Calcium in PDB 6zqx: Crystal Structure of Tetrameric Fibrinogen-Like Recognition Domain of FIBCD1 with N,N'-Diacetyl Chitobiose Ligand Bound

Protein crystallography data

The structure of Crystal Structure of Tetrameric Fibrinogen-Like Recognition Domain of FIBCD1 with N,N'-Diacetyl Chitobiose Ligand Bound, PDB code: 6zqx 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) 59.41 / 1.84
Space group P 4
Cell size a, b, c (Å), α, β, γ (°) 118.67, 118.67, 44.23, 90, 90, 90
R / Rfree (%) 16.1 / 17.6

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Tetrameric Fibrinogen-Like Recognition Domain of FIBCD1 with N,N'-Diacetyl Chitobiose Ligand Bound (pdb code 6zqx). 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 N,N'-Diacetyl Chitobiose Ligand Bound, PDB code: 6zqx:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 6zqx

Go back to Calcium Binding Sites List in 6zqx
Calcium binding site 1 out of 2 in the Crystal Structure of Tetrameric Fibrinogen-Like Recognition Domain of FIBCD1 with N,N'-Diacetyl Chitobiose 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 N,N'-Diacetyl Chitobiose Ligand Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca501

b:28.3
occ:1.00
OD1 A:ASP395 2.3 29.4 1.0
O A:HOH688 2.3 22.9 1.0
O A:SER397 2.4 34.7 1.0
OD2 A:ASP393 2.4 31.5 1.0
O A:ASN399 2.4 28.7 1.0
O A:HOH725 2.5 31.5 1.0
OD1 A:ASP393 2.5 28.5 1.0
CG A:ASP393 2.8 28.6 1.0
CG A:ASP395 3.1 29.9 1.0
OD2 A:ASP395 3.4 27.6 1.0
C A:SER397 3.4 34.9 1.0
C A:ASN399 3.5 34.4 1.0
N A:SER397 4.0 31.0 1.0
O A:HOH727 4.0 41.8 1.0
CA A:SER397 4.1 34.6 1.0
O A:ASP395 4.2 28.8 1.0
N A:ASN400 4.2 27.2 1.0
N A:ASN399 4.3 41.2 1.0
CB A:ASP393 4.3 26.5 1.0
CB A:SER397 4.3 34.7 1.0
CA A:ASN400 4.3 25.6 1.0
C A:GLU398 4.3 41.0 1.0
CA A:ASN399 4.4 40.7 1.0
C A:ASP395 4.4 30.1 1.0
CB A:ASP395 4.5 27.6 1.0
N A:GLU398 4.5 37.2 1.0
N A:ASP395 4.5 25.4 1.0
O A:GLU398 4.6 38.3 1.0
CA A:ASP395 4.7 28.1 1.0
O A:HOH695 4.8 34.5 1.0
CA A:GLU398 4.8 41.4 1.0
OG A:SER397 4.9 34.6 1.0

Calcium binding site 2 out of 2 in 6zqx

Go back to Calcium Binding Sites List in 6zqx
Calcium binding site 2 out of 2 in the Crystal Structure of Tetrameric Fibrinogen-Like Recognition Domain of FIBCD1 with N,N'-Diacetyl Chitobiose 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 N,N'-Diacetyl Chitobiose Ligand Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca501

b:25.6
occ:1.00
O B:HOH662 2.3 28.7 1.0
OD1 B:ASP395 2.3 23.7 1.0
O B:ASN399 2.3 28.3 1.0
O B:HOH733 2.4 32.2 1.0
OD2 B:ASP393 2.4 26.0 1.0
O B:SER397 2.5 31.2 1.0
OD1 B:ASP393 2.6 24.7 1.0
CG B:ASP393 2.8 27.4 1.0
CG B:ASP395 3.2 25.9 1.0
C B:ASN399 3.5 30.0 1.0
OD2 B:ASP395 3.5 23.0 1.0
C B:SER397 3.5 33.6 1.0
O B:HOH715 4.0 42.3 1.0
N B:SER397 4.1 29.7 1.0
CA B:SER397 4.2 32.7 1.0
O B:ASP395 4.2 25.9 1.0
N B:ASN400 4.2 26.6 1.0
N B:ASN399 4.3 34.4 1.0
CB B:ASP393 4.3 27.2 1.0
C B:GLU398 4.3 36.2 1.0
CB B:SER397 4.3 33.4 1.0
CA B:ASN400 4.3 24.3 1.0
C B:ASP395 4.4 26.4 1.0
CB B:ASP395 4.5 23.4 1.0
CA B:ASN399 4.5 34.1 1.0
N B:GLU398 4.5 34.2 1.0
O B:GLU398 4.5 34.2 1.0
O B:HOH752 4.5 50.4 1.0
N B:ASP395 4.6 23.5 1.0
O B:HOH668 4.7 32.2 1.0
CA B:ASP395 4.7 23.9 1.0
CA B:GLU398 4.8 38.4 1.0
OG B:SER397 4.9 33.5 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 12:34:36 2021

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