP320 4.5 43.2 1.0 CA C:GLY324 4.7 43.6 1.0 CB C:ASP320 4.7 43.6 1.0 N C:ASN325 4.8 43.1 1.0 CA C:ASP320 4.8 43.6 1.0 CA C:ASN325 4.8 42.8 1.0

Calcium binding site 3 out of 4 in the Fibrinogen Fragment D with "A" Knob Peptide Mimic Gprvve


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Fibrinogen Fragment D with "A" Knob Peptide Mimic Gprvve within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca602 b:29.0 occ:1.00 OD2 E:ASP381 2.2 15.2 1.0 O E:TRP385 2.4 27.9 1.0 OD1 E:ASP383 2.5 22.4 1.0 OD1 E:ASP381 2.8 18.3 1.0 CG E:ASP381 2.8 16.6 1.0 C E:TRP385 3.5 27.7 1.0 CG E:ASP383 3.5 22.1 1.0 OD2 E:ASP383 3.8 23.8 1.0 O E:HOH644 4.1 15.2 1.0 O E:ASP383 4.3 21.8 1.0 CB E:ASP381 4.3 17.6 1.0 CA E:TRP385 4.3 26.6 1.0 N E:TRP385 4.4 25.5 1.0 N E:LEU386 4.4 29.1 1.0 CB E:TRP385 4.5 26.1 1.0 N E:THR387 4.5 33.0 1.0 CG2 E:THR387 4.5 34.1 1.0 CA E:LEU386 4.5 30.6 1.0 O E:THR387 4.6 35.4 1.0 C E:ASP383 4.8 21.8 1.0 CB E:ASP383 4.8 21.4 1.0 CG E:GLN393 4.9 28.4 1.0 N E:ASP383 4.9 20.4 1.0 O E:LYS392 4.9 32.2 1.0

Calcium binding site 4 out of 4 in the Fibrinogen Fragment D with "A" Knob Peptide Mimic Gprvve


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Fibrinogen Fragment D with "A" Knob Peptide Mimic Gprvve within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca603 b:24.1 occ:1.00 O F:GLY324 2.2 25.0 1.0 O F:PHE322 2.3 26.7 1.0 O F:HOH627 2.3 32.8 1.0 OD1 F:ASP320 2.4 27.5 1.0 OD1 F:ASP318 2.5 26.5 1.0 OD2 F:ASP318 2.8 27.4 1.0 CG F:ASP318 2.9 26.5 1.0 C F:GLY324 3.4 25.3 1.0 CG F:ASP320 3.5 27.4 1.0 C F:PHE322 3.5 26.5 1.0 C F:GLU323 3.7 26.2 1.0 O F:GLU323 3.7 26.0 1.0 OD2 F:ASP320 3.8 27.7 1.0 N F:GLY324 4.0 25.9 1.0 CA F:GLU323 4.2 26.5 1.0 CA F:GLY324 4.2 25.5 1.0 N F:GLU323 4.3 26.5 1.0 CB F:ASP318 4.3 25.6 1.0 N F:ASN325 4.3 25.0 1.0 O F:ASP320 4.4 27.3 1.0 N F:PHE322 4.4 26.8 1.0 CA F:ASN325 4.4 24.5 1.0 CA F:PHE322 4.5 26.4 1.0 CB F:PHE322 4.7 26.1 1.0 CB F:ASP320 4.8 26.8 1.0 C F:ASP320 4.8 27.1 1.0 N F:ASP320 4.9 26.2 1.0

L.Betts, B.K.Merenbloom, S.T.Lord. The Structure of Fibrinogen Fragment D with the 'A' Knob Peptide Gprvve. Thromb.Haemost. V. 4 1139 2006.
ISSN: ISSN 0340-6245
PubMed: 16689770
DOI: 10.1111/J.1538-7836.2006.01902.X