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Calcium in PDB 1fzf: Crystal Structure of Fragment Double-D From Human Fibrin with the Peptide Ligand Gly-His-Arg-Pro-Amide

Protein crystallography data

The structure of Crystal Structure of Fragment Double-D From Human Fibrin with the Peptide Ligand Gly-His-Arg-Pro-Amide, PDB code: 1fzf was solved by S.J.Everse, G.Spraggon, L.Veerapandian, R.F.Doolittle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 54.800, 149.400, 234.700, 90.00, 90.00, 90.00
R / Rfree (%) 23.3 / 30.2

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Fragment Double-D From Human Fibrin with the Peptide Ligand Gly-His-Arg-Pro-Amide (pdb code 1fzf). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of Fragment Double-D From Human Fibrin with the Peptide Ligand Gly-His-Arg-Pro-Amide, PDB code: 1fzf:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 1fzf

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Calcium binding site 1 out of 6 in the Crystal Structure of Fragment Double-D From Human Fibrin 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 Crystal Structure of Fragment Double-D From Human Fibrin with the Peptide Ligand Gly-His-Arg-Pro-Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca2

b:52.7
occ:1.00
 O B:TRP385 2.5 73.9 1.0
OD1 B:ASP383 2.5 51.5 1.0
OD1 B:ASP381 2.7 47.5 1.0
OD2 B:ASP381 2.7 51.9 1.0
CG B:ASP381 3.0 47.3 1.0
C B:TRP385 3.4 77.4 1.0
CG B:ASP383 3.5 36.8 1.0
OD2 B:ASP383 3.8 34.7 1.0
CB B:TRP385 4.0 69.7 1.0
CA B:TRP385 4.1 72.0 1.0
O B:ASP383 4.2 41.7 1.0
N B:TRP385 4.3 67.0 1.0
N B:LEU386 4.4 89.5 1.0
CG2 B:THR387 4.4 0.7 1.0
CB B:ASP381 4.5 46.4 1.0
N B:THR387 4.6 0.6 1.0
CA B:LEU386 4.7 0.7 1.0
C B:ASP383 4.8 41.9 1.0
N B:ASP383 4.8 28.9 1.0
CG B:TRP385 4.8 71.0 1.0
CB B:ASP383 4.8 31.3 1.0
CG B:GLN393 4.9 92.7 1.0
CA B:ASP383 5.0 36.6 1.0

Calcium binding site 2 out of 6 in 1fzf

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Calcium binding site 2 out of 6 in the Crystal Structure of Fragment Double-D From Human Fibrin 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 Crystal Structure of Fragment Double-D From Human Fibrin with the Peptide Ligand Gly-His-Arg-Pro-Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1

b:31.0
occ:1.00
 O C:PHE322 2.4 28.6 1.0
OD1 C:ASP320 2.5 24.9 1.0
OD2 C:ASP318 2.5 36.6 1.0
OD1 C:ASP318 2.6 33.0 1.0
O C:GLY324 2.6 32.3 1.0
CG C:ASP318 2.8 32.1 1.0
C C:PHE322 3.6 31.0 1.0
CG C:ASP320 3.6 28.5 1.0
C C:GLY324 3.7 30.3 1.0
O C:ASP320 3.9 41.2 1.0
C C:GLU323 4.1 37.8 1.0
OD2 C:ASP320 4.1 27.4 1.0
CB C:ASP318 4.2 27.5 1.0
O C:GLU323 4.2 43.7 1.0
N C:GLY324 4.3 30.7 1.0
N C:PHE322 4.4 37.7 1.0
CA C:PHE322 4.5 31.4 1.0
N C:GLU323 4.5 36.0 1.0
CA C:GLU323 4.5 41.0 1.0
C C:ASP320 4.5 39.1 1.0
N C:ASP320 4.6 40.3 1.0
CA C:GLY324 4.6 25.4 1.0
N C:ASN325 4.7 26.0 1.0
CA C:ASN325 4.7 21.7 1.0
CB C:PHE322 4.8 33.1 1.0
CB C:ASP320 4.8 36.8 1.0
CA C:ASP320 4.9 41.0 1.0
C C:ASP318 5.0 34.1 1.0

Calcium binding site 3 out of 6 in 1fzf

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Calcium binding site 3 out of 6 in the Crystal Structure of Fragment Double-D From Human Fibrin 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 Crystal Structure of Fragment Double-D From Human Fibrin with the Peptide Ligand Gly-His-Arg-Pro-Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca4

b:39.3
occ:1.00
 OD1 C:ASP294 2.5 55.0 1.0
O C:ASP298 2.6 61.7 1.0
O C:GLY296 2.7 54.3 1.0
O C:ASP297 3.2 84.8 1.0
C C:GLY296 3.4 56.3 1.0
CB C:ASP301 3.4 45.6 1.0
CG C:ASP294 3.5 60.4 1.0
OD2 C:ASP301 3.5 56.2 1.0
CG C:ASP301 3.5 54.8 1.0
C C:ASP298 3.6 58.9 1.0
N C:GLY296 3.6 65.1 1.0
CA C:GLY296 3.8 61.6 1.0
CA C:PRO299 3.9 47.3 1.0
C C:ASP297 4.0 76.7 1.0
OD2 C:ASP294 4.1 66.7 1.0
N C:PRO299 4.1 50.2 1.0
OD1 C:ASP301 4.3 62.7 1.0
C C:PRO299 4.3 44.7 1.0
O C:PRO299 4.3 50.4 1.0
N C:ASP297 4.3 65.9 1.0
CA C:ASP294 4.4 44.7 1.0
N C:PHE295 4.4 45.2 1.0
C C:ASP294 4.5 44.3 1.0
CB C:ASP294 4.5 55.1 1.0
N C:ASP298 4.6 69.1 1.0
N C:ASP301 4.6 43.8 1.0
CA C:ASP301 4.6 44.6 1.0
CA C:ASP298 4.7 65.7 1.0
C C:PHE295 4.7 51.3 1.0
CA C:ASP297 4.8 78.8 1.0

Calcium binding site 4 out of 6 in 1fzf

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Calcium binding site 4 out of 6 in the Crystal Structure of Fragment Double-D From Human Fibrin 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 Crystal Structure of Fragment Double-D From Human Fibrin with the Peptide Ligand Gly-His-Arg-Pro-Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca2

b:45.4
occ:1.00
 O E:TRP385 2.4 73.7 1.0
OD1 E:ASP383 2.5 45.1 1.0
OD2 E:ASP381 2.7 54.2 1.0
OD1 E:ASP381 2.9 47.6 1.0
CG E:ASP381 3.1 46.9 1.0
C E:TRP385 3.3 77.0 1.0
CG E:ASP383 3.7 41.4 1.0
O E:ASP383 3.7 49.1 1.0
CA E:TRP385 4.1 73.0 1.0
N E:LEU386 4.1 88.1 1.0
N E:TRP385 4.1 68.0 1.0
CB E:TRP385 4.2 72.3 1.0
OD2 E:ASP383 4.2 41.6 1.0
CA E:LEU386 4.3 98.6 1.0
C E:ASP383 4.5 46.1 1.0
N E:THR387 4.5 0.4 1.0
N E:ASP383 4.6 36.9 1.0
CB E:ASP381 4.7 43.1 1.0
CG2 E:THR387 4.8 0.2 1.0
CA E:ASP383 4.8 41.7 1.0
CB E:ASP383 4.8 39.5 1.0
C E:LEU386 4.9 0.8 1.0

Calcium binding site 5 out of 6 in 1fzf

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Calcium binding site 5 out of 6 in the Crystal Structure of Fragment Double-D From Human Fibrin 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 5 of Crystal Structure of Fragment Double-D From Human Fibrin with the Peptide Ligand Gly-His-Arg-Pro-Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca3

b:71.9
occ:1.00
 OD2 E:ASP261 2.6 27.7 1.0
OE2 F:GLU132 2.7 65.1 1.0
O E:GLY263 2.9 44.3 1.0
CG E:ASP261 3.5 35.6 1.0
OD1 E:ASP261 3.6 42.1 1.0
CD F:GLU132 3.9 62.5 1.0
C E:GLY263 4.0 34.2 1.0
CA E:GLY263 4.4 30.1 1.0
CG F:GLU132 4.6 58.0 1.0
CE D:LYS157 4.8 65.1 1.0
OE1 F:GLU132 4.8 63.9 1.0
CB E:ASP261 4.9 30.6 1.0
N E:GLY263 4.9 23.5 1.0
OE1 F:GLN136 4.9 57.5 1.0

Calcium binding site 6 out of 6 in 1fzf

Go back to Calcium Binding Sites List in 1fzf
Calcium binding site 6 out of 6 in the Crystal Structure of Fragment Double-D From Human Fibrin 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 6 of Crystal Structure of Fragment Double-D From Human Fibrin with the Peptide Ligand Gly-His-Arg-Pro-Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca1

b:26.4
occ:1.00
 O F:PHE322 2.2 26.9 1.0
OD1 F:ASP320 2.4 29.9 1.0
OD2 F:ASP318 2.6 37.6 1.0
O F:GLY324 2.6 21.7 1.0
OD1 F:ASP318 2.6 23.9 1.0
CG F:ASP318 2.9 32.4 1.0
C F:PHE322 3.4 26.7 1.0
CG F:ASP320 3.5 29.2 1.0
C F:GLY324 3.7 22.0 1.0
O F:ASP320 3.9 33.7 1.0
OD2 F:ASP320 4.0 31.6 1.0
C F:GLU323 4.0 36.9 1.0
O F:GLU323 4.2 46.1 1.0
N F:PHE322 4.2 28.7 1.0
N F:GLY324 4.2 30.1 1.0
CB F:ASP318 4.3 32.4 1.0
CA F:PHE322 4.3 26.4 1.0
N F:GLU323 4.4 30.0 1.0
CA F:GLU323 4.4 34.5 1.0
C F:ASP320 4.5 32.8 1.0
CA F:GLY324 4.6 22.1 1.0
N F:ASP320 4.6 36.1 1.0
CB F:PHE322 4.6 26.2 1.0
N F:ASN325 4.7 19.2 1.0
CB F:ASP320 4.8 29.9 1.0
CA F:ASN325 4.8 22.3 1.0
CA F:ASP320 4.8 33.2 1.0

Reference:

S.J.Everse, G.Spraggon, L.Veerapandian, R.F.Doolittle. Conformational Changes in Fragments D and Double-D From Human Fibrin(Ogen) Upon Binding the Peptide Ligand Gly-His-Arg-Pro-Amide. Biochemistry V. 38 2941 1999.
ISSN: ISSN 0006-2960
PubMed: 10074346
DOI: 10.1021/BI982626W
Page generated: Thu Jul 11 08:23:53 2024

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