Calcium in PDB 3bvh: Crystal Structure of Recombinant GAMMAD364A Fibrinogen Fragment D with the Peptide Ligand Gly-Pro-Arg-Pro-Amide

The structure of Crystal Structure of Recombinant GAMMAD364A Fibrinogen Fragment D with the Peptide Ligand Gly-Pro-Arg-Pro-Amide, PDB code: 3bvh was solved by S.R.Bowley, B.K.Merenbloom, L.Betts, N.Okumura, A.Heroux, O.V.Gorkun, S.T.Lord, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	89.844, 94.913, 225.754, 90.00, 90.00, 90.00
R / Rfree (%)	22 / 26

The binding sites of Calcium atom in the Crystal Structure of Recombinant GAMMAD364A Fibrinogen Fragment D with the Peptide Ligand Gly-Pro-Arg-Pro-Amide (pdb code 3bvh). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Recombinant GAMMAD364A Fibrinogen Fragment D with the Peptide Ligand Gly-Pro-Arg-Pro-Amide, PDB code: 3bvh:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of Recombinant GAMMAD364A Fibrinogen Fragment D with the Peptide Ligand Gly-Pro-Arg-Pro-Amide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Recombinant GAMMAD364A Fibrinogen Fragment D with the Peptide Ligand Gly-Pro-Arg-Pro-Amide within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1 b:25.9 occ:1.00 O B:HOH520 2.1 21.8 1.0 OD2 B:ASP381 2.3 24.1 1.0 O B:HOH501 2.5 21.8 1.0 O B:TRP385 2.5 27.3 1.0 O B:HOH507 2.5 26.8 1.0 OD1 B:ASP383 2.5 20.6 1.0 O B:HOH547 2.6 56.9 1.0 OD1 B:ASP381 2.9 25.8 1.0 CG B:ASP381 3.0 25.4 1.0 CG B:ASP383 3.4 21.0 1.0 C B:TRP385 3.6 28.0 1.0 OD2 B:ASP383 3.7 20.9 1.0 N B:TRP385 4.3 25.2 1.0 O B:ASP383 4.3 20.3 1.0 CA B:TRP385 4.3 26.4 1.0 CB B:TRP385 4.4 26.2 1.0 CB B:ASP381 4.4 23.4 1.0 N B:LEU386 4.6 30.9 1.0 N B:ASP383 4.6 16.4 1.0 C B:ASP383 4.7 19.3 1.0 CG2 B:THR387 4.7 40.0 1.0 CB B:ASP383 4.7 17.8 1.0 N B:THR387 4.8 37.5 1.0 CA B:LEU386 4.8 34.1 1.0 CA B:ASP383 4.9 18.1 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Recombinant GAMMAD364A Fibrinogen Fragment D with the Peptide Ligand Gly-Pro-Arg-Pro-Amide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Recombinant GAMMAD364A Fibrinogen Fragment D with the Peptide Ligand Gly-Pro-Arg-Pro-Amide within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1 b:31.5 occ:1.00 OD1 C:ASP320 2.3 30.7 1.0 O C:PHE322 2.3 28.9 1.0 OD1 C:ASP318 2.4 29.9 1.0 O C:GLY324 2.4 26.6 1.0 O C:HOH400 2.5 24.3 1.0 OD2 C:ASP318 2.5 31.5 1.0 CG C:ASP318 2.7 29.2 1.0 CG C:ASP320 3.2 32.2 1.0 OD2 C:ASP320 3.4 36.0 1.0 C C:PHE322 3.5 30.0 1.0 C C:GLY324 3.6 27.4 1.0 C C:GLU323 4.0 28.4 1.0 O C:GLU323 4.1 28.1 1.0 CB C:ASP318 4.1 28.8 1.0 N C:GLY324 4.2 27.4 1.0 N C:PHE322 4.3 32.0 1.0 O C:ASP320 4.3 26.2 1.0 CA C:PHE322 4.3 29.8 1.0 CA C:GLU323 4.4 30.9 1.0 N C:GLU323 4.4 30.3 1.0 CA C:ASN325 4.5 29.4 1.0 CB C:PHE322 4.5 30.9 1.0 N C:ASN325 4.5 28.8 1.0 CA C:GLY324 4.5 27.6 1.0 CB C:ASP320 4.6 30.3 1.0 C C:ASP320 4.6 28.3 1.0 N C:ASP320 4.7 28.2 1.0 O C:HOH452 4.8 32.3 1.0 CA C:ASP320 4.8 28.1 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Recombinant GAMMAD364A Fibrinogen Fragment D with the Peptide Ligand Gly-Pro-Arg-Pro-Amide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Recombinant GAMMAD364A Fibrinogen Fragment D with the Peptide Ligand Gly-Pro-Arg-Pro-Amide within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca1 b:49.6 occ:1.00 OD2 E:ASP381 2.4 37.9 1.0 O E:TRP385 2.5 54.8 1.0 O E:HOH463 2.5 26.4 1.0 OD1 E:ASP383 2.5 43.8 1.0 OD1 E:ASP381 2.9 38.1 1.0 CG E:ASP381 3.0 38.2 1.0 CG E:ASP383 3.2 44.7 1.0 OD2 E:ASP383 3.3 47.0 1.0 C E:TRP385 3.7 55.2 1.0 O E:ASP383 4.2 43.7 1.0 CG2 E:THR387 4.4 63.7 1.0 CA E:TRP385 4.4 54.3 1.0 N E:TRP385 4.5 52.9 1.0 CB E:ASP381 4.5 37.4 1.0 CB E:TRP385 4.5 55.3 1.0 CB E:ASP383 4.6 42.8 1.0 N E:LEU386 4.7 56.7 1.0 N E:ASP383 4.8 40.1 1.0 N E:THR387 4.8 60.4 1.0 C E:ASP383 4.8 44.1 1.0 CA E:LEU386 4.8 58.4 1.0 CG E:GLN393 4.9 44.1 1.0 CA E:ASP383 5.0 42.6 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Recombinant GAMMAD364A Fibrinogen Fragment D with the Peptide Ligand Gly-Pro-Arg-Pro-Amide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Recombinant GAMMAD364A Fibrinogen Fragment D with the Peptide Ligand Gly-Pro-Arg-Pro-Amide within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca1 b:51.5 occ:1.00 O F:PHE322 2.3 63.5 1.0 O F:GLY324 2.4 63.3 1.0 OD1 F:ASP320 2.7 50.3 1.0 OD1 F:ASP318 2.7 50.5 1.0 OD2 F:ASP318 2.9 52.2 1.0 CG F:ASP318 3.0 50.8 1.0 CG F:ASP320 3.4 52.8 1.0 C F:PHE322 3.5 63.1 1.0 C F:GLY324 3.6 62.9 1.0 OD2 F:ASP320 3.6 52.7 1.0 O F:ASP320 4.0 48.6 1.0 C F:GLU323 4.1 64.1 1.0 N F:GLY324 4.1 63.5 1.0 N F:PHE322 4.3 61.0 1.0 O F:GLU323 4.3 63.6 1.0 CA F:PHE322 4.3 62.9 1.0 CB F:ASP318 4.3 49.1 1.0 CA F:GLY324 4.4 62.9 1.0 N F:GLU323 4.4 64.2 1.0 N F:ASN325 4.5 62.1 1.0 CA F:GLU323 4.5 65.1 1.0 N F:ASP320 4.6 48.8 1.0 CB F:PHE322 4.6 64.7 1.0 C F:ASP320 4.6 52.2 1.0 CA F:ASN325 4.6 61.3 1.0 CB F:ASP320 4.7 52.4 1.0 O F:HOH421 4.7 43.1 1.0 CA F:ASP320 4.9 51.2 1.0 CG F:PHE322 5.0 67.4 1.0

S.R.Bowley, B.K.Merenbloom, N.Okumura, L.Betts, A.Heroux, O.V.Gorkun, S.T.Lord. Polymerization-Defective Fibrinogen Variant GAMMAD364A Binds Knob "A" Peptide Mimic. Biochemistry V. 47 8607 2008.
ISSN: ISSN 0006-2960
PubMed: 18642883
DOI: 10.1021/BI8000769