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

The structure of Crystal Structure of Fragment D of GAMMAD298,301A Fibrinogen with the Peptide Ligand Gly-His-Arg-Pro-Amide, PDB code: 2oyh 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)	18.00 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	89.164, 94.119, 226.730, 90.00, 90.00, 90.00
R / Rfree (%)	22 / 25.9

The binding sites of Calcium atom in the Crystal Structure of Fragment D of GAMMAD298,301A Fibrinogen with the Peptide Ligand Gly-His-Arg-Pro-Amide (pdb code 2oyh). 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-His-Arg-Pro-Amide, PDB code: 2oyh:
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-His-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-His-Arg-Pro-Amide within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2 b:57.5 occ:1.00 OD2 B:ASP381 2.3 44.1 1.0 O B:HOH509 2.4 45.7 1.0 O B:TRP385 2.4 62.6 1.0 OD1 B:ASP383 2.5 49.6 1.0 OD1 B:ASP381 2.6 44.7 1.0 CG B:ASP381 2.8 43.5 1.0 CG B:ASP383 3.1 48.6 1.0 OD2 B:ASP383 3.2 49.5 1.0 C B:TRP385 3.6 63.3 1.0 O B:ASP383 3.8 46.5 1.0 N B:TRP385 4.3 58.5 1.0 CB B:ASP381 4.3 40.7 1.0 CA B:TRP385 4.4 62.0 1.0 N B:ASP383 4.4 43.6 1.0 C B:ASP383 4.5 47.5 1.0 CB B:ASP383 4.5 48.1 1.0 N B:LEU386 4.6 65.6 1.0 CB B:TRP385 4.6 64.6 1.0 CA B:ASP383 4.7 45.9 1.0 CA B:LEU386 4.7 68.0 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-His-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-His-Arg-Pro-Amide within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1 b:49.9 occ:1.00 O C:PHE322 2.1 50.5 1.0 OD1 C:ASP320 2.3 44.0 1.0 O C:GLY324 2.4 47.9 1.0 O C:HOH431 2.6 37.8 1.0 OD2 C:ASP318 2.6 48.6 1.0 OD1 C:ASP318 2.7 45.6 1.0 CG C:ASP318 2.9 46.8 1.0 CG C:ASP320 3.2 45.4 1.0 C C:PHE322 3.3 50.6 1.0 OD2 C:ASP320 3.5 47.2 1.0 C C:GLY324 3.6 48.3 1.0 O C:ASP320 3.9 43.9 1.0 C C:GLU323 4.0 48.9 1.0 N C:PHE322 4.0 49.3 1.0 CA C:PHE322 4.2 49.5 1.0 O C:GLU323 4.2 48.1 1.0 N C:GLY324 4.2 47.9 1.0 N C:GLU323 4.3 51.2 1.0 CB C:ASP318 4.3 45.8 1.0 CA C:GLU323 4.4 51.8 1.0 C C:ASP320 4.4 44.5 1.0 CB C:PHE322 4.5 50.2 1.0 CA C:GLY324 4.5 47.5 1.0 CB C:ASP320 4.5 43.8 1.0 N C:ASN325 4.5 48.3 1.0 CA C:ASN325 4.6 47.6 1.0 N C:ASP320 4.6 42.3 1.0 CA C:ASP320 4.8 43.2 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-His-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-His-Arg-Pro-Amide within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca2 b:40.5 occ:1.00 OD2 E:ASP381 2.4 34.8 1.0 OD1 E:ASP383 2.4 35.8 1.0 O E:TRP385 2.5 37.5 1.0 O E:HOH542 2.6 35.4 1.0 O E:HOH547 2.7 27.3 1.0 OD1 E:ASP381 2.7 33.5 1.0 O E:HOH540 2.8 31.4 1.0 CG E:ASP381 2.9 31.9 1.0 CG E:ASP383 3.3 33.5 1.0 OD2 E:ASP383 3.5 34.5 1.0 C E:TRP385 3.6 37.6 1.0 O E:ASP383 4.1 30.0 1.0 N E:TRP385 4.1 33.5 1.0 O E:HOH550 4.2 43.5 1.0 CA E:TRP385 4.3 36.1 1.0 CB E:TRP385 4.4 33.0 1.0 CB E:ASP381 4.4 31.6 1.0 N E:ASP383 4.4 26.6 1.0 C E:ASP383 4.5 30.3 1.0 CB E:ASP383 4.6 30.0 1.0 N E:LEU386 4.6 41.6 1.0 CA E:ASP383 4.7 29.1 1.0 CA E:LEU386 4.9 45.0 1.0 CG E:GLN393 4.9 38.8 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-His-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-His-Arg-Pro-Amide within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca1 b:40.9 occ:1.00 OD1 F:ASP320 2.3 41.9 1.0 O F:GLY324 2.3 41.8 1.0 O F:PHE322 2.3 47.5 1.0 OD1 F:ASP318 2.4 38.0 1.0 O F:HOH436 2.7 38.1 1.0 OD2 F:ASP318 2.7 42.2 1.0 CG F:ASP318 2.9 39.0 1.0 CG F:ASP320 3.2 39.9 1.0 OD2 F:ASP320 3.5 40.2 1.0 C F:PHE322 3.5 48.1 1.0 C F:GLY324 3.5 42.0 1.0 C F:GLU323 4.1 45.7 1.0 O F:GLU323 4.2 43.7 1.0 N F:PHE322 4.2 46.7 1.0 N F:GLY324 4.2 43.5 1.0 CA F:PHE322 4.3 47.4 1.0 CB F:ASP318 4.3 37.2 1.0 CA F:ASN325 4.4 39.0 1.0 N F:ASN325 4.4 41.4 1.0 O F:ASP320 4.4 40.9 1.0 CA F:GLY324 4.4 42.7 1.0 CB F:PHE322 4.5 47.3 1.0 N F:GLU323 4.5 49.1 1.0 CB F:ASP320 4.5 38.6 1.0 N F:ASP320 4.6 36.7 1.0 C F:ASP320 4.6 41.0 1.0 CA F:GLU323 4.6 48.7 1.0 CA F:ASP320 4.8 39.2 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