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Calcium in PDB 2j2p: L-Ficolin Complexed to N-Acetyl-Cystein (150MM)

Protein crystallography data

The structure of L-Ficolin Complexed to N-Acetyl-Cystein (150MM), PDB code: 2j2p 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) 19.97 / 2.80
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 96.400, 96.400, 140.290, 90.00, 90.00, 120.00
R / Rfree (%) 19.7 / 27

Calcium Binding Sites:

The binding sites of Calcium atom in the L-Ficolin Complexed to N-Acetyl-Cystein (150MM) (pdb code 2j2p). 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-Cystein (150MM), PDB code: 2j2p:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 2j2p

Go back to Calcium Binding Sites List in 2j2p
Calcium binding site 1 out of 6 in the L-Ficolin Complexed to N-Acetyl-Cystein (150MM)


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-Cystein (150MM) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1289

b:51.9
occ:0.75
 O A:ASN228 2.3 46.6 1.0
OD1 A:ASP226 2.6 46.4 1.0
OD1 A:ASP224 2.6 47.3 1.0
O A:GLY230 2.9 45.9 1.0
OD2 A:ASP224 3.0 46.8 1.0
CG A:ASP224 3.1 47.2 1.0
O A:ASP226 3.4 43.0 1.0
C A:ASN228 3.5 46.1 1.0
CG A:ASP226 3.6 45.8 1.0
OD2 A:ASP226 4.0 46.3 1.0
C A:GLY230 4.1 45.8 1.0
N A:ASN228 4.1 41.9 1.0
C A:THR229 4.3 47.3 1.0
CA A:ASN228 4.3 45.0 1.0
O A:THR229 4.3 47.4 1.0
C A:ASP226 4.4 42.1 1.0
CB A:ASP224 4.4 47.4 1.0
N A:THR229 4.5 46.9 1.0
N A:GLY230 4.5 47.0 1.0
CA A:THR229 4.6 47.5 1.0
CB A:ASN228 4.7 46.2 1.0
N A:ASP226 4.7 45.2 1.0
CB A:ASP226 4.8 44.7 1.0
CA A:GLY230 4.8 46.4 1.0
CA A:ASP226 4.9 43.8 1.0

Calcium binding site 2 out of 6 in 2j2p

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Calcium binding site 2 out of 6 in the L-Ficolin Complexed to N-Acetyl-Cystein (150MM)


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-Cystein (150MM) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1291

b:12.0
occ:0.75
 OD2 B:ASP224 2.3 21.0 1.0
O B:GLY230 2.3 22.3 1.0
O B:ASN228 2.3 24.5 1.0
OD1 B:ASP226 2.4 21.9 1.0
OD1 B:ASP224 2.8 22.3 1.0
CG B:ASP224 2.9 20.9 1.0
CG B:ASP226 3.4 21.9 1.0
C B:ASN228 3.5 23.9 1.0
C B:GLY230 3.5 22.2 1.0
OD2 B:ASP226 3.8 21.7 1.0
N B:ASN228 4.1 23.4 1.0
C B:THR229 4.2 23.1 1.0
N B:GLY230 4.3 22.4 1.0
CA B:ASN228 4.3 23.5 1.0
CB B:ASP224 4.3 20.3 1.0
O B:ASP226 4.3 22.3 1.0
O B:THR229 4.3 24.8 1.0
CA B:GLY230 4.4 21.9 1.0
N B:ASN231 4.5 21.4 1.0
C B:ASP226 4.5 22.3 1.0
N B:ASP226 4.5 21.4 1.0
CA B:ASN231 4.5 21.2 1.0
N B:THR229 4.5 23.8 1.0
CB B:ASN228 4.5 23.6 1.0
CB B:ASP226 4.6 21.9 1.0
CA B:THR229 4.7 23.1 1.0
CA B:ASP226 4.8 21.9 1.0

Calcium binding site 3 out of 6 in 2j2p

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Calcium binding site 3 out of 6 in the L-Ficolin Complexed to N-Acetyl-Cystein (150MM)


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-Cystein (150MM) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1292

b:32.0
occ:1.00
 O C:ASN228 2.3 25.2 1.0
OD1 C:ASP226 2.4 27.7 1.0
OD2 C:ASP224 2.4 21.4 1.0
OD1 C:ASP224 2.7 22.7 1.0
O C:GLY230 2.7 25.0 1.0
CG C:ASP224 2.9 22.2 1.0
CG C:ASP226 3.3 26.5 1.0
C C:ASN228 3.5 24.9 1.0
OD2 C:ASP226 3.6 26.7 1.0
C C:GLY230 3.8 25.1 1.0
N C:ASN228 4.2 24.7 1.0
C C:THR229 4.2 26.3 1.0
O C:THR229 4.2 27.3 1.0
O C:ASP226 4.3 26.0 1.0
CB C:ASP224 4.4 22.2 1.0
CA C:ASN228 4.4 24.7 1.0
N C:GLY230 4.4 25.9 1.0
N C:ASP226 4.5 24.3 1.0
N C:THR229 4.5 25.3 1.0
C C:ASP226 4.5 25.4 1.0
CB C:ASP226 4.6 25.7 1.0
CA C:THR229 4.6 26.1 1.0
CA C:GLY230 4.6 25.5 1.0
N C:ASN231 4.6 24.4 1.0
CA C:ASP226 4.7 25.3 1.0
CA C:ASN231 4.7 23.5 1.0
CB C:ASN228 4.8 24.7 1.0

Calcium binding site 4 out of 6 in 2j2p

Go back to Calcium Binding Sites List in 2j2p
Calcium binding site 4 out of 6 in the L-Ficolin Complexed to N-Acetyl-Cystein (150MM)


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-Cystein (150MM) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca1289

b:59.7
occ:1.00
 O D:ASN228 2.4 51.1 1.0
OD1 D:ASP224 2.5 48.3 1.0
OD2 D:ASP226 2.7 52.7 1.0
CG D:ASP224 2.9 48.4 1.0
OD2 D:ASP224 2.9 48.6 1.0
O D:GLY230 3.1 50.2 1.0
O D:THR229 3.5 51.4 1.0
C D:ASN228 3.5 51.3 1.0
CG D:ASP226 3.6 52.1 1.0
C D:THR229 3.9 51.2 1.0
OD1 D:ASP226 3.9 52.4 1.0
C D:GLY230 4.2 50.0 1.0
CB D:ASP224 4.2 47.5 1.0
CA D:THR229 4.3 51.4 1.0
N D:THR229 4.3 51.3 1.0
N D:ASN228 4.4 50.9 1.0
O D:ASP226 4.4 50.9 1.0
N D:GLY230 4.5 50.8 1.0
CA D:ASN228 4.6 51.4 1.0
C D:ASP226 4.8 50.7 1.0
N D:ASP226 4.8 49.0 1.0
CA D:GLY230 4.9 50.3 1.0
CB D:ASP226 4.9 50.8 1.0

Calcium binding site 5 out of 6 in 2j2p

Go back to Calcium Binding Sites List in 2j2p
Calcium binding site 5 out of 6 in the L-Ficolin Complexed to N-Acetyl-Cystein (150MM)


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-Cystein (150MM) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca1292

b:18.5
occ:1.00
 OD2 E:ASP224 2.3 19.7 1.0
O E:GLY230 2.4 20.9 1.0
O E:ASN228 2.4 23.3 1.0
OD1 E:ASP226 2.5 22.5 1.0
OD1 E:ASP224 2.8 21.3 1.0
CG E:ASP224 2.9 20.2 1.0
CG E:ASP226 3.3 21.5 1.0
C E:GLY230 3.5 20.7 1.0
C E:ASN228 3.6 22.9 1.0
OD2 E:ASP226 3.6 21.3 1.0
C E:THR229 4.2 21.8 1.0
N E:ASN228 4.2 22.9 1.0
N E:GLY230 4.2 20.9 1.0
CB E:ASP224 4.3 20.3 1.0
O E:THR229 4.3 23.1 1.0
N E:ASN231 4.3 21.1 1.0
CA E:ASN228 4.4 22.9 1.0
O E:ASP226 4.4 22.7 1.0
CA E:GLY230 4.4 20.2 1.0
CA E:ASN231 4.4 21.5 1.0
C E:ASP226 4.5 22.4 1.0
N E:THR229 4.6 22.5 1.0
CB E:ASP226 4.6 21.9 1.0
CB E:ASN228 4.6 23.2 1.0
N E:ASP226 4.6 21.8 1.0
CA E:THR229 4.7 22.1 1.0
CA E:ASP226 4.8 22.0 1.0

Calcium binding site 6 out of 6 in 2j2p

Go back to Calcium Binding Sites List in 2j2p
Calcium binding site 6 out of 6 in the L-Ficolin Complexed to N-Acetyl-Cystein (150MM)


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-Cystein (150MM) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca1292

b:35.6
occ:1.00
 OD2 F:ASP224 2.3 22.9 1.0
O F:ASN228 2.3 25.9 1.0
OD1 F:ASP226 2.5 27.2 1.0
O F:GLY230 2.6 25.6 1.0
CG F:ASP224 2.9 23.2 1.0
OD1 F:ASP224 2.9 23.5 1.0
CG F:ASP226 3.4 25.8 1.0
C F:ASN228 3.5 25.8 1.0
C F:GLY230 3.6 25.6 1.0
OD2 F:ASP226 3.7 25.1 1.0
C F:THR229 4.0 26.6 1.0
O F:THR229 4.0 27.2 1.0
N F:GLY230 4.2 26.2 1.0
N F:ASN228 4.2 25.8 1.0
CB F:ASP224 4.3 23.4 1.0
CA F:ASN228 4.3 25.8 1.0
O F:ASP226 4.3 26.5 1.0
CA F:GLY230 4.4 25.7 1.0
N F:THR229 4.4 26.2 1.0
CA F:THR229 4.5 26.7 1.0
N F:ASN231 4.5 25.1 1.0
C F:ASP226 4.7 25.9 1.0
CB F:ASN228 4.7 26.0 1.0
CB F:ASP226 4.7 25.4 1.0
CA F:ASN231 4.7 24.5 1.0
N F:ASP226 4.8 24.3 1.0
CA F:ASP226 4.9 25.2 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 13:20:15 2024

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