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

Protein crystallography data

The structure of Crystal Structure of Fragment D From Human Fibrinogen with the Peptide Ligand Gly-His-Arg-Pro-Amide, PDB code: 1fzg 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 / 2.50
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 D From Human Fibrinogen with the Peptide Ligand Gly-His-Arg-Pro-Amide (pdb code 1fzg). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Crystal Structure of Fragment D From Human Fibrinogen with the Peptide Ligand Gly-His-Arg-Pro-Amide, PDB code: 1fzg:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 1fzg

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Calcium binding site 1 out of 8 in the Crystal Structure of Fragment D From Human Fibrinogen 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 D From Human Fibrinogen with the Peptide Ligand Gly-His-Arg-Pro-Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca2

b:76.9
occ:1.00
 O B:HOH477 1.4 41.3 1.0
OD2 B:ASP381 2.1 54.3 1.0
OD1 B:ASP383 2.5 45.2 1.0
O B:TRP385 2.5 61.2 1.0
CG B:ASP381 3.1 52.2 1.0
CG B:ASP383 3.3 43.4 1.0
OD1 B:ASP381 3.4 53.1 1.0
OD2 B:ASP383 3.5 42.4 1.0
C B:TRP385 3.6 61.9 1.0
CB B:TRP385 3.9 52.8 1.0
O B:LYS392 4.0 70.7 1.0
CA B:TRP385 4.1 56.7 1.0
CG2 B:THR387 4.2 80.8 1.0
N B:TRP385 4.3 54.9 1.0
CB B:ASP381 4.5 50.3 1.0
CG B:TRP385 4.5 52.5 1.0
CA B:GLN393 4.6 63.3 1.0
N B:THR387 4.6 78.2 1.0
CB B:ASP383 4.7 41.2 1.0
CB B:GLN393 4.8 62.5 1.0
N B:LEU386 4.8 67.5 1.0
CG B:GLN393 4.9 65.1 1.0
O B:THR387 4.9 80.7 1.0
CD2 B:TRP385 5.0 51.3 1.0
CE3 B:TRP385 5.0 48.6 1.0
C B:LYS392 5.0 71.4 1.0

Calcium binding site 2 out of 8 in 1fzg

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Calcium binding site 2 out of 8 in the Crystal Structure of Fragment D From Human Fibrinogen 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 D From Human Fibrinogen with the Peptide Ligand Gly-His-Arg-Pro-Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca3

b:93.9
occ:1.00
 OD2 B:ASP261 2.5 42.0 1.0
OE2 C:GLU132 3.0 61.0 1.0
O B:GLY263 3.0 41.4 1.0
OD1 B:ASP261 3.2 42.6 1.0
CG B:ASP261 3.2 39.3 1.0
CD C:GLU132 3.7 58.3 1.0
C B:GLY263 3.8 37.8 1.0
CA B:GLY263 4.0 35.9 1.0
CG C:GLU132 4.1 54.6 1.0
N B:GLY263 4.4 38.2 1.0
OE1 C:GLN136 4.4 54.3 1.0
OE1 C:GLU132 4.6 60.6 1.0
CB B:ASP261 4.7 38.3 1.0
NE2 C:GLN136 4.8 56.3 1.0
N B:ARG264 4.8 36.7 1.0
CD C:GLN136 5.0 53.5 1.0

Calcium binding site 3 out of 8 in 1fzg

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Calcium binding site 3 out of 8 in the Crystal Structure of Fragment D From Human Fibrinogen 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 D From Human Fibrinogen with the Peptide Ligand Gly-His-Arg-Pro-Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1

b:48.2
occ:1.00
 O C:GLY324 2.2 48.3 1.0
OD1 C:ASP320 2.2 43.8 1.0
O C:HOH416 2.3 35.8 1.0
OD1 C:ASP318 2.4 46.7 1.0
O C:PHE322 2.4 48.8 1.0
OD2 C:ASP318 2.7 45.9 1.0
CG C:ASP318 2.8 44.5 1.0
CG C:ASP320 3.2 44.7 1.0
C C:GLY324 3.3 51.5 1.0
C C:PHE322 3.5 51.0 1.0
OD2 C:ASP320 3.7 46.4 1.0
N C:GLY324 4.1 55.9 1.0
C C:GLU323 4.1 56.6 1.0
CB C:ASP318 4.2 42.9 1.0
N C:ASN325 4.2 51.5 1.0
N C:PHE322 4.3 49.5 1.0
O C:GLU323 4.3 58.4 1.0
CA C:GLY324 4.3 53.4 1.0
CA C:ASN325 4.4 50.1 1.0
N C:GLU323 4.4 53.8 1.0
CA C:PHE322 4.4 50.9 1.0
N C:ASP320 4.4 42.5 1.0
O C:ASP320 4.4 48.9 1.0
CB C:ASP320 4.5 43.9 1.0
CA C:GLU323 4.6 57.1 1.0
CB C:PHE322 4.6 51.8 1.0
C C:ASP320 4.6 48.2 1.0
CA C:ASP320 4.7 45.0 1.0

Calcium binding site 4 out of 8 in 1fzg

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Calcium binding site 4 out of 8 in the Crystal Structure of Fragment D From Human Fibrinogen 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 D From Human Fibrinogen with the Peptide Ligand Gly-His-Arg-Pro-Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca4

b:99.7
occ:1.00
 CB C:ASP301 1.7 54.1 1.0
O C:HOH408 1.8 27.9 1.0
CG C:ASP301 1.9 56.8 1.0
OD2 C:ASP301 2.2 55.0 1.0
O C:ASP298 2.4 60.9 1.0
OD1 C:ASP301 2.9 59.5 1.0
OD1 C:ASP294 3.0 48.4 1.0
CA C:ASP301 3.1 54.5 1.0
O C:GLY296 3.2 48.5 1.0
N C:ASP301 3.2 54.3 1.0
C C:ASP298 3.5 60.4 1.0
N C:LYS302 3.8 52.9 1.0
CA C:ASP294 3.9 46.9 1.0
CG C:ASP294 4.0 50.3 1.0
N C:PHE295 4.0 47.3 1.0
C C:ASP301 4.0 54.6 1.0
C C:PRO299 4.2 56.6 1.0
C C:ASP294 4.3 47.9 1.0
C C:GLY296 4.3 50.6 1.0
O C:HOH422 4.3 56.5 1.0
O C:PRO299 4.3 57.5 1.0
N C:GLY296 4.3 50.8 1.0
N C:PRO299 4.4 59.7 1.0
CA C:ASP298 4.4 61.3 1.0
C C:SER300 4.4 54.7 1.0
CA C:PRO299 4.5 59.3 1.0
N C:ASP298 4.5 59.4 1.0
CB C:ASP294 4.5 48.8 1.0
N C:SER300 4.5 53.6 1.0
CB C:ASP298 4.7 60.9 1.0
OD1 C:ASP298 4.7 60.7 1.0
O C:PHE293 4.7 48.0 1.0
O C:HOH419 4.7 65.9 1.0
C C:ASP297 4.8 59.0 1.0
CA C:LYS302 5.0 52.4 1.0
O C:ASP297 5.0 57.9 1.0
CA C:SER300 5.0 54.7 1.0
CA C:GLY296 5.0 50.9 1.0

Calcium binding site 5 out of 8 in 1fzg

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Calcium binding site 5 out of 8 in the Crystal Structure of Fragment D From Human Fibrinogen 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 D From Human Fibrinogen with the Peptide Ligand Gly-His-Arg-Pro-Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca2

b:55.9
occ:1.00
 OD2 E:ASP381 2.1 53.8 1.0
O E:HOH88 2.3 53.0 1.0
O E:TRP385 2.4 70.9 1.0
OD1 E:ASP383 2.6 53.4 1.0
OD1 E:ASP381 2.7 51.2 1.0
CG E:ASP381 2.7 51.4 1.0
CG E:ASP383 3.2 50.5 1.0
OD2 E:ASP383 3.4 53.0 1.0
C E:TRP385 3.5 71.1 1.0
O E:ASP383 3.8 55.6 1.0
N E:TRP385 4.1 64.1 1.0
CB E:ASP381 4.2 49.4 1.0
CA E:TRP385 4.2 67.7 1.0
NE2 E:GLN393 4.3 79.5 1.0
N E:ASP383 4.3 45.4 1.0
C E:ASP383 4.4 52.5 1.0
CB E:TRP385 4.4 68.4 1.0
CB E:ASP383 4.4 49.2 1.0
N E:LEU386 4.5 76.8 1.0
CA E:ASP383 4.6 49.4 1.0
CA E:LEU386 4.7 81.6 1.0
N E:THR387 4.8 84.6 1.0

Calcium binding site 6 out of 8 in 1fzg

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Calcium binding site 6 out of 8 in the Crystal Structure of Fragment D From Human Fibrinogen 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 D From Human Fibrinogen with the Peptide Ligand Gly-His-Arg-Pro-Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca3

b:71.0
occ:1.00
 OE2 F:GLU132 2.3 65.2 1.0
O F:HOH416 2.6 61.3 1.0
OD1 E:ASP261 2.8 43.4 1.0
OD2 E:ASP261 2.9 46.7 1.0
O E:GLY263 3.0 44.6 1.0
CG E:ASP261 3.2 41.8 1.0
CD F:GLU132 3.5 63.7 1.0
C E:GLY263 3.8 41.3 1.0
CA E:GLY263 3.9 37.9 1.0
OE1 F:GLU132 4.3 66.0 1.0
N E:GLY263 4.3 37.5 1.0
CG F:GLU132 4.3 60.2 1.0
CB E:ASP261 4.7 37.9 1.0
O E:HOH6 4.8 53.3 1.0
CE D:LYS157 4.8 54.8 1.0
OE1 F:GLN136 4.9 45.8 1.0
N E:ARG264 4.9 44.9 1.0

Calcium binding site 7 out of 8 in 1fzg

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Calcium binding site 7 out of 8 in the Crystal Structure of Fragment D From Human Fibrinogen 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 7 of Crystal Structure of Fragment D From Human Fibrinogen with the Peptide Ligand Gly-His-Arg-Pro-Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca1

b:37.5
occ:1.00
 O F:GLY324 2.1 38.1 1.0
O F:HOH407 2.1 39.4 1.0
OD1 F:ASP320 2.2 38.5 1.0
OD1 F:ASP318 2.3 30.3 1.0
OD2 F:ASP318 2.3 36.9 1.0
O F:PHE322 2.4 42.3 1.0
CG F:ASP318 2.6 35.4 1.0
CG F:ASP320 3.1 37.2 1.0
C F:GLY324 3.3 41.4 1.0
OD2 F:ASP320 3.4 38.1 1.0
C F:PHE322 3.5 42.8 1.0
CB F:ASP318 4.1 36.6 1.0
O F:HOH414 4.1 47.8 1.0
C F:GLU323 4.1 50.5 1.0
N F:ASN325 4.1 41.5 1.0
CA F:ASN325 4.2 40.0 1.0
N F:GLY324 4.2 48.9 1.0
O F:GLU323 4.2 51.1 1.0
CB F:ASP320 4.3 34.0 1.0
N F:PHE322 4.3 34.3 1.0
CA F:PHE322 4.3 37.2 1.0
CA F:GLY324 4.3 41.7 1.0
CB F:PHE322 4.4 34.0 1.0
C F:ASP320 4.5 36.9 1.0
N F:ASP320 4.5 37.0 1.0
N F:GLU323 4.5 45.1 1.0
CA F:ASP320 4.6 35.3 1.0
O F:ASP320 4.6 37.3 1.0
CA F:GLU323 4.8 50.4 1.0
N F:LYS321 4.9 37.2 1.0

Calcium binding site 8 out of 8 in 1fzg

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Calcium binding site 8 out of 8 in the Crystal Structure of Fragment D From Human Fibrinogen 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 8 of Crystal Structure of Fragment D From Human Fibrinogen with the Peptide Ligand Gly-His-Arg-Pro-Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca4

b:0.0
occ:1.00
 OD1 F:ASP294 2.3 65.8 1.0
O F:ASP298 2.7 54.7 1.0
CG F:ASP294 3.0 64.7 1.0
OD2 F:ASP294 3.4 67.8 1.0
N F:GLY296 3.4 60.0 1.0
CA F:GLY296 3.5 60.2 1.0
C F:ASP298 3.5 55.5 1.0
OD2 F:ASP301 3.5 53.0 1.0
CB F:ASP301 3.6 48.1 1.0
CG F:ASP301 3.8 51.2 1.0
CB F:ASP294 4.0 61.6 1.0
N F:ASP298 4.1 61.8 1.0
CA F:ASP294 4.1 58.4 1.0
C F:GLY296 4.1 61.6 1.0
O F:PRO299 4.1 50.6 1.0
N F:ASP297 4.2 63.3 1.0
CA F:PRO299 4.2 52.9 1.0
N F:PRO299 4.2 54.6 1.0
C F:ASP294 4.3 58.1 1.0
N F:PHE295 4.3 57.5 1.0
N F:ASP301 4.4 45.6 1.0
C F:PRO299 4.4 49.9 1.0
CA F:ASP298 4.5 57.8 1.0
CA F:ASP301 4.6 45.6 1.0
C F:PHE295 4.7 59.7 1.0
OD1 F:ASP301 4.8 52.9 1.0
N F:LYS302 4.9 45.6 1.0
O F:GLY296 4.9 62.7 1.0
O F:ASP294 5.0 59.7 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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