Calcium in PDB 3h32: Crystal Structure of D-Dimer From Human Fibrin Complexed with Gly-His- Arg-Pro-Tyr-Amide

The structure of Crystal Structure of D-Dimer From Human Fibrin Complexed with Gly-His- Arg-Pro-Tyr-Amide, PDB code: 3h32 was solved by R.F.Doolittle, L.Pandi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 3.60
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	264.720, 97.320, 132.490, 90.00, 122.78, 90.00
R / Rfree (%)	26.3 / 32

The binding sites of Calcium atom in the Crystal Structure of D-Dimer From Human Fibrin Complexed with Gly-His- Arg-Pro-Tyr-Amide (pdb code 3h32). 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 D-Dimer From Human Fibrin Complexed with Gly-His- Arg-Pro-Tyr-Amide, PDB code: 3h32:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of D-Dimer From Human Fibrin Complexed with Gly-His- Arg-Pro-Tyr-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 D-Dimer From Human Fibrin Complexed with Gly-His- Arg-Pro-Tyr-Amide within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca501 b:74.6 occ:1.00 O C:PHE322 1.8 86.4 1.0 OD2 C:ASP318 1.9 78.6 1.0 O C:GLU323 2.2 88.3 1.0 OD2 C:ASP320 2.5 80.0 1.0 C C:GLU323 2.6 88.2 1.0 CG C:ASP318 2.6 79.0 1.0 OD1 C:ASP318 2.7 77.8 1.0 C C:PHE322 2.9 86.6 1.0 CA C:GLU323 3.1 88.1 1.0 CG C:ASP320 3.3 81.8 1.0 C C:GLY324 3.3 87.4 1.0 N C:ASN325 3.3 88.0 1.0 N C:GLY324 3.4 87.9 1.0 N C:GLU323 3.4 87.2 1.0 OD1 C:ASP320 3.4 81.7 1.0 O C:GLY324 3.6 87.3 1.0 CA C:ASN325 3.6 89.0 1.0 CA C:GLY324 3.9 87.7 1.0 CB C:ASP318 4.1 79.5 1.0 CA C:PHE322 4.2 85.3 1.0 N C:PHE322 4.4 85.5 1.0 CB C:ASN325 4.5 88.7 1.0 CB C:GLU323 4.6 89.2 1.0 CB C:PHE322 4.6 82.4 1.0 C C:ASN325 4.8 89.6 1.0 CB C:ASP320 4.8 82.3 1.0 O C:ASP320 4.8 82.2 1.0 N C:CYS326 4.8 90.1 1.0 CG C:PHE322 4.8 80.5 1.0 N C:ASP320 5.0 82.2 1.0 CA C:ASP318 5.0 80.5 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of D-Dimer From Human Fibrin Complexed with Gly-His- Arg-Pro-Tyr-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 D-Dimer From Human Fibrin Complexed with Gly-His- Arg-Pro-Tyr-Amide within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca502 b:40.7 occ:1.00 O B:TRP385 2.1 85.0 1.0 OD1 B:ASP383 2.2 82.6 1.0 OD1 B:ASP381 2.4 79.7 1.0 CG B:ASP383 3.2 80.2 1.0 C B:TRP385 3.3 84.8 1.0 CG B:ASP381 3.4 80.1 1.0 OD2 B:ASP383 3.4 80.4 1.0 OD2 B:ASP381 3.7 81.7 1.0 CB B:TRP385 4.2 85.0 1.0 CA B:TRP385 4.2 84.3 1.0 N B:LEU386 4.2 85.2 1.0 CG2 B:THR387 4.2 91.1 1.0 N B:THR387 4.2 86.8 1.0 CA B:LEU386 4.3 85.4 1.0 O B:THR387 4.4 89.0 1.0 O B:LYS392 4.4 81.1 1.0 N B:TRP385 4.4 83.8 1.0 CB B:ASP383 4.5 79.6 1.0 O B:ASP383 4.6 78.7 1.0 CB B:ASP381 4.7 79.8 1.0 CG B:TRP385 4.8 85.7 1.0 C B:LEU386 4.8 84.8 1.0 C B:ASP383 4.9 79.6 1.0 CG B:GLN393 4.9 81.2 1.0 N B:ASP383 4.9 78.9 1.0 CA B:ASP383 5.0 78.9 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of D-Dimer From Human Fibrin Complexed with Gly-His- Arg-Pro-Tyr-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 D-Dimer From Human Fibrin Complexed with Gly-His- Arg-Pro-Tyr-Amide within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca501 b:0.6 occ:1.00 CA F:GLY324 2.0 89.7 1.0 N F:GLY324 2.4 90.2 1.0 C F:GLU323 2.7 89.9 1.0 O F:GLU323 2.8 90.7 1.0 C F:GLY324 3.0 89.3 1.0 N F:ASN325 3.0 89.1 1.0 CG F:GLU323 3.9 87.7 1.0 CA F:GLU323 3.9 89.4 1.0 CB F:GLU323 4.0 88.6 1.0 O F:GLY324 4.2 89.0 1.0 CE2 F:PHE322 4.3 79.8 1.0 CZ F:PHE322 4.4 78.6 1.0 CA F:ASN325 4.5 89.5 1.0 N F:GLU323 4.7 88.5 1.0 OD1 F:ASN325 4.7 90.2 1.0 CD2 F:PHE322 4.7 81.5 1.0 CE1 F:PHE322 4.9 78.6 1.0 CB F:ASN325 5.0 89.0 1.0 O F:PHE322 5.0 88.1 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of D-Dimer From Human Fibrin Complexed with Gly-His- Arg-Pro-Tyr-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 D-Dimer From Human Fibrin Complexed with Gly-His- Arg-Pro-Tyr-Amide within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca502 b:26.6 occ:1.00 OD1 E:ASP383 2.1 79.8 1.0 OD1 E:ASP381 2.2 82.8 1.0 O E:TRP385 2.3 84.8 1.0 CG E:ASP383 2.9 79.7 1.0 OD2 E:ASP383 3.0 81.1 1.0 CG E:ASP381 3.0 82.2 1.0 OD2 E:ASP381 3.2 83.2 1.0 C E:TRP385 3.5 84.2 1.0 CA E:TRP385 4.3 84.6 1.0 CB E:ASP383 4.3 80.1 1.0 O E:ASP383 4.4 81.1 1.0 CB E:TRP385 4.4 86.3 1.0 CB E:ASP381 4.4 81.1 1.0 N E:LEU386 4.4 84.4 1.0 N E:TRP385 4.4 85.6 1.0 CA E:LEU386 4.5 84.5 1.0 N E:ASP383 4.6 80.2 1.0 N E:THR387 4.7 86.5 1.0 O E:THR387 4.7 89.3 1.0 C E:ASP383 4.7 81.3 1.0 CA E:ASP383 4.8 80.6 1.0 CG2 E:THR387 4.8 92.2 1.0 CG E:GLN393 4.8 81.4 1.0 NE2 E:GLN393 4.9 83.9 1.0 O E:LYS392 5.0 79.7 1.0

L.Pandi, J.M.Kollman, F.Lopez-Lira, J.M.Burrows, M.Riley, R.F.Doolittle. Two Families of Synthetic Peptides That Enhance Fibrin Turbidity and Delay Fibrinolysis By Different Mechanisms. Biochemistry V. 48 7201 2009.
ISSN: ISSN 0006-2960
PubMed: 19588915
DOI: 10.1021/BI900647G