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Calcium in PDB 1fzd: Structure of Recombinant Alphaec Domain From Human Fibrinogen-420

Protein crystallography data

The structure of Structure of Recombinant Alphaec Domain From Human Fibrinogen-420, PDB code: 1fzd was solved by G.Spraggon, D.Applegate, S.J.Everse, J.-Z.Zhang, L.Veerapandian, C.Redman, R.F.Doolittle, G.Grieninger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.10
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 71.250, 105.180, 71.140, 104.60, 108.95, 71.47
R / Rfree (%) 19.5 / 25.5

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of Recombinant Alphaec Domain From Human Fibrinogen-420 (pdb code 1fzd). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Structure of Recombinant Alphaec Domain From Human Fibrinogen-420, PDB code: 1fzd:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 1fzd

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Calcium binding site 1 out of 8 in the Structure of Recombinant Alphaec Domain From Human Fibrinogen-420


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Recombinant Alphaec Domain From Human Fibrinogen-420 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1

b:17.5
occ:1.00
 OD2 A:ASP772 2.3 9.1 1.0
O A:GLU778 2.3 22.8 1.0
OD1 A:ASP774 2.3 13.8 1.0
O A:TRP776 2.4 16.7 1.0
O A:HOH871 2.5 17.8 1.0
O A:HOH895 2.5 26.7 1.0
OD1 A:ASP772 2.6 13.7 1.0
CG A:ASP772 2.8 12.2 1.0
CG A:ASP774 3.2 13.2 1.0
OD2 A:ASP774 3.4 14.1 1.0
C A:GLU778 3.5 21.6 1.0
C A:TRP776 3.5 20.2 1.0
N A:TRP776 4.0 22.1 1.0
O A:HOH850 4.1 34.6 1.0
O A:ASP774 4.1 15.7 1.0
N A:GLU778 4.2 24.9 1.0
CA A:TRP776 4.2 19.8 1.0
C A:GLU777 4.3 24.5 1.0
CB A:TRP776 4.3 19.2 1.0
N A:ASN779 4.3 18.7 1.0
CB A:ASP772 4.3 13.1 1.0
CA A:ASN779 4.3 18.0 1.0
CA A:GLU778 4.4 25.7 1.0
N A:ASP774 4.4 12.8 1.0
O A:GLU777 4.4 24.1 1.0
C A:ASP774 4.5 17.0 1.0
CB A:ASP774 4.5 15.3 1.0
O A:HOH893 4.6 35.3 1.0
N A:GLU777 4.6 21.0 1.0
CA A:ASP774 4.7 13.8 1.0
CA A:GLU777 4.7 25.8 1.0
N A:CYS780 5.0 16.6 1.0

Calcium binding site 2 out of 8 in 1fzd

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Calcium binding site 2 out of 8 in the Structure of Recombinant Alphaec Domain From Human Fibrinogen-420


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Recombinant Alphaec Domain From Human Fibrinogen-420 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1

b:19.0
occ:1.00
 O B:TRP776 2.3 17.9 1.0
OD2 B:ASP772 2.3 16.0 1.0
O B:GLU778 2.4 21.0 1.0
OD1 B:ASP774 2.4 19.2 1.0
OD1 B:ASP772 2.5 14.6 1.0
O B:HOH86 2.5 23.7 1.0
O B:HOH109 2.6 27.4 1.0
CG B:ASP772 2.9 14.8 1.0
CG B:ASP774 3.3 16.9 1.0
C B:TRP776 3.5 22.1 1.0
C B:GLU778 3.5 22.8 1.0
OD2 B:ASP774 3.5 17.1 1.0
N B:TRP776 4.1 22.9 1.0
O B:HOH67 4.2 34.4 1.0
C B:GLU777 4.2 26.4 1.0
N B:GLU778 4.2 26.4 1.0
O B:ASP774 4.2 15.6 1.0
CA B:TRP776 4.2 23.3 1.0
N B:ASN779 4.3 17.8 1.0
CA B:ASN779 4.3 16.4 1.0
O B:GLU777 4.3 25.3 1.0
CB B:ASP772 4.4 13.6 1.0
CA B:GLU778 4.4 27.2 1.0
N B:ASP774 4.4 13.7 1.0
N B:GLU777 4.5 23.3 1.0
CB B:TRP776 4.5 22.7 1.0
C B:ASP774 4.5 18.3 1.0
CB B:ASP774 4.6 14.7 1.0
CA B:GLU777 4.6 26.5 1.0
CA B:ASP774 4.7 17.2 1.0
O B:HOH107 4.7 33.9 1.0

Calcium binding site 3 out of 8 in 1fzd

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Calcium binding site 3 out of 8 in the Structure of Recombinant Alphaec Domain From Human Fibrinogen-420


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of Recombinant Alphaec Domain From Human Fibrinogen-420 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1

b:19.2
occ:1.00
 O C:GLU778 2.3 20.0 1.0
OD1 C:ASP774 2.4 17.8 1.0
OD2 C:ASP772 2.5 12.0 1.0
OD1 C:ASP772 2.5 11.4 1.0
O C:TRP776 2.6 23.9 1.0
O C:HOH143 2.7 16.8 1.0
CG C:ASP772 2.8 14.1 1.0
CG C:ASP774 3.1 17.0 1.0
OD2 C:ASP774 3.3 15.5 1.0
C C:GLU778 3.4 19.9 1.0
C C:TRP776 3.7 24.4 1.0
O C:HOH125 4.2 27.8 1.0
N C:TRP776 4.2 20.6 1.0
C C:GLU777 4.2 25.0 1.0
N C:GLU778 4.2 20.8 1.0
N C:ASN779 4.2 17.1 1.0
CA C:ASN779 4.3 16.0 1.0
CB C:ASP772 4.3 13.9 1.0
CA C:GLU778 4.4 23.5 1.0
CA C:TRP776 4.4 23.0 1.0
N C:ASP774 4.4 18.0 1.0
O C:ASP774 4.4 17.4 1.0
CB C:TRP776 4.4 24.1 1.0
CB C:ASP774 4.4 15.6 1.0
O C:GLU777 4.5 24.0 1.0
O C:HOH166 4.5 20.3 1.0
C C:ASP774 4.5 19.5 1.0
N C:GLU777 4.6 25.9 1.0
CA C:ASP774 4.7 18.7 1.0
CA C:GLU777 4.7 28.6 1.0

Calcium binding site 4 out of 8 in 1fzd

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Calcium binding site 4 out of 8 in the Structure of Recombinant Alphaec Domain From Human Fibrinogen-420


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of Recombinant Alphaec Domain From Human Fibrinogen-420 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca1

b:18.7
occ:1.00
 OD2 D:ASP772 2.3 14.8 1.0
O D:TRP776 2.4 23.5 1.0
O D:GLU778 2.5 20.8 1.0
OD1 D:ASP772 2.5 13.1 1.0
OD1 D:ASP774 2.5 17.6 1.0
O D:HOH200 2.6 25.0 1.0
O D:HOH222 2.7 30.0 1.0
CG D:ASP772 2.8 13.6 1.0
CG D:ASP774 3.2 17.9 1.0
OD2 D:ASP774 3.3 18.6 1.0
C D:GLU778 3.5 21.7 1.0
C D:TRP776 3.6 26.2 1.0
N D:TRP776 4.1 23.9 1.0
O D:HOH220 4.2 30.0 1.0
N D:GLU778 4.2 24.9 1.0
N D:ASN779 4.2 18.6 1.0
C D:GLU777 4.2 27.7 1.0
O D:ASP774 4.3 18.4 1.0
CA D:ASN779 4.3 19.4 1.0
CA D:TRP776 4.3 24.1 1.0
CB D:ASP772 4.3 11.9 1.0
CA D:GLU778 4.4 25.6 1.0
O D:GLU777 4.4 25.1 1.0
CB D:TRP776 4.4 24.2 1.0
N D:ASP774 4.4 17.2 1.0
CB D:ASP774 4.5 17.5 1.0
C D:ASP774 4.5 18.4 1.0
O D:HOH183 4.5 28.1 1.0
N D:GLU777 4.5 27.7 1.0
CA D:ASP774 4.7 17.1 1.0
CA D:GLU777 4.7 29.3 1.0

Calcium binding site 5 out of 8 in 1fzd

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Calcium binding site 5 out of 8 in the Structure of Recombinant Alphaec Domain From Human Fibrinogen-420


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of Recombinant Alphaec Domain From Human Fibrinogen-420 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca1

b:50.4
occ:1.00
 OD1 E:ASP774 2.1 54.4 1.0
O E:GLU778 2.2 55.1 1.0
O E:TRP776 2.3 59.2 1.0
O E:HOH253 2.6 55.2 1.0
OD2 E:ASP772 2.6 54.1 1.0
OD1 E:ASP772 2.8 54.3 1.0
CG E:ASP772 3.0 55.1 1.0
CG E:ASP774 3.1 54.2 1.0
C E:TRP776 3.3 60.2 1.0
C E:GLU778 3.4 56.2 1.0
OD2 E:ASP774 3.5 53.7 1.0
N E:TRP776 4.0 58.9 1.0
O E:GLU777 4.0 59.6 1.0
C E:GLU777 4.0 60.6 1.0
CA E:TRP776 4.1 59.5 1.0
N E:GLU778 4.2 59.3 1.0
CB E:TRP776 4.2 60.0 1.0
N E:ASN779 4.2 52.8 1.0
CA E:ASN779 4.3 49.2 1.0
N E:GLU777 4.3 61.5 1.0
O E:ASP774 4.4 54.2 1.0
CA E:GLU778 4.4 58.8 1.0
CB E:ASP772 4.4 54.5 1.0
CB E:ASP774 4.5 54.4 1.0
C E:ASP774 4.5 55.0 1.0
CA E:GLU777 4.5 62.4 1.0
O E:HOH269 4.7 52.2 1.0
N E:ASP774 4.7 53.4 1.0
CA E:ASP774 4.7 54.5 1.0
C E:GLN775 5.0 58.7 1.0
N E:GLN775 5.0 56.3 1.0

Calcium binding site 6 out of 8 in 1fzd

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Calcium binding site 6 out of 8 in the Structure of Recombinant Alphaec Domain From Human Fibrinogen-420


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of Recombinant Alphaec Domain From Human Fibrinogen-420 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca1

b:51.7
occ:1.00
 O F:GLU778 2.0 53.8 1.0
OD1 F:ASP774 2.1 52.3 1.0
O F:TRP776 2.4 61.9 1.0
OD2 F:ASP772 2.5 54.0 1.0
O F:HOH307 2.8 49.5 1.0
OD1 F:ASP772 3.0 54.3 1.0
CG F:ASP774 3.1 52.4 1.0
CG F:ASP772 3.2 53.7 1.0
C F:GLU778 3.2 55.4 1.0
C F:TRP776 3.3 62.0 1.0
OD2 F:ASP774 3.5 52.3 1.0
N F:TRP776 3.8 58.9 1.0
CA F:TRP776 3.9 60.9 1.0
CB F:TRP776 3.9 61.5 1.0
N F:GLU778 4.0 60.8 1.0
N F:ASN779 4.0 52.2 1.0
CA F:ASN779 4.1 48.3 1.0
CA F:GLU778 4.2 59.1 1.0
C F:GLU777 4.2 62.3 1.0
O F:ASP774 4.3 51.2 1.0
N F:GLU777 4.4 63.1 1.0
CB F:ASP774 4.4 51.3 1.0
O F:GLU777 4.5 62.0 1.0
C F:ASP774 4.5 51.7 1.0
CB F:ASP772 4.6 52.3 1.0
N F:ASP774 4.6 49.4 1.0
CA F:GLU777 4.7 63.7 1.0
CA F:ASP774 4.8 51.4 1.0
O F:HOH277 4.8 50.8 1.0
N F:CYS780 4.9 40.2 1.0
CG F:TRP776 4.9 61.8 1.0

Calcium binding site 7 out of 8 in 1fzd

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Calcium binding site 7 out of 8 in the Structure of Recombinant Alphaec Domain From Human Fibrinogen-420


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Structure of Recombinant Alphaec Domain From Human Fibrinogen-420 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca1

b:53.3
occ:1.00
 O G:GLU778 2.1 56.0 1.0
OD2 G:ASP772 2.4 51.7 1.0
OD1 G:ASP772 2.5 50.5 1.0
O G:TRP776 2.7 65.8 1.0
OD1 G:ASP774 2.7 56.1 1.0
CG G:ASP772 2.8 51.6 1.0
O G:HOH357 3.1 62.3 1.0
C G:GLU778 3.3 58.3 1.0
CG G:ASP774 3.4 56.9 1.0
OD2 G:ASP774 3.6 56.6 1.0
C G:TRP776 3.7 66.4 1.0
N G:TRP776 4.1 64.0 1.0
C G:GLU777 4.2 66.2 1.0
N G:GLU778 4.2 64.1 1.0
CB G:ASP772 4.2 50.9 1.0
O G:GLU777 4.2 66.1 1.0
N G:ASN779 4.2 54.6 1.0
CA G:GLU778 4.3 61.6 1.0
N G:ASP774 4.3 51.9 1.0
CA G:TRP776 4.3 65.7 1.0
C G:ASP774 4.4 56.8 1.0
CA G:ASN779 4.4 50.6 1.0
O G:ASP774 4.4 56.2 1.0
CB G:TRP776 4.5 67.7 1.0
CB G:ASP774 4.5 55.7 1.0
CA G:ASP774 4.6 55.3 1.0
N G:GLU777 4.6 66.7 1.0
CA G:GLU777 4.7 67.4 1.0
O G:HOH355 4.8 72.0 1.0
N G:GLN775 4.8 58.5 1.0
O G:ASP772 4.9 52.0 1.0

Calcium binding site 8 out of 8 in 1fzd

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Calcium binding site 8 out of 8 in the Structure of Recombinant Alphaec Domain From Human Fibrinogen-420


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Structure of Recombinant Alphaec Domain From Human Fibrinogen-420 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca1

b:67.8
occ:1.00
 OD2 H:ASP772 2.3 62.3 1.0
O H:GLU778 2.3 70.7 1.0
OD2 H:ASP774 2.6 72.3 1.0
OD1 H:ASP772 2.9 62.2 1.0
O H:TRP776 3.0 81.7 1.0
CG H:ASP772 3.0 62.3 1.0
CG H:ASP774 3.3 72.6 1.0
C H:TRP776 3.5 81.8 1.0
C H:GLU778 3.5 71.5 1.0
OD1 H:ASP774 3.8 72.7 1.0
C H:GLU777 4.1 79.4 1.0
N H:TRP776 4.1 80.4 1.0
CA H:TRP776 4.1 81.8 1.0
CB H:TRP776 4.1 82.9 1.0
N H:GLU777 4.2 81.8 1.0
N H:GLU778 4.2 76.8 1.0
O H:GLU777 4.3 79.3 1.0
CB H:ASP774 4.3 72.5 1.0
CA H:ASN779 4.3 63.2 1.0
N H:ASN779 4.3 67.3 1.0
CA H:GLU777 4.4 81.4 1.0
N H:ASP774 4.4 69.3 1.0
O H:ASP774 4.4 74.4 1.0
CB H:ASP772 4.4 63.1 1.0
C H:ASP774 4.5 74.2 1.0
CA H:GLU778 4.5 74.1 1.0
CA H:ASP774 4.6 72.0 1.0
O H:HOH395 4.9 57.9 1.0

Reference:

G.Spraggon, D.Applegate, S.J.Everse, J.Z.Zhang, L.Veerapandian, C.Redman, R.F.Doolittle, G.Grieninger. Crystal Structure of A Recombinant Alphaec Domain From Human Fibrinogen-420. Proc.Natl.Acad.Sci.Usa V. 95 9099 1998.
ISSN: ISSN 0027-8424
PubMed: 9689040
DOI: 10.1073/PNAS.95.16.9099
Page generated: Sat Dec 12 02:56:48 2020

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