Calcium in PDB 1n86: Crystal Structure of Human D-Dimer From Cross-Linked Fibrin Complexed with Gpr and Ghrpldk Peptide Ligands.

The structure of Crystal Structure of Human D-Dimer From Cross-Linked Fibrin Complexed with Gpr and Ghrpldk Peptide Ligands., PDB code: 1n86 was solved by Z.Yang, L.Pandi, R.F.Doolittle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 3.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	52.328, 130.093, 298.313, 90.00, 90.00, 90.00
R / Rfree (%)	22.6 / 28.9

The binding sites of Calcium atom in the Crystal Structure of Human D-Dimer From Cross-Linked Fibrin Complexed with Gpr and Ghrpldk Peptide Ligands. (pdb code 1n86). 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 Human D-Dimer From Cross-Linked Fibrin Complexed with Gpr and Ghrpldk Peptide Ligands., PDB code: 1n86:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of Human D-Dimer From Cross-Linked Fibrin Complexed with Gpr and Ghrpldk Peptide 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 Human D-Dimer From Cross-Linked Fibrin Complexed with Gpr and Ghrpldk Peptide Ligands. within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1 b:52.7 occ:1.00 OD1 B:ASP383 2.1 79.8 1.0 O B:TRP385 2.3 58.1 1.0 OD2 B:ASP381 2.3 79.5 1.0 OD1 B:ASP381 2.5 84.5 1.0 CG B:ASP381 2.7 79.3 1.0 CG B:ASP383 3.1 77.8 1.0 C B:TRP385 3.4 58.6 1.0 OD2 B:ASP383 3.5 78.9 1.0 CB B:TRP385 3.9 71.6 1.0 O B:ASP383 3.9 72.6 1.0 CA B:TRP385 4.1 62.2 1.0 CB B:ASP381 4.2 72.6 1.0 O B:LYS392 4.3 80.0 1.0 N B:TRP385 4.3 66.2 1.0 N B:ASP383 4.4 64.9 1.0 N B:LEU386 4.4 62.8 1.0 CB B:ASP383 4.4 78.3 1.0 C B:ASP383 4.5 74.2 1.0 CA B:LEU386 4.6 71.5 1.0 CA B:ASP383 4.7 72.9 1.0 CA B:GLN393 4.9 73.8 1.0 CG B:TRP385 4.9 65.8 1.0 N B:ASN382 4.9 66.8 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Human D-Dimer From Cross-Linked Fibrin Complexed with Gpr and Ghrpldk Peptide 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 Human D-Dimer From Cross-Linked Fibrin Complexed with Gpr and Ghrpldk Peptide Ligands. within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca2 b:81.7 occ:1.00 O E:TRP385 2.1 86.0 1.0 OD2 E:ASP381 2.5 0.3 1.0 OD1 E:ASP383 2.6 90.9 1.0 OD1 E:ASP381 2.8 1.0 1.0 CG E:ASP381 3.0 0.3 1.0 C E:TRP385 3.3 84.9 1.0 CG E:ASP383 3.6 91.0 1.0 CB E:TRP385 4.0 76.8 1.0 OD2 E:ASP383 4.0 90.7 1.0 CA E:TRP385 4.2 82.3 1.0 N E:LEU386 4.2 89.3 1.0 O E:LYS392 4.2 92.9 1.0 O E:ASP383 4.2 65.3 1.0 CA E:LEU386 4.3 96.6 1.0 CB E:ASP381 4.4 98.4 1.0 N E:TRP385 4.5 93.9 1.0 N E:THR387 4.6 0.3 1.0 CG E:TRP385 4.9 73.5 1.0 OG1 E:THR387 4.9 0.1 1.0 N E:ASP383 4.9 78.5 1.0 CD2 E:LEU386 4.9 0.7 1.0 C E:ASP383 4.9 76.5 1.0 C E:LEU386 4.9 99.8 1.0 CB E:ASP383 5.0 89.3 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Human D-Dimer From Cross-Linked Fibrin Complexed with Gpr and Ghrpldk Peptide 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 Human D-Dimer From Cross-Linked Fibrin Complexed with Gpr and Ghrpldk Peptide Ligands. within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca3 b:54.6 occ:1.00 OD1 C:ASP320 2.3 57.7 1.0 OD1 C:ASP318 2.3 47.1 1.0 OD2 C:ASP318 2.4 43.6 1.0 O C:GLY324 2.4 50.0 1.0 O C:PHE322 2.5 70.1 1.0 CG C:ASP318 2.6 53.9 1.0 CG C:ASP320 3.2 64.4 1.0 O C:ASP320 3.4 65.4 1.0 OD2 C:ASP320 3.6 60.4 1.0 C C:GLY324 3.7 59.5 1.0 C C:PHE322 3.7 66.8 1.0 O C:GLU323 3.9 56.6 1.0 CB C:ASP318 4.1 45.8 1.0 C C:GLU323 4.2 63.2 1.0 C C:ASP320 4.3 62.6 1.0 N C:ASP320 4.4 69.2 1.0 N C:PHE322 4.4 57.0 1.0 CA C:ASN325 4.4 66.4 1.0 CB C:ASP320 4.5 64.9 1.0 CA C:PHE322 4.5 66.9 1.0 N C:ASN325 4.5 60.8 1.0 N C:GLY324 4.5 63.1 1.0 CA C:ASP320 4.6 64.6 1.0 CA C:GLY324 4.6 63.7 1.0 N C:GLU323 4.7 69.7 1.0 CB C:PHE322 4.8 74.1 1.0 CA C:GLU323 4.8 70.0 1.0 C C:ASP318 4.9 55.2 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Human D-Dimer From Cross-Linked Fibrin Complexed with Gpr and Ghrpldk Peptide 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 Human D-Dimer From Cross-Linked Fibrin Complexed with Gpr and Ghrpldk Peptide Ligands. within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca4 b:54.6 occ:1.00 O F:PHE322 2.4 64.4 1.0 OD1 F:ASP318 2.4 45.5 1.0 OD1 F:ASP320 2.5 66.4 1.0 O F:GLY324 2.6 64.6 1.0 OD2 F:ASP318 2.6 52.2 1.0 CG F:ASP318 2.8 51.3 1.0 CG F:ASP320 3.4 65.8 1.0 O F:ASP320 3.4 58.1 1.0 C F:PHE322 3.6 65.0 1.0 O F:GLU323 3.7 80.1 1.0 C F:GLY324 3.8 72.2 1.0 OD2 F:ASP320 3.9 78.5 1.0 C F:GLU323 4.1 80.2 1.0 CB F:ASP318 4.2 53.8 1.0 C F:ASP320 4.4 57.8 1.0 N F:PHE322 4.4 53.8 1.0 N F:ASP320 4.5 59.3 1.0 CA F:PHE322 4.5 61.0 1.0 N F:GLY324 4.5 76.3 1.0 N F:GLU323 4.6 73.9 1.0 CA F:ASN325 4.6 73.0 1.0 CB F:ASP320 4.6 64.0 1.0 N F:ASN325 4.7 70.6 1.0 CA F:GLY324 4.7 75.3 1.0 CA F:GLU323 4.7 81.5 1.0 CA F:ASP320 4.7 59.3 1.0 CB F:PHE322 4.9 71.2 1.0

Z.Yang, L.Pandi, R.F.Doolittle. The Crystal Structure of Fragment Double-D From Cross-Linked Lamprey Fibrin Reveals Isopeptide Linkages Across An Unexpected D-D Interface. Biochemistry V. 41 15610 2002.
ISSN: ISSN 0006-2960
PubMed: 12501189
DOI: 10.1021/BI026666I