Calcium in PDB 1n73: Fibrin D-Dimer, Lamprey Complexed with the Peptide Ligand: Gly-His- Arg-Pro-Amide

The structure of Fibrin D-Dimer, Lamprey Complexed with the Peptide Ligand: Gly-His- Arg-Pro-Amide, PDB code: 1n73 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 / 2.90
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	49.732, 99.302, 120.732, 99.58, 101.46, 92.36
R / Rfree (%)	25.8 / 28.9

The binding sites of Calcium atom in the Fibrin D-Dimer, Lamprey Complexed with the Peptide Ligand: Gly-His- Arg-Pro-Amide (pdb code 1n73). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Fibrin D-Dimer, Lamprey Complexed with the Peptide Ligand: Gly-His- Arg-Pro-Amide, PDB code: 1n73:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Fibrin D-Dimer, Lamprey Complexed 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 Fibrin D-Dimer, Lamprey Complexed with the Peptide Ligand: Gly-His- Arg-Pro-Amide within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1 b:50.1 occ:1.00 O C:TYR320 2.3 52.1 1.0 O C:GLY322 2.4 46.2 1.0 OD1 C:ASP318 2.4 50.6 1.0 OD2 C:ASP316 2.5 43.0 1.0 OD1 C:ASP316 2.9 45.1 1.0 CG C:ASP316 3.0 43.2 1.0 CG C:ASP318 3.4 48.9 1.0 C C:TYR320 3.4 50.0 1.0 C C:GLY322 3.5 47.2 1.0 OD2 C:ASP318 3.6 51.4 1.0 C C:GLU321 3.9 48.8 1.0 N C:GLY322 4.0 48.0 1.0 O C:GLU321 4.1 47.4 1.0 N C:TYR320 4.2 47.9 1.0 CA C:TYR320 4.2 48.3 1.0 CA C:GLY322 4.3 47.9 1.0 N C:GLU321 4.3 50.9 1.0 CB C:ASP316 4.4 42.8 1.0 CB C:TYR320 4.4 48.9 1.0 CA C:GLU321 4.4 50.0 1.0 N C:SER323 4.5 47.4 1.0 CA C:SER323 4.6 47.5 1.0 CB C:ASP318 4.7 46.4 1.0 O C:ASP318 4.7 46.7 1.0 C C:ASP318 4.8 45.6 1.0 N C:ASP318 4.9 44.1 1.0

Calcium binding site 2 out of 4 in the Fibrin D-Dimer, Lamprey Complexed 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 Fibrin D-Dimer, Lamprey Complexed with the Peptide Ligand: Gly-His- Arg-Pro-Amide within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca2 b:62.3 occ:1.00 OD1 F:ASP318 2.3 52.6 1.0 O F:TYR320 2.3 49.0 1.0 O F:GLY322 2.3 44.7 1.0 OD2 F:ASP316 2.4 43.4 1.0 OD1 F:ASP316 2.8 41.1 1.0 CG F:ASP316 2.9 42.5 1.0 CG F:ASP318 3.2 50.8 1.0 C F:TYR320 3.4 48.9 1.0 OD2 F:ASP318 3.5 52.8 1.0 C F:GLY322 3.5 48.2 1.0 C F:GLU321 4.0 52.0 1.0 N F:GLY322 4.1 51.9 1.0 N F:TYR320 4.1 46.4 1.0 CA F:TYR320 4.2 47.7 1.0 O F:GLU321 4.2 51.9 1.0 CB F:ASP316 4.3 41.7 1.0 CB F:TYR320 4.3 47.5 1.0 CA F:GLY322 4.3 49.2 1.0 N F:GLU321 4.4 50.2 1.0 N F:SER323 4.4 49.6 1.0 CA F:GLU321 4.5 51.4 1.0 CA F:SER323 4.5 50.2 1.0 CB F:ASP318 4.6 46.9 1.0 O F:ASP318 4.7 46.6 1.0 C F:ASP318 4.7 45.0 1.0 N F:ASP318 4.8 41.5 1.0 CA F:ASP318 4.9 44.1 1.0

Calcium binding site 3 out of 4 in the Fibrin D-Dimer, Lamprey Complexed 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 Fibrin D-Dimer, Lamprey Complexed with the Peptide Ligand: Gly-His- Arg-Pro-Amide within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca3 b:52.0 occ:1.00 OD2 B:ASP401 2.0 49.9 1.0 OD1 B:ASP403 2.4 58.2 1.0 O B:TRP405 2.5 62.7 1.0 O B:LYS412 2.5 57.6 1.0 CG B:ASP401 2.9 47.9 1.0 OD1 B:ASP401 3.0 51.5 1.0 O B:ASN406 3.2 64.6 1.0 CG B:ASP403 3.4 57.4 1.0 C B:TRP405 3.5 61.4 1.0 OD2 B:ASP403 3.7 57.5 1.0 C B:LYS412 3.7 57.8 1.0 C B:ASN406 3.8 63.9 1.0 CB B:LYS412 4.2 57.8 1.0 CA B:TRP405 4.2 60.0 1.0 O B:ASP409 4.2 58.8 1.0 N B:TRP405 4.2 59.0 1.0 CB B:TRP405 4.2 59.5 1.0 CB B:ASP401 4.3 48.3 1.0 N B:PRO407 4.3 63.6 1.0 O B:PRO407 4.4 64.6 1.0 N B:ASN406 4.4 62.2 1.0 CA B:PRO407 4.4 64.7 1.0 CA B:LYS412 4.5 58.0 1.0 CA B:ASN406 4.6 62.9 1.0 O B:ASP403 4.7 56.8 1.0 N B:HIS413 4.7 56.0 1.0 C B:PRO407 4.7 64.7 1.0 CB B:ASP403 4.7 57.2 1.0 CA B:HIS413 4.8 57.0 1.0 C B:ASP403 4.9 55.6 1.0 N B:ASP403 4.9 53.1 1.0

Calcium binding site 4 out of 4 in the Fibrin D-Dimer, Lamprey Complexed 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 Fibrin D-Dimer, Lamprey Complexed with the Peptide Ligand: Gly-His- Arg-Pro-Amide within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca4 b:75.4 occ:1.00 O E:TRP405 2.2 63.9 1.0 OD2 E:ASP401 2.3 51.9 1.0 OD1 E:ASP403 2.3 58.9 1.0 O E:LYS412 2.4 60.3 1.0 CG E:ASP401 3.1 49.6 1.0 O E:ASN406 3.2 66.5 1.0 C E:TRP405 3.2 63.2 1.0 OD1 E:ASP401 3.2 50.2 1.0 CG E:ASP403 3.3 59.9 1.0 C E:LYS412 3.6 61.0 1.0 OD2 E:ASP403 3.6 62.1 1.0 C E:ASN406 3.7 64.8 1.0 CA E:TRP405 3.9 63.3 1.0 CB E:TRP405 4.0 63.3 1.0 CB E:LYS412 4.0 59.6 1.0 N E:TRP405 4.0 62.9 1.0 N E:ASN406 4.2 63.4 1.0 O E:ASP409 4.3 59.0 1.0 N E:PRO407 4.3 65.4 1.0 CA E:LYS412 4.4 60.6 1.0 CA E:PRO407 4.5 65.7 1.0 CA E:ASN406 4.5 64.2 1.0 CB E:ASP401 4.5 49.7 1.0 O E:PRO407 4.6 65.8 1.0 N E:HIS413 4.6 61.0 1.0 O E:ASP403 4.7 57.7 1.0 CB E:ASP403 4.7 58.6 1.0 CG E:TRP405 4.7 63.7 1.0 CA E:HIS413 4.8 61.0 1.0 C E:ASP403 4.8 57.7 1.0 C E:PRO407 4.9 65.7 1.0 N E:ASP403 4.9 54.0 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