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Calcium in PDB 1fze: Crystal Structure of Fragment Double-D From Human Fibrin

Protein crystallography data

The structure of Crystal Structure of Fragment Double-D From Human Fibrin, PDB code: 1fze 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 / 3.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 108.000, 48.600, 166.400, 90.00, 104.40, 90.00
R / Rfree (%) 25.1 / 31.8

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Fragment Double-D From Human Fibrin (pdb code 1fze). 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, PDB code: 1fze:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 1fze

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Calcium binding site 1 out of 6 in the Crystal Structure of Fragment Double-D From Human Fibrin


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca2

b:63.5
occ:1.00
 O B:TRP385 2.5 74.1 1.0
OD1 B:ASP381 2.5 45.4 1.0
OD1 B:ASP383 2.6 39.0 1.0
OD2 B:ASP381 2.7 43.7 1.0
CG B:ASP381 2.8 42.2 1.0
C B:TRP385 3.5 69.2 1.0
CG B:ASP383 3.7 44.2 1.0
OD2 B:ASP383 4.1 52.1 1.0
CB B:ASP381 4.2 37.5 1.0
N B:LEU386 4.3 75.2 1.0
O B:ASP383 4.4 52.1 1.0
CA B:LEU386 4.4 79.7 1.0
CA B:TRP385 4.4 60.0 1.0
CB B:TRP385 4.5 53.2 1.0
N B:TRP385 4.6 62.4 1.0
O B:THR387 4.7 0.9 1.0
N B:ASP383 4.7 41.5 1.0
C B:LEU386 4.8 86.8 1.0
C B:ASP383 4.9 50.5 1.0
CB B:ASP383 5.0 43.8 1.0

Calcium binding site 2 out of 6 in 1fze

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Calcium binding site 2 out of 6 in the Crystal Structure of Fragment Double-D From Human Fibrin


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca3

b:35.6
occ:1.00
 O B:GLY263 2.3 30.0 1.0
OE2 C:GLU132 2.4 47.7 1.0
OD2 B:ASP261 2.6 41.6 1.0
OD2 B:ASP398 2.7 59.9 1.0
CG B:ASP398 3.2 56.0 1.0
OD1 B:ASP261 3.2 43.2 1.0
CG B:ASP261 3.3 39.3 1.0
C B:GLY263 3.5 18.1 1.0
OD1 B:ASP398 3.5 60.8 1.0
CD C:GLU132 3.7 44.8 1.0
OH B:TYR378 3.8 44.4 1.0
CA B:ASP398 4.0 43.0 1.0
CA B:GLY263 4.1 15.7 1.0
CB B:ASP398 4.1 49.9 1.0
OE1 C:GLN136 4.3 28.0 1.0
CE2 B:TYR378 4.4 48.0 1.0
OE1 C:GLU132 4.5 44.7 1.0
N B:ARG264 4.6 20.6 1.0
CG C:GLU132 4.6 42.1 1.0
N B:GLY263 4.6 22.0 1.0
CZ B:TYR378 4.6 45.0 1.0
N B:ASP398 4.7 41.9 1.0
CB B:ASP261 4.8 29.5 1.0
CA B:ARG264 4.9 26.2 1.0

Calcium binding site 3 out of 6 in 1fze

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Calcium binding site 3 out of 6 in the Crystal Structure of Fragment Double-D From Human Fibrin


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1

b:39.0
occ:1.00
 O C:GLY324 2.3 40.7 1.0
O C:PHE322 2.4 48.6 1.0
OD1 C:ASP320 2.6 20.5 1.0
OD2 C:ASP318 2.6 51.0 1.0
OD1 C:ASP318 2.8 53.2 1.0
CG C:ASP318 2.9 48.5 1.0
C C:GLY324 3.3 35.5 1.0
O C:GLU323 3.4 40.7 1.0
C C:PHE322 3.5 43.6 1.0
CG C:ASP320 3.5 25.1 1.0
C C:GLU323 3.6 39.3 1.0
OD2 C:ASP320 3.8 39.4 1.0
N C:GLY324 3.9 27.9 1.0
CA C:GLY324 4.1 25.2 1.0
N C:ASN325 4.2 27.7 1.0
CB C:ASP318 4.3 44.4 1.0
N C:GLU323 4.3 45.7 1.0
CA C:GLU323 4.3 43.3 1.0
O C:ASP320 4.3 24.5 1.0
CA C:ASN325 4.4 26.5 1.0
CA C:PHE322 4.4 39.6 1.0
N C:PHE322 4.5 36.2 1.0
CB C:PHE322 4.6 42.0 1.0
CB C:ASP320 4.9 21.2 1.0
C C:ASP320 4.9 28.5 1.0

Calcium binding site 4 out of 6 in 1fze

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Calcium binding site 4 out of 6 in the Crystal Structure of Fragment Double-D From Human Fibrin


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca2

b:44.0
occ:1.00
 O E:TRP385 2.3 62.4 1.0
OD1 E:ASP383 2.5 41.0 1.0
OD1 E:ASP381 2.6 42.3 1.0
OD2 E:ASP381 2.6 49.9 1.0
CG E:ASP381 2.9 43.8 1.0
C E:TRP385 3.3 62.5 1.0
CG E:ASP383 3.5 39.5 1.0
OD2 E:ASP383 3.9 36.5 1.0
CB E:TRP385 4.2 51.1 1.0
CA E:TRP385 4.2 57.4 1.0
N E:LEU386 4.2 71.5 1.0
CB E:ASP381 4.3 41.7 1.0
CA E:LEU386 4.4 78.8 1.0
O E:ASP383 4.4 55.2 1.0
N E:TRP385 4.4 58.9 1.0
N E:ASP383 4.7 40.1 1.0
O E:THR387 4.7 0.4 1.0
C E:LEU386 4.8 85.2 1.0
CB E:ASP383 4.8 40.8 1.0
O E:LYS392 4.8 80.2 1.0
C E:ASP383 4.8 50.2 1.0

Calcium binding site 5 out of 6 in 1fze

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Calcium binding site 5 out of 6 in the Crystal Structure of Fragment Double-D From Human Fibrin


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca3

b:36.2
occ:1.00
 O E:GLY263 2.3 25.7 1.0
OD2 E:ASP398 2.6 46.1 1.0
OE2 F:GLU132 2.6 48.1 1.0
OD2 E:ASP261 2.7 35.0 1.0
CG E:ASP398 3.0 46.3 1.0
OD1 E:ASP261 3.1 35.3 1.0
OD1 E:ASP398 3.3 51.8 1.0
CG E:ASP261 3.3 31.5 1.0
C E:GLY263 3.4 16.2 1.0
CA E:ASP398 3.8 37.4 1.0
CD F:GLU132 3.9 45.0 1.0
CB E:ASP398 3.9 43.8 1.0
OH E:TYR378 3.9 35.5 1.0
CA E:GLY263 3.9 16.0 1.0
CE2 E:TYR378 4.3 42.6 1.0
N E:GLY263 4.4 22.8 1.0
N E:ARG264 4.5 20.0 1.0
OE1 F:GLN136 4.5 35.2 1.0
CZ E:TYR378 4.5 42.3 1.0
N E:ASP398 4.6 43.1 1.0
OE1 F:GLU132 4.6 44.5 1.0
CB E:ASP261 4.8 21.4 1.0
CG F:GLU132 4.8 46.6 1.0
C E:ASP398 4.8 32.1 1.0
CA E:ARG264 4.9 31.0 1.0

Calcium binding site 6 out of 6 in 1fze

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Calcium binding site 6 out of 6 in the Crystal Structure of Fragment Double-D From Human Fibrin


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca1

b:37.6
occ:1.00
 O F:PHE322 2.4 35.8 1.0
OD1 F:ASP318 2.5 55.9 1.0
OD1 F:ASP320 2.5 9.8 1.0
OD2 F:ASP318 2.8 57.0 1.0
O F:GLY324 2.8 32.1 1.0
CG F:ASP318 2.9 54.2 1.0
CG F:ASP320 3.6 23.0 1.0
C F:PHE322 3.6 36.4 1.0
O F:GLU323 3.8 41.3 1.0
O F:ASP320 3.8 36.4 1.0
C F:GLY324 3.8 34.1 1.0
C F:GLU323 4.0 39.4 1.0
OD2 F:ASP320 4.0 33.1 1.0
CB F:ASP318 4.2 46.0 1.0
N F:GLY324 4.4 37.6 1.0
N F:PHE322 4.4 39.5 1.0
N F:GLU323 4.5 38.9 1.0
CA F:GLU323 4.5 41.6 1.0
CA F:PHE322 4.5 37.1 1.0
C F:ASP320 4.6 33.5 1.0
CA F:GLY324 4.6 37.9 1.0
N F:ASP320 4.7 35.2 1.0
N F:ASN325 4.8 29.5 1.0
CB F:ASP320 4.8 27.6 1.0
CB F:PHE322 4.8 31.9 1.0
CA F:ASN325 4.9 27.5 1.0
CA F:ASP320 4.9 31.1 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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