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Calcium in PDB 2j3o: L-Ficolin Complexed to N-Acetyl-D-Glucosamine

Protein crystallography data

The structure of L-Ficolin Complexed to N-Acetyl-D-Glucosamine, PDB code: 2j3o 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) 19.00 / 2.65
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 200.520, 84.510, 144.090, 90.00, 123.57, 90.00
R / Rfree (%) 22.8 / 28.3

Calcium Binding Sites:

The binding sites of Calcium atom in the L-Ficolin Complexed to N-Acetyl-D-Glucosamine (pdb code 2j3o). 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-D-Glucosamine, PDB code: 2j3o:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 2j3o

Go back to Calcium Binding Sites List in 2j3o
Calcium binding site 1 out of 6 in the L-Ficolin Complexed to N-Acetyl-D-Glucosamine


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-D-Glucosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1289

b:78.7
occ:1.00
 O A:GLY230 2.3 58.7 0.0
OD2 A:ASP224 2.6 60.6 1.0
C A:GLY230 3.0 59.5 1.0
O A:ASN228 3.0 58.4 1.0
OD1 A:ASP224 3.2 63.0 1.0
C A:ASN228 3.3 59.2 1.0
CG A:ASP224 3.3 60.3 1.0
OD1 A:ASP226 3.3 57.7 1.0
CB A:ASN228 3.4 59.7 1.0
N A:GLY230 3.5 61.0 1.0
N A:ASN231 3.7 60.0 1.0
CG A:ASP226 3.7 57.0 1.0
OD2 A:ASP226 3.7 57.8 1.0
CA A:GLY230 3.7 59.8 1.0
CA A:ASN228 3.8 59.1 1.0
C A:THR229 3.9 59.5 1.0
N A:THR229 3.9 59.7 1.0
CA A:ASN231 4.0 60.1 1.0
N A:ASN228 4.1 58.3 1.0
CG A:ASN228 4.1 61.8 1.0
O A:ASP226 4.2 55.3 1.0
OD1 A:ASN228 4.4 62.1 1.0
O A:THR229 4.4 58.7 0.0
CA A:THR229 4.4 59.5 1.0
N A:CYS232 4.5 59.1 1.0
OD1 A:ASN231 4.6 65.6 1.0
C A:ASP226 4.6 56.6 1.0
CB A:ASP224 4.8 59.0 1.0
C A:ASN231 4.8 58.8 1.0
CB A:ASP226 4.8 55.9 1.0
ND2 A:ASN228 4.9 60.8 1.0

Calcium binding site 2 out of 6 in 2j3o

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


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-D-Glucosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1291

b:60.3
occ:1.00
 O B:ASN228 2.3 52.9 1.0
OD2 B:ASP224 2.4 49.1 1.0
OD1 B:ASP226 2.5 46.0 1.0
OD1 B:ASP224 2.5 43.5 1.0
O B:GLY230 2.7 46.2 1.0
CG B:ASP224 2.7 46.4 1.0
CG B:ASP226 3.5 47.2 1.0
C B:ASN228 3.5 51.5 1.0
OD2 B:ASP226 3.9 46.4 1.0
C B:GLY230 3.9 47.4 1.0
C B:THR229 4.1 49.4 1.0
CB B:ASP224 4.2 47.1 1.0
N B:ASN228 4.3 51.9 1.0
O B:ASP226 4.3 49.4 1.0
CA B:THR229 4.3 49.8 1.0
O B:THR229 4.3 50.0 1.0
N B:GLY230 4.4 48.2 1.0
N B:THR229 4.4 50.2 1.0
CA B:ASN228 4.5 51.4 1.0
C B:ASP226 4.5 48.6 1.0
N B:ASP226 4.6 47.0 1.0
CB B:ASP226 4.7 47.6 1.0
CA B:GLY230 4.7 47.0 1.0
CA B:ASP226 4.8 47.7 1.0
N B:ASN231 4.9 46.5 1.0
CB B:ASN228 5.0 51.4 1.0

Calcium binding site 3 out of 6 in 2j3o

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


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-D-Glucosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1291

b:61.6
occ:1.00
 OD1 C:ASP226 2.3 54.6 1.0
O C:GLY230 2.4 55.1 1.0
O C:ASN228 2.4 53.9 1.0
OD2 C:ASP224 2.4 48.0 1.0
OD1 C:ASP224 2.8 47.8 1.0
CG C:ASP224 2.9 47.7 1.0
CG C:ASP226 3.3 53.1 1.0
C C:ASN228 3.5 53.2 1.0
C C:GLY230 3.6 54.8 1.0
OD2 C:ASP226 3.7 53.7 1.0
C C:THR229 4.1 52.9 1.0
N C:ASN228 4.2 52.6 1.0
N C:GLY230 4.2 53.6 1.0
CB C:ASP224 4.3 47.7 1.0
O C:THR229 4.3 54.5 1.0
CA C:ASN228 4.4 52.8 1.0
N C:THR229 4.4 53.2 1.0
CA C:THR229 4.4 52.9 1.0
CA C:GLY230 4.5 54.5 1.0
O C:ASP226 4.5 49.4 1.0
N C:ASN231 4.5 54.5 1.0
CB C:ASP226 4.6 50.6 1.0
CA C:ASN231 4.6 54.7 1.0
N C:ASP226 4.7 48.2 1.0
C C:ASP226 4.7 49.9 1.0
CB C:ASN228 4.7 52.5 1.0
CA C:ASP226 4.9 49.4 1.0

Calcium binding site 4 out of 6 in 2j3o

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


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

b:75.2
occ:1.00
 O D:GLY230 2.3 58.9 1.0
O D:ASN228 2.3 61.3 1.0
OD2 D:ASP224 2.4 65.5 1.0
OD1 D:ASP226 2.7 58.8 1.0
OD1 D:ASP224 2.7 63.5 1.0
CG D:ASP224 2.8 64.1 1.0
C D:GLY230 3.3 58.5 1.0
O D:THR229 3.4 60.4 1.0
CG D:ASP226 3.5 59.2 1.0
C D:ASN228 3.5 60.5 1.0
C D:THR229 3.6 59.7 1.0
OD2 D:ASP226 3.7 58.5 1.0
N D:GLY230 4.0 58.6 1.0
CA D:GLY230 4.1 58.5 1.0
N D:ASN231 4.1 58.0 1.0
CA D:THR229 4.2 59.6 1.0
CB D:ASP224 4.2 62.1 1.0
CA D:ASN231 4.3 57.6 1.0
N D:THR229 4.3 60.2 1.0
N D:ASN228 4.5 60.1 1.0
CA D:ASN228 4.6 60.0 1.0
O D:ASP226 4.6 58.3 1.0
CB D:ASN228 4.9 59.7 1.0
CB D:ASP226 4.9 58.1 1.0

Calcium binding site 5 out of 6 in 2j3o

Go back to Calcium Binding Sites List in 2j3o
Calcium binding site 5 out of 6 in the L-Ficolin Complexed to N-Acetyl-D-Glucosamine


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-D-Glucosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca1290

b:60.1
occ:1.00
 O E:GLY230 2.2 58.6 1.0
OD2 E:ASP224 2.2 60.8 1.0
OD1 E:ASP226 2.3 60.6 1.0
O E:ASN228 2.4 59.6 1.0
OD1 E:ASP224 2.5 61.0 1.0
CG E:ASP224 2.7 59.5 1.0
CG E:ASP226 3.2 58.8 1.0
C E:GLY230 3.4 59.3 1.0
OD2 E:ASP226 3.4 59.2 1.0
C E:ASN228 3.6 59.2 1.0
O E:THR229 4.0 59.7 1.0
O E:ASP226 4.1 56.1 1.0
C E:THR229 4.1 58.9 1.0
CB E:ASP224 4.2 58.1 1.0
N E:ASN228 4.2 58.1 1.0
N E:ASN231 4.3 59.0 1.0
CA E:ASN231 4.3 58.2 1.0
N E:GLY230 4.3 58.8 1.0
CA E:GLY230 4.4 59.0 1.0
CA E:ASN228 4.4 59.2 1.0
C E:ASP226 4.5 56.9 1.0
CB E:ASP226 4.5 57.7 1.0
N E:ASP226 4.5 56.3 1.0
N E:THR229 4.6 58.8 1.0
CA E:THR229 4.6 58.9 1.0
CA E:ASP226 4.7 56.9 1.0
CB E:ASN228 4.9 59.5 1.0

Calcium binding site 6 out of 6 in 2j3o

Go back to Calcium Binding Sites List in 2j3o
Calcium binding site 6 out of 6 in the L-Ficolin Complexed to N-Acetyl-D-Glucosamine


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-D-Glucosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca1289

b:72.4
occ:1.00
 O F:ASN228 2.2 61.3 1.0
OD1 F:ASP226 2.3 61.4 1.0
O F:GLY230 2.5 60.7 1.0
OD2 F:ASP224 2.5 60.2 1.0
OD1 F:ASP224 3.0 62.2 1.0
CG F:ASP224 3.1 61.6 1.0
C F:ASN228 3.4 62.0 1.0
CG F:ASP226 3.5 61.5 1.0
C F:GLY230 3.7 61.0 1.0
O F:THR229 3.8 60.3 1.0
C F:THR229 3.9 60.5 1.0
OD2 F:ASP226 4.1 62.4 1.0
CA F:THR229 4.1 61.1 1.0
N F:THR229 4.2 61.8 1.0
O F:ASP226 4.3 61.2 1.0
O F:HOH2021 4.3 60.6 1.0
N F:GLY230 4.3 60.1 1.0
N F:ASN228 4.4 62.2 1.0
CA F:ASN228 4.4 62.2 1.0
CB F:ASP224 4.5 60.5 1.0
N F:ASN231 4.6 60.9 1.0
C F:ASP226 4.6 60.6 1.0
CA F:GLY230 4.6 60.4 1.0
CA F:ASN231 4.6 60.2 1.0
N F:ASP226 4.7 59.8 1.0
CB F:ASP226 4.7 60.4 1.0
CA F:ASP226 4.9 59.9 1.0
C F:LEU227 4.9 62.2 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 13:21:07 2024

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