Calcium in PDB 1ltj: Crystal Structure of Recombinant Human Fibrinogen Fragment D with the Peptide Ligands Gly-Pro-Arg-Pro-Amide and Gly-His-Arg-Pro-Amide

The structure of Crystal Structure of Recombinant Human Fibrinogen Fragment D with the Peptide Ligands Gly-Pro-Arg-Pro-Amide and Gly-His-Arg-Pro-Amide, PDB code: 1ltj was solved by M.S.Kostelansky, L.Betts, 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)	18.02 / 2.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	89.284, 94.218, 226.936, 90.00, 90.00, 90.00
R / Rfree (%)	21.2 / 27

The binding sites of Calcium atom in the Crystal Structure of Recombinant Human Fibrinogen Fragment D with the Peptide Ligands Gly-Pro-Arg-Pro-Amide and Gly-His-Arg-Pro-Amide (pdb code 1ltj). 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 Human Fibrinogen Fragment D with the Peptide Ligands Gly-Pro-Arg-Pro-Amide and Gly-His-Arg-Pro-Amide, PDB code: 1ltj:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of Recombinant Human Fibrinogen Fragment D with the Peptide Ligands Gly-Pro-Arg-Pro-Amide and 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 Recombinant Human Fibrinogen Fragment D with the Peptide Ligands Gly-Pro-Arg-Pro-Amide and Gly-His-Arg-Pro-Amide within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2 b:58.1 occ:1.00 O B:HOH497 2.3 30.1 1.0 OD1 B:ASP383 2.4 52.5 1.0 O B:TRP385 2.5 64.0 1.0 OD2 B:ASP381 2.5 36.9 1.0 OD1 B:ASP381 2.7 36.6 1.0 CG B:ASP383 2.9 52.9 1.0 CG B:ASP381 3.0 38.4 1.0 OD2 B:ASP383 3.0 53.1 1.0 C B:TRP385 3.5 64.2 1.0 O B:ASP383 3.9 52.4 1.0 N B:TRP385 4.3 61.6 1.0 CA B:TRP385 4.3 63.5 1.0 CB B:ASP383 4.3 52.4 1.0 CB B:TRP385 4.3 65.3 1.0 N B:ASP383 4.4 48.4 1.0 C B:ASP383 4.5 53.0 1.0 CG2 B:THR387 4.5 70.6 1.0 CB B:ASP381 4.5 38.1 1.0 N B:LEU386 4.5 65.8 1.0 CA B:ASP383 4.6 51.5 1.0 CA B:LEU386 4.7 67.0 1.0 N B:THR387 4.7 68.6 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Recombinant Human Fibrinogen Fragment D with the Peptide Ligands Gly-Pro-Arg-Pro-Amide and 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 Recombinant Human Fibrinogen Fragment D with the Peptide Ligands Gly-Pro-Arg-Pro-Amide and Gly-His-Arg-Pro-Amide within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1 b:39.4 occ:1.00 O C:PHE322 2.1 55.1 1.0 O C:HOH428 2.3 40.8 1.0 O C:GLY324 2.4 50.3 1.0 OD1 C:ASP320 2.5 42.9 1.0 OD1 C:ASP318 2.6 44.3 1.0 OD2 C:ASP318 2.7 45.6 1.0 CG C:ASP318 2.9 44.6 1.0 C C:PHE322 3.3 54.0 1.0 CG C:ASP320 3.4 43.5 1.0 C C:GLY324 3.6 51.0 1.0 OD2 C:ASP320 3.7 41.2 1.0 O C:ASP320 3.8 44.5 1.0 C C:GLU323 3.9 54.6 1.0 O C:GLU323 3.9 54.9 1.0 N C:PHE322 4.0 50.9 1.0 N C:GLY324 4.1 52.9 1.0 CA C:PHE322 4.2 52.0 1.0 N C:GLU323 4.2 55.4 1.0 CA C:GLU323 4.3 56.4 1.0 CB C:ASP318 4.3 44.7 1.0 C C:ASP320 4.4 43.8 1.0 CA C:GLY324 4.5 51.5 1.0 N C:ASN325 4.5 50.7 1.0 CA C:ASN325 4.5 49.9 1.0 CB C:PHE322 4.6 50.8 1.0 N C:ASP320 4.6 41.2 1.0 CB C:ASP320 4.7 43.3 1.0 CA C:ASP320 4.8 42.7 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Recombinant Human Fibrinogen Fragment D with the Peptide Ligands Gly-Pro-Arg-Pro-Amide and 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 Recombinant Human Fibrinogen Fragment D with the Peptide Ligands Gly-Pro-Arg-Pro-Amide and Gly-His-Arg-Pro-Amide within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca2 b:35.0 occ:1.00 OD1 E:ASP383 2.3 34.7 1.0 O E:HOH534 2.5 28.3 1.0 O E:TRP385 2.5 37.0 1.0 OD2 E:ASP381 2.6 29.8 1.0 OD1 E:ASP381 2.6 32.4 1.0 O E:HOH516 2.8 21.6 1.0 CG E:ASP381 3.0 29.1 1.0 CG E:ASP383 3.1 29.7 1.0 OD2 E:ASP383 3.4 29.5 1.0 C E:TRP385 3.6 33.8 1.0 O E:ASP383 4.0 30.0 1.0 N E:TRP385 4.0 27.6 1.0 CA E:TRP385 4.2 31.0 1.0 C E:ASP383 4.4 27.8 1.0 CB E:TRP385 4.4 28.9 1.0 CB E:ASP383 4.5 28.9 1.0 N E:ASP383 4.5 26.8 1.0 CB E:ASP381 4.5 29.4 1.0 N E:LEU386 4.6 36.0 1.0 CG E:GLN393 4.6 34.7 1.0 CA E:ASP383 4.7 27.6 1.0 CA E:LEU386 4.8 38.8 1.0 N E:THR387 4.9 41.8 1.0 O E:LYS392 5.0 38.4 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Recombinant Human Fibrinogen Fragment D with the Peptide Ligands Gly-Pro-Arg-Pro-Amide and 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 Recombinant Human Fibrinogen Fragment D with the Peptide Ligands Gly-Pro-Arg-Pro-Amide and Gly-His-Arg-Pro-Amide within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca1 b:30.1 occ:1.00 O F:GLY324 2.3 31.1 1.0 OD1 F:ASP320 2.3 31.9 1.0 OD1 F:ASP318 2.4 26.1 1.0 O F:PHE322 2.4 36.1 1.0 O F:HOH414 2.5 14.0 1.0 OD2 F:ASP318 2.7 30.8 1.0 CG F:ASP318 2.8 28.5 1.0 CG F:ASP320 3.2 34.1 1.0 OD2 F:ASP320 3.5 34.4 1.0 C F:GLY324 3.5 32.2 1.0 C F:PHE322 3.6 36.3 1.0 N F:GLY324 4.0 33.7 1.0 C F:GLU323 4.0 35.0 1.0 CB F:ASP318 4.2 29.2 1.0 O F:GLU323 4.4 34.1 1.0 CA F:GLY324 4.4 32.0 1.0 N F:ASN325 4.4 33.2 1.0 CA F:GLU323 4.4 35.6 1.0 CA F:ASN325 4.4 33.0 1.0 N F:GLU323 4.4 36.5 1.0 N F:PHE322 4.4 36.5 1.0 CA F:PHE322 4.5 36.2 1.0 O F:ASP320 4.5 34.8 1.0 CB F:ASP320 4.6 34.6 1.0 N F:ASP320 4.6 32.2 1.0 CB F:PHE322 4.7 37.1 1.0 C F:ASP320 4.7 35.1 1.0 CA F:ASP320 4.9 34.4 1.0

M.S.Kostelansky, L.Betts, O.V.Gorkun, S.T.Lord. 2.8 A Crystal Structures of Recombinant Fibrinogen Fragment D with and Without Two Peptide Ligands: Ghrp Binding to the "B" Site Disrupts Its Nearby Calcium-Binding Site. Biochemistry V. 41 12124 2002.
ISSN: ISSN 0006-2960
PubMed: 12356313
DOI: 10.1021/BI0261894