Calcium in PDB 1fzf: Crystal Structure of Fragment Double-D From Human Fibrin with the Peptide Ligand Gly-His-Arg-Pro-Amide

The structure of Crystal Structure of Fragment Double-D From Human Fibrin with the Peptide Ligand Gly-His-Arg-Pro-Amide, PDB code: 1fzf was solved by S.J.Everse, G.Spraggon, L.Veerapandian, R.F.Doolittle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	54.800, 149.400, 234.700, 90.00, 90.00, 90.00
R / Rfree (%)	23.3 / 30.2

The binding sites of Calcium atom in the Crystal Structure of Fragment Double-D From Human Fibrin with the Peptide Ligand Gly-His-Arg-Pro-Amide (pdb code 1fzf). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of Fragment Double-D From Human Fibrin with the Peptide Ligand Gly-His-Arg-Pro-Amide, PDB code: 1fzf:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Crystal Structure of Fragment Double-D From Human Fibrin 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 Double-D From Human Fibrin with the Peptide Ligand Gly-His-Arg-Pro-Amide within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2 b:52.7 occ:1.00 O B:TRP385 2.5 73.9 1.0 OD1 B:ASP383 2.5 51.5 1.0 OD1 B:ASP381 2.7 47.5 1.0 OD2 B:ASP381 2.7 51.9 1.0 CG B:ASP381 3.0 47.3 1.0 C B:TRP385 3.4 77.4 1.0 CG B:ASP383 3.5 36.8 1.0 OD2 B:ASP383 3.8 34.7 1.0 CB B:TRP385 4.0 69.7 1.0 CA B:TRP385 4.1 72.0 1.0 O B:ASP383 4.2 41.7 1.0 N B:TRP385 4.3 67.0 1.0 N B:LEU386 4.4 89.5 1.0 CG2 B:THR387 4.4 0.7 1.0 CB B:ASP381 4.5 46.4 1.0 N B:THR387 4.6 0.6 1.0 CA B:LEU386 4.7 0.7 1.0 C B:ASP383 4.8 41.9 1.0 N B:ASP383 4.8 28.9 1.0 CG B:TRP385 4.8 71.0 1.0 CB B:ASP383 4.8 31.3 1.0 CG B:GLN393 4.9 92.7 1.0 CA B:ASP383 5.0 36.6 1.0

Calcium binding site 2 out of 6 in the Crystal Structure of Fragment Double-D From Human Fibrin 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 Double-D From Human Fibrin with the Peptide Ligand Gly-His-Arg-Pro-Amide within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1 b:31.0 occ:1.00 O C:PHE322 2.4 28.6 1.0 OD1 C:ASP320 2.5 24.9 1.0 OD2 C:ASP318 2.5 36.6 1.0 OD1 C:ASP318 2.6 33.0 1.0 O C:GLY324 2.6 32.3 1.0 CG C:ASP318 2.8 32.1 1.0 C C:PHE322 3.6 31.0 1.0 CG C:ASP320 3.6 28.5 1.0 C C:GLY324 3.7 30.3 1.0 O C:ASP320 3.9 41.2 1.0 C C:GLU323 4.1 37.8 1.0 OD2 C:ASP320 4.1 27.4 1.0 CB C:ASP318 4.2 27.5 1.0 O C:GLU323 4.2 43.7 1.0 N C:GLY324 4.3 30.7 1.0 N C:PHE322 4.4 37.7 1.0 CA C:PHE322 4.5 31.4 1.0 N C:GLU323 4.5 36.0 1.0 CA C:GLU323 4.5 41.0 1.0 C C:ASP320 4.5 39.1 1.0 N C:ASP320 4.6 40.3 1.0 CA C:GLY324 4.6 25.4 1.0 N C:ASN325 4.7 26.0 1.0 CA C:ASN325 4.7 21.7 1.0 CB C:PHE322 4.8 33.1 1.0 CB C:ASP320 4.8 36.8 1.0 CA C:ASP320 4.9 41.0 1.0 C C:ASP318 5.0 34.1 1.0

Calcium binding site 3 out of 6 in the Crystal Structure of Fragment Double-D From Human Fibrin 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 Double-D From Human Fibrin with the Peptide Ligand Gly-His-Arg-Pro-Amide within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca4 b:39.3 occ:1.00 OD1 C:ASP294 2.5 55.0 1.0 O C:ASP298 2.6 61.7 1.0 O C:GLY296 2.7 54.3 1.0 O C:ASP297 3.2 84.8 1.0 C C:GLY296 3.4 56.3 1.0 CB C:ASP301 3.4 45.6 1.0 CG C:ASP294 3.5 60.4 1.0 OD2 C:ASP301 3.5 56.2 1.0 CG C:ASP301 3.5 54.8 1.0 C C:ASP298 3.6 58.9 1.0 N C:GLY296 3.6 65.1 1.0 CA C:GLY296 3.8 61.6 1.0 CA C:PRO299 3.9 47.3 1.0 C C:ASP297 4.0 76.7 1.0 OD2 C:ASP294 4.1 66.7 1.0 N C:PRO299 4.1 50.2 1.0 OD1 C:ASP301 4.3 62.7 1.0 C C:PRO299 4.3 44.7 1.0 O C:PRO299 4.3 50.4 1.0 N C:ASP297 4.3 65.9 1.0 CA C:ASP294 4.4 44.7 1.0 N C:PHE295 4.4 45.2 1.0 C C:ASP294 4.5 44.3 1.0 CB C:ASP294 4.5 55.1 1.0 N C:ASP298 4.6 69.1 1.0 N C:ASP301 4.6 43.8 1.0 CA C:ASP301 4.6 44.6 1.0 CA C:ASP298 4.7 65.7 1.0 C C:PHE295 4.7 51.3 1.0 CA C:ASP297 4.8 78.8 1.0

Calcium binding site 4 out of 6 in the Crystal Structure of Fragment Double-D From Human Fibrin 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 Double-D From Human Fibrin with the Peptide Ligand Gly-His-Arg-Pro-Amide within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca2 b:45.4 occ:1.00 O E:TRP385 2.4 73.7 1.0 OD1 E:ASP383 2.5 45.1 1.0 OD2 E:ASP381 2.7 54.2 1.0 OD1 E:ASP381 2.9 47.6 1.0 CG E:ASP381 3.1 46.9 1.0 C E:TRP385 3.3 77.0 1.0 CG E:ASP383 3.7 41.4 1.0 O E:ASP383 3.7 49.1 1.0 CA E:TRP385 4.1 73.0 1.0 N E:LEU386 4.1 88.1 1.0 N E:TRP385 4.1 68.0 1.0 CB E:TRP385 4.2 72.3 1.0 OD2 E:ASP383 4.2 41.6 1.0 CA E:LEU386 4.3 98.6 1.0 C E:ASP383 4.5 46.1 1.0 N E:THR387 4.5 0.4 1.0 N E:ASP383 4.6 36.9 1.0 CB E:ASP381 4.7 43.1 1.0 CG2 E:THR387 4.8 0.2 1.0 CA E:ASP383 4.8 41.7 1.0 CB E:ASP383 4.8 39.5 1.0 C E:LEU386 4.9 0.8 1.0

Calcium binding site 5 out of 6 in the Crystal Structure of Fragment Double-D From Human Fibrin 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 5 of Crystal Structure of Fragment Double-D From Human Fibrin with the Peptide Ligand Gly-His-Arg-Pro-Amide within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca3 b:71.9 occ:1.00 OD2 E:ASP261 2.6 27.7 1.0 OE2 F:GLU132 2.7 65.1 1.0 O E:GLY263 2.9 44.3 1.0 CG E:ASP261 3.5 35.6 1.0 OD1 E:ASP261 3.6 42.1 1.0 CD F:GLU132 3.9 62.5 1.0 C E:GLY263 4.0 34.2 1.0 CA E:GLY263 4.4 30.1 1.0 CG F:GLU132 4.6 58.0 1.0 CE D:LYS157 4.8 65.1 1.0 OE1 F:GLU132 4.8 63.9 1.0 CB E:ASP261 4.9 30.6 1.0 N E:GLY263 4.9 23.5 1.0 OE1 F:GLN136 4.9 57.5 1.0

Calcium binding site 6 out of 6 in the Crystal Structure of Fragment Double-D From Human Fibrin 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 6 of Crystal Structure of Fragment Double-D From Human Fibrin with the Peptide Ligand Gly-His-Arg-Pro-Amide within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca1 b:26.4 occ:1.00 O F:PHE322 2.2 26.9 1.0 OD1 F:ASP320 2.4 29.9 1.0 OD2 F:ASP318 2.6 37.6 1.0 O F:GLY324 2.6 21.7 1.0 OD1 F:ASP318 2.6 23.9 1.0 CG F:ASP318 2.9 32.4 1.0 C F:PHE322 3.4 26.7 1.0 CG F:ASP320 3.5 29.2 1.0 C F:GLY324 3.7 22.0 1.0 O F:ASP320 3.9 33.7 1.0 OD2 F:ASP320 4.0 31.6 1.0 C F:GLU323 4.0 36.9 1.0 O F:GLU323 4.2 46.1 1.0 N F:PHE322 4.2 28.7 1.0 N F:GLY324 4.2 30.1 1.0 CB F:ASP318 4.3 32.4 1.0 CA F:PHE322 4.3 26.4 1.0 N F:GLU323 4.4 30.0 1.0 CA F:GLU323 4.4 34.5 1.0 C F:ASP320 4.5 32.8 1.0 CA F:GLY324 4.6 22.1 1.0 N F:ASP320 4.6 36.1 1.0 CB F:PHE322 4.6 26.2 1.0 N F:ASN325 4.7 19.2 1.0 CB F:ASP320 4.8 29.9 1.0 CA F:ASN325 4.8 22.3 1.0 CA F:ASP320 4.8 33.2 1.0

S.J.Everse, G.Spraggon, L.Veerapandian, R.F.Doolittle. Conformational Changes in Fragments D and Double-D From Human Fibrin(Ogen) Upon Binding the Peptide Ligand Gly-His-Arg-Pro-Amide. Biochemistry V. 38 2941 1999.
ISSN: ISSN 0006-2960
PubMed: 10074346
DOI: 10.1021/BI982626W