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Calcium in PDB 2j3u: L-Ficolin Complexed to Galactose

Protein crystallography data

The structure of L-Ficolin Complexed to Galactose, PDB code: 2j3u 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 / 2.15
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 (%) 18.8 / 23.7

Calcium Binding Sites:

The binding sites of Calcium atom in the L-Ficolin Complexed to Galactose (pdb code 2j3u). 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 Galactose, PDB code: 2j3u:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 2j3u

Go back to Calcium Binding Sites List in 2j3u
Calcium binding site 1 out of 6 in the L-Ficolin Complexed to Galactose


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 Galactose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1289

b:83.3
occ:1.00
 OD1 A:ASP226 2.3 38.2 1.0
O A:ASN228 2.4 38.2 1.0
OD2 A:ASP224 2.7 38.5 1.0
OD1 A:ASP224 3.0 38.3 1.0
O A:GLY230 3.2 39.0 1.0
CG A:ASP224 3.2 38.8 1.0
CG A:ASP226 3.5 37.5 1.0
C A:ASN228 3.6 38.3 1.0
O A:ASP226 4.0 38.0 1.0
N A:ASN228 4.1 38.2 1.0
OD2 A:ASP226 4.1 36.8 1.0
C A:ASP226 4.1 37.9 1.0
C A:GLY230 4.3 38.9 1.0
CA A:ASN228 4.4 38.3 1.0
N A:ASP226 4.4 38.2 1.0
C A:THR229 4.4 38.8 1.0
O A:THR229 4.5 38.9 1.0
CA A:ASP226 4.6 38.1 1.0
CB A:ASP226 4.6 38.0 1.0
C A:LEU227 4.6 38.1 1.0
N A:LEU227 4.6 38.1 1.0
N A:THR229 4.6 38.6 1.0
CB A:ASP224 4.7 38.6 1.0
CA A:THR229 4.7 38.9 1.0
N A:GLY230 4.7 38.9 1.0
CA A:LEU227 4.9 38.0 1.0
CB A:ASN228 4.9 38.0 1.0

Calcium binding site 2 out of 6 in 2j3u

Go back to Calcium Binding Sites List in 2j3u
Calcium binding site 2 out of 6 in the L-Ficolin Complexed to Galactose


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 Galactose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1292

b:26.9
occ:1.00
 O B:GLY230 2.3 36.7 1.0
O B:ASN228 2.4 33.3 1.0
O B:HOH2056 2.4 20.2 1.0
OD1 B:ASP226 2.4 35.5 1.0
OD2 B:ASP224 2.4 38.5 1.0
O B:HOH2055 2.5 28.1 1.0
OD1 B:ASP224 2.6 39.4 1.0
CG B:ASP224 2.9 38.0 1.0
CG B:ASP226 3.2 35.4 1.0
OD2 B:ASP226 3.4 35.5 1.0
C B:ASN228 3.5 34.4 1.0
C B:GLY230 3.5 35.8 1.0
N B:ASN228 4.0 34.7 1.0
O B:HOH2054 4.1 35.1 1.0
O B:ASP226 4.2 34.2 1.0
N B:GLY230 4.2 33.9 1.0
CA B:ASN228 4.2 34.5 1.0
C B:THR229 4.2 34.5 1.0
CB B:ASP224 4.4 35.6 1.0
CA B:GLY230 4.4 35.0 1.0
C B:ASP226 4.4 34.4 1.0
N B:ASN231 4.4 35.6 1.0
CB B:ASN228 4.4 35.2 1.0
N B:THR229 4.5 34.1 1.0
CA B:ASN231 4.5 36.6 1.0
O B:THR229 4.5 34.9 1.0
O B:HOH2059 4.5 40.4 1.0
CB B:ASP226 4.5 34.8 1.0
N B:ASP226 4.6 35.0 1.0
CA B:THR229 4.7 34.3 1.0
O B:HOH2060 4.7 29.5 1.0
CA B:ASP226 4.7 34.7 1.0
N B:LEU227 5.0 34.3 1.0

Calcium binding site 3 out of 6 in 2j3u

Go back to Calcium Binding Sites List in 2j3u
Calcium binding site 3 out of 6 in the L-Ficolin Complexed to Galactose


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 Galactose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1292

b:42.8
occ:1.00
 O C:ASN228 2.3 39.5 1.0
O C:GLY230 2.3 37.9 1.0
OD1 C:ASP226 2.4 35.5 1.0
OD2 C:ASP224 2.4 37.5 1.0
OD1 C:ASP224 2.8 39.4 1.0
CG C:ASP224 3.0 37.8 1.0
CG C:ASP226 3.2 36.8 1.0
C C:ASN228 3.4 39.6 1.0
C C:GLY230 3.5 37.8 1.0
OD2 C:ASP226 3.5 36.8 1.0
N C:ASN228 4.0 38.9 1.0
C C:THR229 4.1 39.2 1.0
CA C:ASN228 4.1 39.4 1.0
N C:GLY230 4.2 38.9 1.0
O C:THR229 4.2 39.3 1.0
O C:ASP226 4.3 37.8 1.0
CB C:ASN228 4.3 38.9 1.0
N C:THR229 4.4 39.7 1.0
N C:ASN231 4.4 37.6 1.0
CA C:GLY230 4.4 38.0 1.0
CA C:ASN231 4.4 37.2 1.0
C C:ASP226 4.5 38.0 1.0
CB C:ASP224 4.5 36.8 1.0
CA C:THR229 4.5 39.6 1.0
CB C:ASP226 4.6 37.0 1.0
N C:ASP226 4.7 37.0 1.0
CA C:ASP226 4.8 37.1 1.0

Calcium binding site 4 out of 6 in 2j3u

Go back to Calcium Binding Sites List in 2j3u
Calcium binding site 4 out of 6 in the L-Ficolin Complexed to Galactose


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 Galactose within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca1289

b:62.3
occ:1.00
 O D:ASN228 2.2 39.2 1.0
O D:GLY230 2.3 38.8 1.0
OD1 D:ASP226 2.5 38.9 1.0
OD2 D:ASP224 2.7 38.2 1.0
OD1 D:ASP224 2.9 37.2 1.0
CG D:ASP224 3.1 37.7 1.0
C D:ASN228 3.4 39.1 1.0
CG D:ASP226 3.4 38.3 1.0
C D:GLY230 3.5 38.9 1.0
OD2 D:ASP226 3.7 38.3 1.0
C D:THR229 4.0 39.1 1.0
N D:GLY230 4.1 39.1 1.0
O D:THR229 4.1 39.0 1.0
N D:ASN228 4.2 39.0 1.0
CA D:ASN228 4.2 39.2 1.0
N D:THR229 4.3 39.1 1.0
CA D:GLY230 4.4 39.0 1.0
CA D:THR229 4.4 39.2 1.0
O D:ASP226 4.4 37.8 1.0
N D:ASN231 4.5 38.7 1.0
CB D:ASN228 4.6 39.1 1.0
C D:ASP226 4.6 38.0 1.0
CB D:ASP224 4.6 38.1 1.0
CA D:ASN231 4.6 38.7 1.0
N D:ASP226 4.6 38.0 1.0
CB D:ASP226 4.7 38.3 1.0
CA D:ASP226 4.9 38.1 1.0

Calcium binding site 5 out of 6 in 2j3u

Go back to Calcium Binding Sites List in 2j3u
Calcium binding site 5 out of 6 in the L-Ficolin Complexed to Galactose


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 Galactose within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca1291

b:23.7
occ:1.00
 OD1 E:ASP226 2.3 35.3 1.0
O E:GLY230 2.3 35.2 1.0
O E:HOH2046 2.3 24.2 1.0
OD2 E:ASP224 2.4 36.6 1.0
O E:ASN228 2.4 34.3 1.0
O E:HOH2042 2.4 24.9 1.0
OD1 E:ASP224 2.6 40.2 1.0
CG E:ASP224 2.8 38.2 1.0
CG E:ASP226 3.2 36.0 1.0
OD2 E:ASP226 3.4 36.7 1.0
C E:GLY230 3.5 34.8 1.0
C E:ASN228 3.5 34.5 1.0
N E:ASN228 4.1 35.6 1.0
O E:HOH2041 4.2 32.8 1.0
O E:ASP226 4.2 35.0 1.0
N E:GLY230 4.2 32.8 1.0
C E:THR229 4.2 33.8 1.0
CA E:ASN228 4.2 35.0 1.0
CB E:ASP224 4.3 36.3 1.0
CA E:GLY230 4.4 33.9 1.0
N E:ASN231 4.4 34.5 1.0
O E:THR229 4.4 33.5 1.0
CA E:ASN231 4.5 35.0 1.0
C E:ASP226 4.5 35.4 1.0
CB E:ASN228 4.5 35.2 1.0
O E:HOH2044 4.5 35.7 1.0
CB E:ASP226 4.5 35.6 1.0
N E:THR229 4.5 34.5 1.0
N E:ASP226 4.6 35.5 1.0
CA E:THR229 4.7 33.5 1.0
CA E:ASP226 4.7 35.5 1.0

Calcium binding site 6 out of 6 in 2j3u

Go back to Calcium Binding Sites List in 2j3u
Calcium binding site 6 out of 6 in the L-Ficolin Complexed to Galactose


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 Galactose within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca1292

b:40.3
occ:1.00
 O F:ASN228 2.3 38.7 1.0
O F:HOH2045 2.3 29.8 1.0
O F:GLY230 2.3 37.4 1.0
OD1 F:ASP226 2.4 38.0 1.0
OD2 F:ASP224 2.4 36.0 1.0
OD1 F:ASP224 2.7 37.2 1.0
CG F:ASP224 2.9 36.8 1.0
CG F:ASP226 3.2 39.0 1.0
C F:ASN228 3.3 39.6 1.0
OD2 F:ASP226 3.4 38.6 1.0
C F:GLY230 3.5 37.5 1.0
N F:ASN228 3.9 40.3 1.0
CA F:ASN228 4.1 40.2 1.0
O F:ASP226 4.1 40.8 1.0
N F:GLY230 4.1 38.7 1.0
C F:THR229 4.1 40.1 1.0
CB F:ASN228 4.3 40.0 1.0
N F:THR229 4.3 39.8 1.0
C F:ASP226 4.4 40.5 1.0
CA F:GLY230 4.4 37.6 1.0
CB F:ASP224 4.4 36.1 1.0
N F:ASN231 4.4 37.0 1.0
O F:THR229 4.5 41.2 1.0
CA F:THR229 4.5 40.3 1.0
CB F:ASP226 4.5 39.1 1.0
CA F:ASN231 4.5 36.3 1.0
N F:ASP226 4.7 39.6 1.0
CA F:ASP226 4.7 39.6 1.0
O F:HOH2047 4.8 44.9 1.0
N F:LEU227 5.0 40.9 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 13:27:31 2024

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