Calcium in PDB 2oyi: Crystal Structure of Fragment D of GAMMAD298,301A Fibrinogen with the Peptide Ligand Gly-Pro-Arg-Pro-Amide

The structure of Crystal Structure of Fragment D of GAMMAD298,301A Fibrinogen with the Peptide Ligand Gly-Pro-Arg-Pro-Amide, PDB code: 2oyi was solved by M.S.Kostelansky, 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)	17.97 / 2.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	88.988, 94.038, 226.353, 90.00, 90.00, 90.00
R / Rfree (%)	21.6 / 25.6

The binding sites of Calcium atom in the Crystal Structure of Fragment D of GAMMAD298,301A Fibrinogen with the Peptide Ligand Gly-Pro-Arg-Pro-Amide (pdb code 2oyi). 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 Fragment D of GAMMAD298,301A Fibrinogen with the Peptide Ligand Gly-Pro-Arg-Pro-Amide, PDB code: 2oyi:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of Fragment D of GAMMAD298,301A Fibrinogen 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 Fragment D of GAMMAD298,301A Fibrinogen with the Peptide Ligand Gly-Pro-Arg-Pro-Amide within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2 b:55.0 occ:1.00 OD2 B:ASP381 2.2 46.3 1.0 O B:TRP385 2.3 61.8 1.0 OD1 B:ASP383 2.3 54.1 1.0 O B:HOH488 2.5 41.0 1.0 OD1 B:ASP381 2.9 43.9 1.0 CG B:ASP381 2.9 44.5 1.0 CG B:ASP383 3.0 52.3 1.0 OD2 B:ASP383 3.2 52.1 1.0 C B:TRP385 3.4 62.5 1.0 O B:ASP383 4.1 49.0 1.0 N B:TRP385 4.2 59.1 1.0 CA B:TRP385 4.2 61.6 1.0 CB B:TRP385 4.3 63.3 1.0 CB B:ASP381 4.4 41.6 1.0 N B:LEU386 4.4 64.6 1.0 CB B:ASP383 4.4 50.5 1.0 N B:THR387 4.5 67.7 1.0 CG2 B:THR387 4.6 70.1 1.0 C B:ASP383 4.6 49.2 1.0 CA B:LEU386 4.6 66.3 1.0 N B:ASP383 4.6 45.8 1.0 CA B:ASP383 4.8 48.1 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Fragment D of GAMMAD298,301A Fibrinogen 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 Fragment D of GAMMAD298,301A Fibrinogen with the Peptide Ligand Gly-Pro-Arg-Pro-Amide within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1 b:44.1 occ:1.00 O C:PHE322 2.0 44.4 1.0 OD1 C:ASP320 2.2 41.3 1.0 O C:GLY324 2.4 45.5 1.0 OD1 C:ASP318 2.5 41.8 1.0 O C:HOH424 2.6 31.7 1.0 OD2 C:ASP318 2.7 42.3 1.0 CG C:ASP318 2.9 41.3 1.0 CG C:ASP320 3.1 43.1 1.0 C C:PHE322 3.2 44.6 1.0 OD2 C:ASP320 3.5 45.6 1.0 C C:GLY324 3.7 46.2 1.0 O C:ASP320 3.8 41.0 1.0 C C:GLU323 3.9 48.1 1.0 O C:GLU323 3.9 47.6 1.0 N C:PHE322 4.0 42.3 1.0 CA C:PHE322 4.1 43.0 1.0 N C:GLY324 4.2 47.5 1.0 N C:GLU323 4.2 46.5 1.0 C C:ASP320 4.3 39.8 1.0 CA C:GLU323 4.3 49.0 1.0 CB C:ASP318 4.3 39.9 1.0 CB C:ASP320 4.5 40.8 1.0 CB C:PHE322 4.5 41.8 1.0 N C:ASP320 4.5 34.7 1.0 CA C:GLY324 4.5 46.5 1.0 CA C:ASN325 4.6 44.8 1.0 N C:ASN325 4.6 45.7 1.0 CA C:ASP320 4.7 38.5 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Fragment D of GAMMAD298,301A Fibrinogen 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 Fragment D of GAMMAD298,301A Fibrinogen with the Peptide Ligand Gly-Pro-Arg-Pro-Amide within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca2 b:29.6 occ:1.00 OD2 E:ASP381 2.4 24.6 1.0 O E:TRP385 2.4 29.5 1.0 OD1 E:ASP383 2.4 27.1 1.0 O E:HOH516 2.7 16.3 1.0 OD1 E:ASP381 2.7 26.5 1.0 CG E:ASP381 2.9 25.1 1.0 CG E:ASP383 3.3 24.0 1.0 OD2 E:ASP383 3.5 24.6 1.0 C E:TRP385 3.6 26.8 1.0 N E:TRP385 4.4 23.1 1.0 CB E:ASP381 4.4 24.2 1.0 CA E:TRP385 4.5 25.1 1.0 CB E:TRP385 4.6 23.5 1.0 N E:ASP383 4.6 20.6 1.0 N E:LEU386 4.6 29.7 1.0 CB E:ASP383 4.6 23.1 1.0 O E:ASP383 4.7 22.7 1.0 CA E:LEU386 4.7 32.9 1.0 N E:THR387 4.7 35.4 1.0 C E:ASP383 4.8 23.0 1.0 OG1 E:THR387 4.9 37.5 1.0 CA E:ASP383 4.9 22.5 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Fragment D of GAMMAD298,301A Fibrinogen 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 Fragment D of GAMMAD298,301A Fibrinogen with the Peptide Ligand Gly-Pro-Arg-Pro-Amide within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca1 b:29.8 occ:1.00 O F:GLY324 2.2 33.1 1.0 OD1 F:ASP318 2.4 25.5 1.0 OD1 F:ASP320 2.4 29.6 1.0 O F:PHE322 2.5 34.3 1.0 O F:HOH412 2.6 12.7 1.0 OD2 F:ASP318 2.6 32.8 1.0 CG F:ASP318 2.8 28.8 1.0 C F:GLY324 3.4 34.1 1.0 CG F:ASP320 3.4 31.6 1.0 C F:PHE322 3.6 34.8 1.0 OD2 F:ASP320 3.8 30.4 1.0 C F:GLU323 4.2 33.6 1.0 CB F:ASP318 4.2 27.8 1.0 O F:GLU323 4.2 31.0 1.0 N F:GLY324 4.2 33.8 1.0 N F:PHE322 4.3 34.9 1.0 N F:ASN325 4.3 33.6 1.0 CA F:GLY324 4.4 32.1 1.0 CA F:PHE322 4.4 34.6 1.0 CA F:ASN325 4.4 31.1 1.0 CB F:PHE322 4.6 32.5 1.0 N F:GLU323 4.6 36.7 1.0 O F:ASP320 4.6 35.7 1.0 N F:ASP320 4.7 31.0 1.0 CB F:ASP320 4.7 32.5 1.0 CA F:GLU323 4.8 35.8 1.0 C F:ASP320 4.8 35.1 1.0 CA F:ASP320 5.0 33.3 1.0

M.S.Kostelansky, K.C.Lounes, L.F.Ping, S.K.Dickerson, O.V.Gorkun, S.T.Lord. Probing the GAMMA2 Calcium-Binding Site: Studies with GAMMAD298,301A Fibrinogen Reveal Changes in the GAMMA294-301 Loop That Alter the Integrity of the "A" Polymerization Site. Biochemistry V. 46 5114 2007.
ISSN: ISSN 0006-2960
PubMed: 17411074
DOI: 10.1021/BI602607A