Calcium in PDB 1fzc: Crystal Structure of Fragment Double-D From Human Fibrin with Two Different Bound Ligands

The structure of Crystal Structure of Fragment Double-D From Human Fibrin with Two Different Bound Ligands, PDB code: 1fzc was solved by S.J.Everse, G.Spraggon, L.Veerapandian, M.Riley, R.F.Doolittle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	83.443, 95.600, 113.641, 90.00, 90.19, 90.00
R / Rfree (%)	22 / 29

The binding sites of Calcium atom in the Crystal Structure of Fragment Double-D From Human Fibrin with Two Different Bound Ligands (pdb code 1fzc). 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 Double-D From Human Fibrin with Two Different Bound Ligands, PDB code: 1fzc:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of Fragment Double-D From Human Fibrin with Two Different Bound Ligands


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 Two Different Bound Ligands within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2 b:4.6 occ:1.00 O B:HOH595 2.3 44.0 1.0 O B:TRP385 2.3 28.3 1.0 OD2 B:ASP381 2.4 37.0 1.0 OD1 B:ASP383 2.6 20.7 1.0 O B:HOH570 2.6 47.3 1.0 OD1 B:ASP381 2.8 37.5 1.0 CG B:ASP381 3.1 36.1 1.0 CG B:ASP383 3.3 20.4 1.0 C B:TRP385 3.5 31.9 1.0 OD2 B:ASP383 3.6 25.1 1.0 N B:TRP385 4.2 26.4 1.0 CA B:TRP385 4.3 27.9 1.0 CB B:TRP385 4.4 22.9 1.0 N B:ASP383 4.4 21.5 1.0 CB B:ASP383 4.4 19.6 1.0 C B:ASP383 4.4 23.2 1.0 O B:ASP383 4.5 21.0 1.0 N B:LEU386 4.5 37.9 1.0 CB B:ASP381 4.5 31.5 1.0 CA B:ASP383 4.6 21.8 1.0 CA B:LEU386 4.7 43.2 1.0 N B:THR387 4.8 51.0 1.0 O B:LYS392 4.9 38.1 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Fragment Double-D From Human Fibrin with Two Different Bound Ligands


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 Two Different Bound Ligands within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1 b:3.3 occ:1.00 OD1 C:ASP320 2.3 24.7 1.0 OD2 C:ASP318 2.4 38.8 1.0 O C:GLY324 2.4 41.2 1.0 OD1 C:ASP318 2.6 39.9 1.0 O C:PHE322 2.6 48.1 1.0 CG C:ASP318 2.8 40.7 1.0 CG C:ASP320 3.3 30.8 1.0 C C:GLY324 3.6 40.9 1.0 OD2 C:ASP320 3.6 33.0 1.0 C C:PHE322 3.7 46.3 1.0 O C:ASP320 4.1 34.8 1.0 N C:PHE322 4.3 44.3 1.0 CB C:ASP318 4.3 38.5 1.0 O C:GLU323 4.3 38.5 1.0 C C:GLU323 4.3 44.2 1.0 CA C:PHE322 4.4 44.5 1.0 N C:ASN325 4.4 39.2 1.0 CA C:ASN325 4.4 37.7 1.0 N C:ASP320 4.4 32.7 1.0 N C:GLY324 4.5 41.7 1.0 C C:ASP320 4.6 35.2 1.0 N C:GLU323 4.6 46.8 1.0 CB C:ASP320 4.6 30.6 1.0 CA C:GLY324 4.6 39.9 1.0 CB C:PHE322 4.7 44.7 1.0 CA C:ASP320 4.8 34.7 1.0 CA C:GLU323 4.8 47.2 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Fragment Double-D From Human Fibrin with Two Different Bound Ligands


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 Two Different Bound Ligands within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca2 b:3.0 occ:1.00 OD2 E:ASP381 2.5 27.5 1.0 O E:TRP385 2.5 27.7 1.0 O E:HOH475 2.6 18.5 1.0 OD1 E:ASP383 2.7 22.5 1.0 O E:HOH517 3.1 40.9 1.0 CG E:ASP381 3.1 29.6 1.0 OD1 E:ASP381 3.1 26.4 1.0 CG E:ASP383 3.5 19.8 1.0 OD2 E:ASP383 3.5 18.9 1.0 C E:TRP385 3.7 28.8 1.0 N E:TRP385 4.3 24.8 1.0 CA E:TRP385 4.4 27.0 1.0 O E:ASP383 4.4 20.9 1.0 CB E:TRP385 4.6 23.3 1.0 N E:LEU386 4.6 31.9 1.0 CB E:ASP381 4.6 24.9 1.0 N E:ASP383 4.7 22.5 1.0 CA E:LEU386 4.7 34.9 1.0 C E:ASP383 4.7 24.4 1.0 CB E:ASP383 4.7 18.7 1.0 N E:THR387 4.8 39.6 1.0 CA E:ASP383 4.9 23.1 1.0 O E:ASP381 5.0 26.2 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Fragment Double-D From Human Fibrin with Two Different Bound Ligands


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 Two Different Bound Ligands within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca1 b:3.6 occ:1.00 O F:GLY324 2.2 26.1 1.0 OD2 F:ASP318 2.4 32.2 1.0 OD1 F:ASP320 2.5 21.9 1.0 O F:PHE322 2.7 39.6 1.0 O F:HOH475 2.7 49.2 1.0 OD1 F:ASP318 2.9 31.3 1.0 CG F:ASP318 3.0 31.6 1.0 CG F:ASP320 3.3 25.6 1.0 OD2 F:ASP320 3.4 25.4 1.0 C F:GLY324 3.5 30.1 1.0 C F:PHE322 3.5 37.9 1.0 C F:GLU323 4.2 37.0 1.0 CB F:PHE322 4.2 34.8 1.0 CA F:ASN325 4.2 31.8 1.0 N F:GLY324 4.2 34.4 1.0 CA F:PHE322 4.2 36.5 1.0 N F:PHE322 4.3 33.8 1.0 N F:ASN325 4.4 29.1 1.0 O F:ASP320 4.4 27.0 1.0 N F:GLU323 4.4 39.2 1.0 O F:HOH428 4.4 37.7 1.0 O F:GLU323 4.5 35.5 1.0 N F:ASP320 4.5 26.8 1.0 CA F:GLY324 4.5 31.9 1.0 CB F:ASP320 4.5 25.9 1.0 CB F:ASP318 4.5 32.5 1.0 C F:ASP320 4.6 29.1 1.0 CA F:GLU323 4.6 40.1 1.0 CA F:ASP320 4.7 29.7 1.0 O F:HOH476 4.8 47.9 1.0 N F:CYS326 5.0 30.6 1.0 CG F:PHE322 5.0 35.4 1.0

S.J.Everse, G.Spraggon, L.Veerapandian, M.Riley, R.F.Doolittle. Crystal Structure of Fragment Double-D From Human Fibrin with Two Different Bound Ligands. Biochemistry V. 37 8637 1998.
ISSN: ISSN 0006-2960
PubMed: 9628725
DOI: 10.1021/BI9804129