Calcium in PDB 3hus: Crystal Structure of Recombinant Gamma N308K Fibrinogen Fragment D with the Peptide Ligand Gly-Pro-Arg-Pro-Amide

The structure of Crystal Structure of Recombinant Gamma N308K Fibrinogen Fragment D with the Peptide Ligand Gly-Pro-Arg-Pro-Amide, PDB code: 3hus was solved by S.T.Lord, S.R.Bowley, N.Okumura, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.25 / 3.04
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	95.009, 95.009, 448.382, 90.00, 90.00, 90.00
R / Rfree (%)	22 / 28.8

The binding sites of Calcium atom in the Crystal Structure of Recombinant Gamma N308K Fibrinogen Fragment D with the Peptide Ligand Gly-Pro-Arg-Pro-Amide (pdb code 3hus). 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 Gamma N308K Fibrinogen Fragment D with the Peptide Ligand Gly-Pro-Arg-Pro-Amide, PDB code: 3hus:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of Recombinant Gamma N308K Fibrinogen Fragment D with the Peptide Ligand Gly-Pro-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 Gamma N308K Fibrinogen Fragment D with the Peptide Ligand Gly-Pro-Arg-Pro-Amide within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2 b:69.2 occ:1.00 O B:HOH1 2.6 41.3 1.0 O B:ASP383 2.7 61.0 1.0 OD1 B:ASP383 2.9 60.7 1.0 O B:TRP385 3.0 64.5 1.0 OD2 B:ASP381 3.1 57.2 1.0 C B:TRP385 3.7 64.5 1.0 C B:ASP383 3.7 61.1 1.0 CG B:ASP381 3.7 57.3 1.0 OD1 B:ASP381 3.8 56.8 1.0 N B:TRP385 3.9 63.6 1.0 CG B:ASP383 4.0 60.9 1.0 N B:ASP383 4.1 60.0 1.0 CA B:TRP385 4.3 64.3 1.0 CA B:ASP383 4.3 60.7 1.0 N B:LEU386 4.5 65.0 1.0 C B:ASN382 4.6 59.3 1.0 N B:GLY384 4.7 61.7 1.0 CA B:LEU386 4.7 65.5 1.0 C B:GLY384 4.7 63.0 1.0 CB B:ASP383 4.7 60.7 1.0 OD2 B:ASP383 4.8 60.9 1.0 CA B:GLY384 4.9 62.5 1.0 CB B:TRP385 4.9 64.4 1.0 N B:ASN382 5.0 58.3 1.0 C B:ASP381 5.0 57.9 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Recombinant Gamma N308K Fibrinogen Fragment D with the Peptide Ligand Gly-Pro-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 Gamma N308K Fibrinogen Fragment D with the Peptide Ligand Gly-Pro-Arg-Pro-Amide within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1 b:68.9 occ:1.00 O C:PHE322 2.6 64.5 1.0 OD1 C:ASP318 3.3 62.3 1.0 OD1 C:ASP320 3.5 61.7 1.0 O C:ASP320 3.6 62.7 1.0 CG C:ASP318 3.7 62.0 1.0 O C:GLY324 3.8 64.8 1.0 OD2 C:ASP318 3.8 62.1 1.0 C C:PHE322 3.9 64.5 1.0 O C:GLU323 4.2 65.2 1.0 C C:GLU323 4.5 65.1 1.0 CG C:ASP320 4.5 62.2 1.0 N C:PHE322 4.5 64.0 1.0 C C:ASP320 4.5 62.8 1.0 CB C:ASP318 4.7 61.7 1.0 CA C:GLU323 4.7 65.2 1.0 N C:GLU323 4.7 64.8 1.0 N C:ASP320 4.8 62.3 1.0 CA C:PHE322 4.8 64.4 1.0 C C:GLY324 4.9 64.8 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Recombinant Gamma N308K Fibrinogen Fragment D with the Peptide Ligand Gly-Pro-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 Gamma N308K Fibrinogen Fragment D with the Peptide Ligand Gly-Pro-Arg-Pro-Amide within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca2 b:64.1 occ:1.00 OD2 E:ASP381 2.2 57.3 1.0 O E:TRP385 2.5 64.8 1.0 O E:HOH36 2.7 43.1 1.0 CG E:ASP381 3.2 57.1 1.0 OD1 E:ASP381 3.5 56.7 1.0 OD1 E:ASP383 3.6 59.8 1.0 C E:TRP385 3.7 64.8 1.0 O E:THR387 4.2 68.0 1.0 N E:THR387 4.3 67.1 1.0 CA E:LEU386 4.5 66.0 1.0 N E:LEU386 4.5 65.4 1.0 O E:HOH22 4.6 65.2 1.0 CB E:ASP381 4.6 56.9 1.0 CA E:TRP385 4.7 64.3 1.0 CG E:ASP383 4.8 60.0 1.0 O E:ASP383 4.8 60.4 1.0 CB E:TRP385 4.8 64.4 1.0 N E:TRP385 4.9 63.5 1.0 O E:HOH37 4.9 46.8 1.0 C E:LEU386 4.9 66.5 1.0 CG2 E:THR387 5.0 67.4 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Recombinant Gamma N308K Fibrinogen Fragment D with the Peptide Ligand Gly-Pro-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 Gamma N308K Fibrinogen Fragment D with the Peptide Ligand Gly-Pro-Arg-Pro-Amide within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca1 b:90.4 occ:1.00 O F:PHE322 2.6 69.8 1.0 OD1 F:ASP318 3.2 69.6 1.0 O F:GLY324 3.4 68.5 1.0 O F:GLU323 3.5 69.4 1.0 OD1 F:ASP320 3.6 68.7 1.0 CG F:ASP318 3.7 69.0 1.0 C F:PHE322 3.8 69.7 1.0 OD2 F:ASP318 3.8 69.7 1.0 C F:GLU323 3.9 69.4 1.0 CA F:GLU323 4.3 69.6 1.0 O F:ASP320 4.5 69.0 1.0 C F:GLY324 4.5 68.5 1.0 N F:GLU323 4.5 69.7 1.0 N F:GLY324 4.6 69.2 1.0 CG F:ASP320 4.7 69.0 1.0 CB F:ASP318 4.8 68.5 1.0 N F:PHE322 4.8 69.5 1.0 CA F:PHE322 4.9 69.7 1.0 CA F:GLY324 5.0 68.8 1.0

S.R.Bowley, N.Okumura, S.T.Lord. Impaired Protofibril Formation in Fibrinogen GAMMAN308K Is Due to Altered D:D and "A:A" Interactions. Biochemistry V. 48 8656 2009.
ISSN: ISSN 0006-2960
PubMed: 19650644
DOI: 10.1021/BI900239B