Atomistry » Calcium » PDB 1fzd-1g8f » 1fzd
Atomistry »
  Calcium »
    PDB 1fzd-1g8f »
      1fzd »

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

Go back to Calcium Binding Sites List in 1fzd
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

Go back to Calcium Binding Sites List in 1fzd
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

Go back to Calcium Binding Sites List in 1fzd
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

Go back to Calcium Binding Sites List in 1fzd
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

Go back to Calcium Binding Sites List in 1fzd
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

Go back to Calcium Binding Sites List in 1fzd
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

Go back to Calcium Binding Sites List in 1fzd
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

Go back to Calcium Binding Sites List in 1fzd
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: Thu Jul 11 08:23:54 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy