Calcium in PDB 6zqy: Crystal Structure of Tetrameric Fibrinogen-Like Recognition Domain of FIBCD1 with NEU5AC Ligand Bound

Protein crystallography data

The structure of Crystal Structure of Tetrameric Fibrinogen-Like Recognition Domain of FIBCD1 with NEU5AC Ligand Bound, PDB code: 6zqy was solved by A.K.Shrive, T.J.Greenhough, H.M.Williams, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 59.72 / 1.85
Space group P 4
Cell size a, b, c (Å), α, β, γ (°) 119.29, 119.29, 44.21, 90, 90, 90
R / Rfree (%) 17.5 / 19.6

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Tetrameric Fibrinogen-Like Recognition Domain of FIBCD1 with NEU5AC Ligand Bound (pdb code 6zqy). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of Tetrameric Fibrinogen-Like Recognition Domain of FIBCD1 with NEU5AC Ligand Bound, PDB code: 6zqy:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 6zqy

Go back to Calcium Binding Sites List in 6zqy
Calcium binding site 1 out of 2 in the Crystal Structure of Tetrameric Fibrinogen-Like Recognition Domain of FIBCD1 with NEU5AC Ligand Bound


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 Tetrameric Fibrinogen-Like Recognition Domain of FIBCD1 with NEU5AC Ligand Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca501

b:21.5
occ:1.00
OD1 A:ASP395 2.3 22.3 1.0
OD2 A:ASP393 2.4 19.6 1.0
O A:HOH636 2.4 23.7 1.0
O A:SER397 2.4 28.9 1.0
O A:HOH737 2.4 26.7 1.0
O A:ASN399 2.4 25.5 1.0
OD1 A:ASP393 2.5 17.9 1.0
CG A:ASP393 2.7 18.7 1.0
CG A:ASP395 3.2 20.8 1.0
C A:SER397 3.5 28.5 1.0
OD2 A:ASP395 3.5 20.8 1.0
C A:ASN399 3.5 26.5 1.0
O A:HOH645 4.0 44.0 1.0
O A:ASP395 4.1 22.1 1.0
N A:SER397 4.1 25.9 1.0
CA A:SER397 4.2 26.9 1.0
N A:ASN399 4.2 29.6 1.0
CB A:ASP393 4.2 19.0 1.0
N A:ASN400 4.3 23.2 1.0
C A:GLU398 4.3 30.5 1.0
CA A:ASN400 4.4 21.7 1.0
C A:ASP395 4.4 22.2 1.0
CB A:SER397 4.4 26.7 1.0
CA A:ASN399 4.4 29.1 1.0
N A:GLU398 4.4 30.3 1.0
CB A:ASP395 4.5 20.8 1.0
N A:ASP395 4.5 20.2 1.0
O A:HOH660 4.6 27.3 1.0
O A:GLU398 4.6 29.0 1.0
CA A:ASP395 4.7 21.1 1.0
CA A:GLU398 4.7 32.0 1.0
OG A:SER397 4.9 26.3 1.0

Calcium binding site 2 out of 2 in 6zqy

Go back to Calcium Binding Sites List in 6zqy
Calcium binding site 2 out of 2 in the Crystal Structure of Tetrameric Fibrinogen-Like Recognition Domain of FIBCD1 with NEU5AC Ligand Bound


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 Tetrameric Fibrinogen-Like Recognition Domain of FIBCD1 with NEU5AC Ligand Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca501

b:19.7
occ:1.00
O B:HOH714 2.3 21.0 1.0
OD1 B:ASP395 2.3 18.0 1.0
OD2 B:ASP393 2.4 19.0 1.0
O B:ASN399 2.4 23.6 1.0
O B:HOH741 2.4 24.1 1.0
O B:SER397 2.5 25.8 1.0
OD1 B:ASP393 2.5 18.9 1.0
CG B:ASP393 2.7 19.1 1.0
CG B:ASP395 3.2 18.6 1.0
OD2 B:ASP395 3.5 18.6 1.0
C B:ASN399 3.5 23.9 1.0
C B:SER397 3.5 27.5 1.0
O B:HOH738 4.0 38.7 1.0
N B:SER397 4.1 24.9 1.0
CA B:SER397 4.2 25.7 1.0
CB B:ASP393 4.2 19.6 1.0
O B:ASP395 4.2 18.8 1.0
N B:ASN400 4.3 20.9 1.0
N B:ASN399 4.3 28.0 1.0
C B:GLU398 4.3 29.6 1.0
CB B:SER397 4.4 25.7 1.0
CA B:ASN400 4.4 19.1 1.0
O B:HOH751 4.4 40.9 1.0
C B:ASP395 4.4 19.7 1.0
CB B:ASP395 4.5 18.8 1.0
CA B:ASN399 4.5 27.0 1.0
O B:GLU398 4.5 30.1 1.0
N B:GLU398 4.5 29.2 1.0
N B:ASP395 4.6 18.6 1.0
CA B:ASP395 4.7 19.1 1.0
O B:HOH699 4.8 21.9 1.0
CA B:GLU398 4.8 31.3 1.0
OG B:SER397 5.0 25.3 1.0
N B:HIS396 5.0 20.9 1.0

Reference:

H.M.Williams, J.B.Moeller, I.Burns, A.Schlosser, G.L.Sorensen, T.J.Greenhough, U.Holmskov, A.K.Shrive. Crystal Structures of Human Immune Protein FIBCD1 Reveal An Extended Ligand Binding Site Compatible with Recognition of Chitin Oligomers To Be Published.
Page generated: Sat Aug 21 12:34:37 2021

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