Calcium in PDB 1rf1: Crystal Structure of Fragment D of GAMMAE132A Fibrinogen with the Peptide Ligand Gly-His-Arg-Pro-Amide

The structure of Crystal Structure of Fragment D of GAMMAE132A Fibrinogen with the Peptide Ligand Gly-His-Arg-Pro-Amide, PDB code: 1rf1 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 / 2.53
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	89.714, 94.683, 228.198, 90.00, 90.00, 90.00
R / Rfree (%)	23.4 / 28.1

The binding sites of Calcium atom in the Crystal Structure of Fragment D of GAMMAE132A Fibrinogen with the Peptide Ligand Gly-His-Arg-Pro-Amide (pdb code 1rf1). 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 GAMMAE132A Fibrinogen with the Peptide Ligand Gly-His-Arg-Pro-Amide, PDB code: 1rf1:
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 GAMMAE132A 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 GAMMAE132A Fibrinogen with the Peptide Ligand Gly-His-Arg-Pro-Amide within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca462 b:47.9 occ:1.00 OD1 B:ASP383 2.3 37.1 1.0 OD2 B:ASP381 2.4 38.5 1.0 O B:TRP385 2.4 51.7 1.0 O B:HOH471 2.5 24.7 1.0 OD1 B:ASP381 2.8 37.0 1.0 CG B:ASP381 2.9 38.0 1.0 CG B:ASP383 3.2 38.3 1.0 OD2 B:ASP383 3.4 39.3 1.0 C B:TRP385 3.5 51.9 1.0 O B:ASP383 4.0 39.3 1.0 N B:TRP385 4.2 47.9 1.0 CA B:TRP385 4.2 50.9 1.0 CB B:TRP385 4.3 53.6 1.0 CB B:ASP381 4.4 35.2 1.0 N B:LEU386 4.5 53.2 1.0 CB B:ASP383 4.5 37.2 1.0 C B:ASP383 4.6 39.0 1.0 N B:ASP383 4.6 35.2 1.0 OG1 B:THR387 4.7 61.5 1.0 CG B:GLN393 4.7 53.8 1.0 CA B:LEU386 4.8 54.0 1.0 CA B:ASP383 4.8 37.6 1.0 N B:THR387 4.9 55.5 1.0 O B:LYS392 5.0 59.3 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Fragment D of GAMMAE132A 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 GAMMAE132A Fibrinogen with the Peptide Ligand Gly-His-Arg-Pro-Amide within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca407 b:37.8 occ:1.00 O C:PHE322 2.1 48.3 1.0 OD1 C:ASP320 2.3 31.2 1.0 O C:GLY324 2.5 42.8 1.0 OD1 C:ASP318 2.7 39.1 1.0 OD2 C:ASP318 2.7 41.2 1.0 CG C:ASP318 3.0 40.7 1.0 CG C:ASP320 3.2 36.1 1.0 C C:PHE322 3.3 48.0 1.0 OD2 C:ASP320 3.5 36.7 1.0 O C:ASP320 3.6 37.8 1.0 C C:GLY324 3.7 43.0 1.0 C C:GLU323 3.9 46.7 1.0 N C:PHE322 4.1 46.2 1.0 O C:GLU323 4.1 46.5 1.0 N C:GLY324 4.2 44.5 1.0 CA C:PHE322 4.2 46.9 1.0 N C:GLU323 4.2 49.0 1.0 CA C:GLU323 4.2 49.4 1.0 C C:ASP320 4.3 38.4 1.0 CB C:ASP318 4.4 39.7 1.0 N C:ASP320 4.4 35.4 1.0 CB C:ASP320 4.5 36.8 1.0 CB C:PHE322 4.6 48.2 1.0 CA C:GLY324 4.6 43.0 1.0 CA C:ASN325 4.6 41.2 1.0 CA C:ASP320 4.6 36.9 1.0 N C:ASN325 4.6 42.5 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Fragment D of GAMMAE132A 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 GAMMAE132A Fibrinogen with the Peptide Ligand Gly-His-Arg-Pro-Amide within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca462 b:25.6 occ:1.00 OD2 E:ASP381 2.2 27.5 1.0 O E:TRP385 2.4 28.5 1.0 O E:HOH541 2.5 16.9 1.0 O E:HOH543 2.5 20.6 1.0 O E:HOH495 2.6 18.6 1.0 OD1 E:ASP383 2.6 17.3 1.0 OD1 E:ASP381 2.7 23.4 1.0 CG E:ASP381 2.8 25.0 1.0 CG E:ASP383 3.4 15.8 1.0 C E:TRP385 3.5 29.5 1.0 OD2 E:ASP383 3.6 14.0 1.0 N E:TRP385 4.2 24.1 1.0 CA E:TRP385 4.2 26.7 1.0 CB E:TRP385 4.2 24.8 1.0 CB E:ASP381 4.3 23.1 1.0 O E:ASP383 4.3 19.1 1.0 N E:LEU386 4.6 32.6 1.0 N E:ASP383 4.7 15.8 1.0 C E:ASP383 4.7 18.9 1.0 CB E:ASP383 4.7 15.1 1.0 OG1 E:THR387 4.8 42.3 1.0 N E:THR387 4.9 37.8 1.0 CA E:LEU386 4.9 35.1 1.0 O E:LYS392 4.9 33.1 1.0 CA E:ASP383 4.9 17.1 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Fragment D of GAMMAE132A 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 GAMMAE132A Fibrinogen with the Peptide Ligand Gly-His-Arg-Pro-Amide within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca407 b:29.8 occ:1.00 OD1 F:ASP320 2.2 23.9 1.0 O F:GLY324 2.3 32.2 1.0 OD1 F:ASP318 2.4 27.8 1.0 O F:HOH434 2.4 24.1 1.0 O F:PHE322 2.4 36.8 1.0 OD2 F:ASP318 2.6 30.3 1.0 CG F:ASP318 2.7 27.3 1.0 CG F:ASP320 3.0 26.7 1.0 OD2 F:ASP320 3.2 28.1 1.0 C F:GLY324 3.5 33.5 1.0 C F:PHE322 3.6 37.3 1.0 N F:PHE322 4.1 37.8 1.0 CB F:ASP318 4.2 27.0 1.0 CA F:ASN325 4.3 32.0 1.0 CA F:PHE322 4.3 37.5 1.0 C F:GLU323 4.3 34.4 1.0 N F:ASN325 4.3 33.6 1.0 N F:GLY324 4.3 32.4 1.0 O F:GLU323 4.3 32.8 1.0 CB F:ASP320 4.4 27.4 1.0 O F:ASP320 4.4 30.0 1.0 CB F:PHE322 4.4 37.3 1.0 CA F:GLY324 4.5 32.7 1.0 N F:ASP320 4.5 26.7 1.0 C F:ASP320 4.6 30.9 1.0 N F:GLU323 4.6 37.8 1.0 CA F:ASP320 4.7 28.9 1.0 CA F:GLU323 4.8 37.5 1.0

M.S.Kostelansky, K.C.Lounes, L.F.Ping, S.K.Dickerson, O.V.Gorkun, S.T.Lord. Calcium-Binding Site BETA2, Adjacent to the "B" Polymerization Site, Modulates Lateral Aggregation of Protofibrils During Fibrin Polymerization. Biochemistry V. 43 2475 2004.
ISSN: ISSN 0006-2960
PubMed: 14992585
DOI: 10.1021/BI0359978