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Calcium in PDB 2j0g: L-Ficolin Complexed to N-Acetyl-Mannosamine

Protein crystallography data

The structure of L-Ficolin Complexed to N-Acetyl-Mannosamine, PDB code: 2j0g 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) 15.00 / 2.85
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 96.940, 96.940, 139.470, 90.00, 90.00, 120.00
R / Rfree (%) 19.3 / 24.8

Calcium Binding Sites:

The binding sites of Calcium atom in the L-Ficolin Complexed to N-Acetyl-Mannosamine (pdb code 2j0g). 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 N-Acetyl-Mannosamine, PDB code: 2j0g:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 2j0g

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Calcium binding site 1 out of 6 in the L-Ficolin Complexed to N-Acetyl-Mannosamine


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 N-Acetyl-Mannosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca500

b:75.2
occ:1.00
 O A:ASP226 2.6 39.1 1.0
OD2 A:ASP224 2.6 34.3 1.0
O A:ASN228 2.8 40.4 1.0
OD1 A:ASP226 2.9 42.6 1.0
CG A:ASP224 3.2 35.7 1.0
OD1 A:ASP224 3.3 35.4 1.0
C A:ASP226 3.7 40.0 1.0
C A:ASN228 3.7 40.6 1.0
O A:GLY230 3.8 46.8 1.0
CG A:ASP226 3.8 42.1 1.0
N A:ASN228 4.2 39.7 1.0
N A:ASP226 4.3 39.0 1.0
CA A:ASP226 4.3 40.1 1.0
CB A:ASP224 4.4 36.8 1.0
CA A:THR229 4.4 42.2 1.0
N A:THR229 4.5 41.4 1.0
OD2 A:ASP226 4.6 41.3 1.0
CA A:ASN228 4.6 39.6 1.0
CB A:ASP226 4.7 40.5 1.0
N A:LEU227 4.7 39.9 1.0
O A:ASP224 4.7 37.4 1.0
C A:THR229 4.7 43.1 1.0
C A:ASP224 4.9 37.3 1.0
C A:ASN225 5.0 37.8 1.0
O A:THR229 5.0 43.0 1.0

Calcium binding site 2 out of 6 in 2j0g

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Calcium binding site 2 out of 6 in the L-Ficolin Complexed to N-Acetyl-Mannosamine


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 N-Acetyl-Mannosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca500

b:27.9
occ:1.00
 O B:ASN228 2.6 38.6 1.0
OD1 B:ASP226 2.6 36.7 1.0
OD2 B:ASP224 2.7 36.9 1.0
OD1 B:ASP224 2.8 38.0 1.0
O B:GLY230 2.8 38.8 1.0
CG B:ASP224 2.9 37.4 1.0
C B:ASN228 3.6 38.7 1.0
CG B:ASP226 3.6 37.5 1.0
C B:GLY230 3.8 38.4 1.0
OD2 B:ASP226 4.0 38.3 1.0
O B:ASP226 4.1 38.6 1.0
N B:ASN228 4.2 38.4 1.0
CB B:ASP224 4.3 37.8 1.0
N B:GLY230 4.3 38.3 1.0
CA B:ASN228 4.3 38.5 1.0
C B:THR229 4.4 38.5 1.0
N B:THR229 4.5 38.8 1.0
C B:ASP226 4.5 38.4 1.0
CA B:GLY230 4.5 38.2 1.0
N B:ASP226 4.7 38.4 1.0
CA B:THR229 4.7 38.5 1.0
N B:ASN231 4.7 38.2 1.0
CB B:ASN228 4.7 39.0 1.0
O B:THR229 4.8 38.8 1.0
CA B:ASN231 4.8 38.0 1.0
CB B:ASP226 4.8 38.0 1.0
CA B:ASP226 4.9 38.4 1.0

Calcium binding site 3 out of 6 in 2j0g

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Calcium binding site 3 out of 6 in the L-Ficolin Complexed to N-Acetyl-Mannosamine


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 N-Acetyl-Mannosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca500

b:38.6
occ:1.00
 O C:ASN228 2.4 38.6 1.0
O C:GLY230 2.5 38.8 1.0
OD2 C:ASP224 2.6 36.7 1.0
OD1 C:ASP226 2.9 36.8 1.0
CG C:ASP224 3.3 37.4 1.0
OD1 C:ASP224 3.3 38.0 1.0
C C:GLY230 3.4 38.4 1.0
C C:ASN228 3.4 38.6 1.0
N C:GLY230 3.8 38.2 1.0
CG C:ASP226 3.9 37.6 1.0
C C:THR229 3.9 38.5 1.0
CA C:GLY230 4.0 38.2 1.0
OD2 C:ASP226 4.1 38.2 1.0
O C:THR229 4.3 38.8 1.0
N C:THR229 4.3 38.8 1.0
CA C:ASN228 4.3 38.5 1.0
N C:ASN231 4.3 38.2 1.0
N C:ASN228 4.3 38.4 1.0
CA C:THR229 4.3 38.5 1.0
CB C:ASN228 4.5 39.0 1.0
CA C:ASN231 4.6 38.0 1.0
O C:ASP226 4.6 38.6 1.0
CB C:ASP224 4.7 37.9 1.0
C C:ASP226 5.0 38.4 1.0

Calcium binding site 4 out of 6 in 2j0g

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Calcium binding site 4 out of 6 in the L-Ficolin Complexed to N-Acetyl-Mannosamine


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 N-Acetyl-Mannosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca500

b:70.8
occ:1.00
 OD1 D:ASP224 2.5 40.3 1.0
O D:ASN228 2.6 45.9 1.0
CA D:THR229 2.6 47.1 1.0
CG D:ASP224 3.1 39.9 1.0
C D:ASN228 3.2 46.2 1.0
N D:THR229 3.3 46.6 1.0
OD2 D:ASP224 3.3 38.8 1.0
C D:THR229 3.3 47.5 1.0
CG2 D:THR229 3.5 47.0 1.0
CB D:THR229 3.6 47.1 1.0
O D:THR229 3.7 47.4 1.0
OD1 D:ASP226 3.7 47.4 1.0
O D:ASP226 3.8 45.0 1.0
N D:GLY230 4.2 47.9 1.0
CB D:ASP224 4.3 40.8 1.0
CA D:ASN228 4.6 45.9 1.0
O D:GLY230 4.6 48.6 1.0
O D:ASP224 4.6 42.1 1.0
N D:ASN228 4.7 45.9 1.0
C D:GLY230 4.7 48.4 1.0
CG D:ASP226 4.7 46.7 1.0
C D:ASP226 4.8 45.5 1.0
OG1 D:THR229 4.8 47.0 1.0

Calcium binding site 5 out of 6 in 2j0g

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Calcium binding site 5 out of 6 in the L-Ficolin Complexed to N-Acetyl-Mannosamine


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 N-Acetyl-Mannosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca500

b:34.0
occ:1.00
 OD1 E:ASP226 2.3 36.6 1.0
O E:ASN228 2.4 38.6 1.0
O E:GLY230 2.4 38.8 1.0
OD2 E:ASP224 2.5 36.8 1.0
OD1 E:ASP224 2.6 38.0 1.0
CG E:ASP224 2.8 37.2 1.0
CG E:ASP226 3.2 37.6 1.0
C E:GLY230 3.5 38.4 1.0
C E:ASN228 3.5 38.7 1.0
OD2 E:ASP226 3.6 38.4 1.0
N E:ASN228 4.0 38.4 1.0
CA E:ASN228 4.1 38.5 1.0
N E:GLY230 4.2 38.2 1.0
O E:ASP226 4.2 38.6 1.0
CB E:ASP224 4.2 37.7 1.0
N E:ASN231 4.3 38.2 1.0
CA E:GLY230 4.3 38.2 1.0
CB E:ASN228 4.4 39.0 1.0
CA E:ASN231 4.4 38.0 1.0
C E:THR229 4.4 38.5 1.0
C E:ASP226 4.5 38.4 1.0
CB E:ASP226 4.5 38.0 1.0
N E:THR229 4.5 38.8 1.0
N E:ASP226 4.6 38.4 1.0
CA E:ASP226 4.7 38.4 1.0
CA E:THR229 4.8 38.5 1.0
O E:THR229 4.9 38.8 1.0

Calcium binding site 6 out of 6 in 2j0g

Go back to Calcium Binding Sites List in 2j0g
Calcium binding site 6 out of 6 in the L-Ficolin Complexed to N-Acetyl-Mannosamine


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 N-Acetyl-Mannosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca500

b:46.2
occ:1.00
 O F:ASN228 2.5 38.6 1.0
OD2 F:ASP224 2.6 36.7 1.0
O F:GLY230 2.7 38.8 1.0
OD1 F:ASP226 3.2 36.8 1.0
CG F:ASP224 3.3 37.3 1.0
OD1 F:ASP224 3.3 38.0 1.0
C F:ASN228 3.4 38.7 1.0
C F:GLY230 3.6 38.4 1.0
C F:THR229 3.8 38.5 1.0
N F:GLY230 3.8 38.2 1.0
O F:THR229 4.1 38.8 1.0
CA F:THR229 4.1 38.5 1.0
CA F:GLY230 4.1 38.2 1.0
N F:THR229 4.2 38.8 1.0
CG F:ASP226 4.3 37.6 1.0
CA F:ASN228 4.3 38.5 1.0
N F:ASN228 4.4 38.4 1.0
N F:ASN231 4.6 38.2 1.0
O F:ASP226 4.6 38.6 1.0
CB F:ASP224 4.6 37.8 1.0
OD2 F:ASP226 4.6 38.2 1.0
CB F:ASN228 4.6 38.9 1.0
CA F:ASN231 4.9 38.0 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 13:12:50 2024

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