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Calcium in PDB 2j0y: L-Ficolin Complexed to B-1,3-D-Glucan

Protein crystallography data

The structure of L-Ficolin Complexed to B-1,3-D-Glucan, PDB code: 2j0y was solved by V.Garlatti, C.Gaboriaud, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.95 / 2.35
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 96.080, 96.080, 140.980, 90.00, 90.00, 120.00
R / Rfree (%) 19.6 / 24.2

Calcium Binding Sites:

The binding sites of Calcium atom in the L-Ficolin Complexed to B-1,3-D-Glucan (pdb code 2j0y). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the L-Ficolin Complexed to B-1,3-D-Glucan, PDB code: 2j0y:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 2j0y

Go back to Calcium Binding Sites List in 2j0y
Calcium binding site 1 out of 6 in the L-Ficolin Complexed to B-1,3-D-Glucan


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of L-Ficolin Complexed to B-1,3-D-Glucan within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1290

b:27.6
occ:1.00
 OD1 B:ASP226 2.3 43.6 1.0
O B:ASN228 2.3 44.3 1.0
O B:HOH2039 2.3 26.2 1.0
O B:HOH2038 2.4 25.6 1.0
O B:GLY230 2.4 44.8 1.0
OD2 B:ASP224 2.5 45.0 1.0
OD1 B:ASP224 2.6 45.4 1.0
CG B:ASP224 2.9 45.1 1.0
CG B:ASP226 3.2 43.5 1.0
C B:ASN228 3.4 44.7 1.0
OD2 B:ASP226 3.5 42.5 1.0
C B:GLY230 3.5 44.7 1.0
N B:ASN228 4.0 44.6 1.0
CA B:ASN228 4.2 44.6 1.0
C B:THR229 4.2 44.7 1.0
O B:ASP226 4.2 44.9 1.0
N B:GLY230 4.2 44.4 1.0
O B:HOH2036 4.3 33.2 1.0
CB B:ASP224 4.4 44.6 1.0
N B:ASN231 4.4 44.5 1.0
CA B:GLY230 4.4 44.6 1.0
C B:ASP226 4.4 44.6 1.0
N B:THR229 4.4 44.7 1.0
CB B:ASN228 4.4 43.9 1.0
O B:THR229 4.5 45.0 1.0
CB B:ASP226 4.5 43.3 1.0
CA B:ASN231 4.5 44.5 1.0
N B:ASP226 4.6 44.7 1.0
CA B:THR229 4.6 44.6 1.0
CA B:ASP226 4.7 44.5 1.0

Calcium binding site 2 out of 6 in 2j0y

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Calcium binding site 2 out of 6 in the L-Ficolin Complexed to B-1,3-D-Glucan


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of L-Ficolin Complexed to B-1,3-D-Glucan within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1293

b:42.1
occ:1.00
 O C:ASN228 2.3 44.3 1.0
OD1 C:ASP226 2.4 43.6 1.0
O C:GLY230 2.5 44.8 1.0
OD2 C:ASP224 2.5 45.0 1.0
OD1 C:ASP224 2.5 45.3 1.0
CG C:ASP224 2.9 45.2 1.0
CG C:ASP226 3.2 43.5 1.0
OD2 C:ASP226 3.4 42.3 1.0
C C:ASN228 3.5 44.7 1.0
C C:GLY230 3.6 44.7 1.0
N C:ASN228 4.1 44.7 1.0
O C:ASP226 4.2 44.9 1.0
CA C:ASN228 4.2 44.6 1.0
C C:THR229 4.2 44.7 1.0
N C:GLY230 4.3 44.4 1.0
CB C:ASP224 4.4 44.6 1.0
C C:ASP226 4.5 44.6 1.0
CB C:ASN228 4.5 44.1 1.0
O C:THR229 4.5 45.0 1.0
N C:THR229 4.5 44.7 1.0
CA C:GLY230 4.5 44.6 1.0
N C:ASN231 4.5 44.6 1.0
CB C:ASP226 4.5 43.4 1.0
N C:ASP226 4.6 44.7 1.0
CA C:ASN231 4.6 44.5 1.0
CA C:THR229 4.6 44.6 1.0
CA C:ASP226 4.7 44.5 1.0

Calcium binding site 3 out of 6 in 2j0y

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Calcium binding site 3 out of 6 in the L-Ficolin Complexed to B-1,3-D-Glucan


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of L-Ficolin Complexed to B-1,3-D-Glucan within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1294

b:46.9
occ:1.00
 O C:ASP222 2.3 39.4 1.0
O C:HOH2034 2.5 32.8 1.0
O C:HOH2051 2.6 37.5 1.0
O C:HOH2033 2.8 30.1 1.0
C C:ASP222 3.5 40.4 1.0
OE1 C:GLN223 4.0 40.9 1.0
CB C:ASP222 4.2 39.5 1.0
CA C:ASP222 4.4 39.9 1.0
O4 C:BGC1289 4.4 47.4 1.0
O C:HOH2035 4.4 28.6 1.0
N C:GLN223 4.5 42.0 1.0
CA C:GLN223 4.6 42.6 1.0
OD2 C:ASP222 4.7 42.6 1.0
CG C:ASP222 4.8 40.6 1.0
CD C:GLN223 4.9 42.3 1.0
CB C:GLN223 5.0 42.8 1.0

Calcium binding site 4 out of 6 in 2j0y

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Calcium binding site 4 out of 6 in the L-Ficolin Complexed to B-1,3-D-Glucan


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of L-Ficolin Complexed to B-1,3-D-Glucan within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca1289

b:28.0
occ:1.00
 OD1 E:ASP226 2.3 43.6 1.0
O E:ASN228 2.3 44.3 1.0
O E:HOH2043 2.3 25.4 1.0
O E:HOH2040 2.4 27.1 1.0
OD2 E:ASP224 2.4 44.9 1.0
O E:GLY230 2.4 44.8 1.0
OD1 E:ASP224 2.6 45.3 1.0
CG E:ASP224 2.8 45.1 1.0
CG E:ASP226 3.2 43.5 1.0
OD2 E:ASP226 3.4 42.4 1.0
C E:ASN228 3.4 44.7 1.0
C E:GLY230 3.5 44.7 1.0
N E:ASN228 4.1 44.6 1.0
CA E:ASN228 4.2 44.6 1.0
C E:THR229 4.2 44.7 1.0
N E:GLY230 4.2 44.4 1.0
O E:ASP226 4.2 44.9 1.0
CB E:ASP224 4.3 44.6 1.0
N E:ASN231 4.4 44.6 1.0
CA E:GLY230 4.4 44.6 1.0
CB E:ASN228 4.4 43.9 1.0
N E:THR229 4.4 44.7 1.0
C E:ASP226 4.5 44.6 1.0
O E:THR229 4.5 45.0 1.0
CB E:ASP226 4.5 43.5 1.0
CA E:ASN231 4.5 44.5 1.0
N E:ASP226 4.6 44.6 1.0
O E:HOH2041 4.6 30.3 1.0
CA E:THR229 4.6 44.6 1.0
CA E:ASP226 4.7 44.5 1.0

Calcium binding site 5 out of 6 in 2j0y

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Calcium binding site 5 out of 6 in the L-Ficolin Complexed to B-1,3-D-Glucan


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of L-Ficolin Complexed to B-1,3-D-Glucan within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca1294

b:38.8
occ:1.00
 O F:ASN228 2.3 44.3 1.0
OD1 F:ASP226 2.3 43.5 1.0
O F:HOH2037 2.4 23.8 1.0
O F:GLY230 2.4 44.8 1.0
OD2 F:ASP224 2.5 45.0 1.0
OD1 F:ASP224 2.6 45.4 1.0
CG F:ASP224 2.9 45.2 1.0
CG F:ASP226 3.1 43.5 1.0
OD2 F:ASP226 3.3 42.4 1.0
C F:ASN228 3.4 44.7 1.0
C F:GLY230 3.5 44.7 1.0
N F:ASN228 4.0 44.7 1.0
CA F:ASN228 4.1 44.6 1.0
C F:THR229 4.2 44.7 1.0
O F:ASP226 4.2 44.9 1.0
N F:GLY230 4.2 44.4 1.0
CB F:ASN228 4.3 44.1 1.0
N F:THR229 4.4 44.7 1.0
C F:ASP226 4.4 44.6 1.0
CA F:GLY230 4.4 44.6 1.0
CB F:ASP226 4.4 43.4 1.0
N F:ASN231 4.4 44.5 1.0
CB F:ASP224 4.5 44.7 1.0
O F:THR229 4.5 45.0 1.0
CA F:ASN231 4.5 44.5 1.0
O F:HOH2035 4.5 29.7 1.0
CA F:THR229 4.5 44.6 1.0
N F:ASP226 4.6 44.7 1.0
CA F:ASP226 4.7 44.5 1.0
N F:LEU227 5.0 44.7 1.0
C F:LEU227 5.0 44.5 1.0

Calcium binding site 6 out of 6 in 2j0y

Go back to Calcium Binding Sites List in 2j0y
Calcium binding site 6 out of 6 in the L-Ficolin Complexed to B-1,3-D-Glucan


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of L-Ficolin Complexed to B-1,3-D-Glucan within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca1295

b:48.6
occ:1.00
 O F:ASP222 2.3 40.0 1.0
O F:HOH2034 2.6 30.2 1.0
O F:HOH2033 2.7 25.7 1.0
C F:ASP222 3.5 40.5 1.0
OE1 F:GLN223 4.0 41.7 1.0
CB F:ASP222 4.1 39.2 1.0
CA F:ASP222 4.3 39.7 1.0
O4 F:BGC1290 4.4 47.6 1.0
OD2 F:ASP222 4.4 40.3 1.0
N F:GLN223 4.5 42.4 1.0
O F:HOH2036 4.5 23.2 1.0
ND2 B:ASN275 4.5 41.1 1.0
CG F:ASP222 4.6 39.6 1.0
CA F:GLN223 4.6 42.8 1.0
CB F:GLN223 4.9 42.5 1.0
CD F:GLN223 4.9 43.4 1.0

Reference:

V.Garlatti, N.Belloy, L.Martin, M.Lacroix, M.Matsushita, Y.Endo, T.Fujita, J.C.Fontecilla-Camps, G.J.Arlaud, N.M.Thielens, C.Gaboriaud. Structural Insights Into the Innate Immune Recognition Specificities of L- and H-Ficolins. Embo J. V. 26 623 2007.
ISSN: ISSN 0261-4189
PubMed: 17215869
DOI: 10.1038/SJ.EMBOJ.7601500
Page generated: Fri Jul 12 13:14:54 2024

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