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Calcium in PDB 2j1g: L-Ficolin Complexed to N-Acetyl-Cystein

Protein crystallography data

The structure of L-Ficolin Complexed to N-Acetyl-Cystein, PDB code: 2j1g 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 / 1.95
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 99.040, 99.040, 142.000, 90.00, 90.00, 120.00
R / Rfree (%) 17.6 / 21

Calcium Binding Sites:

The binding sites of Calcium atom in the L-Ficolin Complexed to N-Acetyl-Cystein (pdb code 2j1g). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the L-Ficolin Complexed to N-Acetyl-Cystein, PDB code: 2j1g:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 2j1g

Go back to Calcium Binding Sites List in 2j1g
Calcium binding site 1 out of 5 in the L-Ficolin Complexed to N-Acetyl-Cystein


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1290

b:25.7
occ:1.00
 O B:ASN228 2.3 25.7 1.0
O B:GLY230 2.3 25.5 1.0
OD1 B:ASP226 2.3 25.8 1.0
OD2 B:ASP224 2.4 27.9 1.0
O B:HOH2154 2.4 22.5 1.0
O B:HOH2159 2.4 30.1 1.0
OD1 B:ASP224 2.6 27.5 1.0
CG B:ASP224 2.8 26.5 1.0
CG B:ASP226 3.2 25.7 1.0
OD2 B:ASP226 3.4 27.5 1.0
C B:ASN228 3.5 26.4 1.0
C B:GLY230 3.5 25.8 1.0
N B:ASN228 4.1 25.9 1.0
O B:HOH2155 4.2 41.6 1.0
N B:GLY230 4.2 24.3 1.0
CA B:ASN228 4.2 26.1 1.0
C B:THR229 4.3 26.0 1.0
O B:ASP226 4.3 25.0 1.0
CB B:ASP224 4.4 26.0 1.0
CA B:ASN231 4.4 26.1 1.0
N B:ASN231 4.4 25.3 1.0
N B:THR229 4.4 25.7 1.0
CB B:ASN228 4.4 26.2 1.0
CA B:GLY230 4.5 25.8 1.0
CB B:ASP226 4.5 25.6 1.0
C B:ASP226 4.5 25.9 1.0
CA B:THR229 4.6 26.0 1.0
O B:HOH2162 4.6 40.8 1.0
O B:HOH2157 4.6 28.9 1.0
O B:THR229 4.6 27.6 1.0
N B:ASP226 4.6 25.2 1.0
CA B:ASP226 4.8 25.3 1.0
O B:HOH2163 5.0 32.7 1.0

Calcium binding site 2 out of 5 in 2j1g

Go back to Calcium Binding Sites List in 2j1g
Calcium binding site 2 out of 5 in the L-Ficolin Complexed to N-Acetyl-Cystein


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

b:29.5
occ:1.00
 OD2 C:ASP224 2.3 29.0 1.0
OD1 C:ASP226 2.3 28.5 1.0
O C:GLY230 2.3 28.1 1.0
O C:ASN228 2.3 29.5 1.0
O C:HOH2127 2.4 29.7 1.0
OD1 C:ASP224 2.6 29.9 1.0
O C:HOH2135 2.6 32.0 1.0
CG C:ASP224 2.8 29.1 1.0
CG C:ASP226 3.1 29.2 1.0
OD2 C:ASP226 3.3 29.0 1.0
C C:ASN228 3.5 29.1 1.0
C C:GLY230 3.5 27.2 1.0
O C:HOH2128 3.8 82.6 1.0
N C:ASN228 4.1 28.8 1.0
C C:THR229 4.2 29.3 1.0
CA C:ASN228 4.2 29.4 1.0
N C:GLY230 4.2 28.1 1.0
CB C:ASP224 4.3 28.2 1.0
O C:HOH2130 4.3 41.0 1.0
CA C:ASN231 4.3 25.7 1.0
O C:ASP226 4.3 27.9 1.0
N C:ASN231 4.4 26.0 1.0
O C:HOH2137 4.4 43.5 1.0
CA C:GLY230 4.4 27.8 1.0
N C:THR229 4.4 29.7 1.0
CB C:ASP226 4.5 28.2 1.0
CB C:ASN228 4.5 29.7 1.0
C C:ASP226 4.5 28.3 1.0
O C:THR229 4.5 29.5 1.0
CA C:THR229 4.6 29.9 1.0
N C:ASP226 4.6 26.8 1.0
O C:HOH2126 4.7 30.9 1.0
CA C:ASP226 4.7 27.6 1.0
N C:LEU227 5.0 28.4 1.0

Calcium binding site 3 out of 5 in 2j1g

Go back to Calcium Binding Sites List in 2j1g
Calcium binding site 3 out of 5 in the L-Ficolin Complexed to N-Acetyl-Cystein


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

b:53.3
occ:1.00
 O D:GLY230 2.3 49.6 1.0
O D:ASN228 2.3 51.0 1.0
OD1 D:ASP226 2.3 48.5 1.0
O D:HOH2068 2.4 58.2 1.0
OD2 D:ASP224 2.4 48.6 1.0
OD1 D:ASP224 2.7 48.3 1.0
CG D:ASP224 2.9 47.9 1.0
CG D:ASP226 3.1 49.0 1.0
OD2 D:ASP226 3.3 49.1 1.0
C D:ASN228 3.5 50.9 1.0
C D:GLY230 3.5 49.4 1.0
N D:ASN228 4.1 50.9 1.0
O D:THR229 4.1 51.5 1.0
C D:THR229 4.1 51.1 1.0
CA D:ASN228 4.2 51.1 1.0
N D:GLY230 4.3 50.6 1.0
O D:HOH2067 4.3 65.7 1.0
CB D:ASP224 4.4 47.6 1.0
N D:ASN231 4.4 48.8 1.0
CB D:ASN228 4.4 51.3 1.0
CA D:ASN231 4.4 47.8 1.0
CA D:GLY230 4.5 50.0 1.0
N D:THR229 4.5 51.2 1.0
CB D:ASP226 4.5 48.5 1.0
O D:ASP226 4.5 48.9 1.0
O D:HOH2066 4.6 54.5 1.0
C D:ASP226 4.6 48.8 1.0
CA D:THR229 4.6 51.0 1.0
N D:ASP226 4.7 47.9 1.0
CA D:ASP226 4.8 48.5 1.0

Calcium binding site 4 out of 5 in 2j1g

Go back to Calcium Binding Sites List in 2j1g
Calcium binding site 4 out of 5 in the L-Ficolin Complexed to N-Acetyl-Cystein


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

b:25.2
occ:1.00
 O E:ASN228 2.3 26.9 1.0
O E:GLY230 2.3 28.7 1.0
O E:HOH2152 2.3 27.3 1.0
OD2 E:ASP224 2.3 33.9 1.0
OD1 E:ASP226 2.4 26.7 1.0
O E:HOH2146 2.5 26.7 1.0
OD1 E:ASP224 2.6 32.5 1.0
CG E:ASP224 2.8 32.8 1.0
CG E:ASP226 3.2 29.4 1.0
OD2 E:ASP226 3.4 30.9 1.0
C E:ASN228 3.4 27.6 1.0
C E:GLY230 3.5 29.7 1.0
N E:ASN228 4.1 28.2 1.0
N E:GLY230 4.2 28.2 1.0
CA E:ASN228 4.2 27.5 1.0
O E:HOH2153 4.3 40.2 1.0
C E:THR229 4.3 28.8 1.0
O E:ASP226 4.3 28.5 1.0
CB E:ASP224 4.3 30.2 1.0
N E:THR229 4.4 27.3 1.0
N E:ASN231 4.4 29.7 1.0
CA E:ASN231 4.5 30.2 1.0
CA E:GLY230 4.5 29.3 1.0
CB E:ASN228 4.5 28.0 1.0
C E:ASP226 4.6 28.6 1.0
CA E:THR229 4.6 27.9 1.0
CB E:ASP226 4.6 27.8 1.0
N E:ASP226 4.6 28.3 1.0
O E:HOH2147 4.7 31.9 1.0
O E:THR229 4.7 28.9 1.0
CA E:ASP226 4.8 28.1 1.0
OD1 E:ASN228 5.0 31.1 1.0

Calcium binding site 5 out of 5 in 2j1g

Go back to Calcium Binding Sites List in 2j1g
Calcium binding site 5 out of 5 in the L-Ficolin Complexed to N-Acetyl-Cystein


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

b:52.3
occ:1.00
 O F:ASN228 2.2 45.4 1.0
OD1 F:ASP226 2.3 39.0 1.0
OD2 F:ASP224 2.4 36.3 1.0
O F:GLY230 2.6 41.1 1.0
OD1 F:ASP224 2.9 39.7 1.0
CG F:ASP224 3.1 38.0 1.0
O F:HOH2077 3.1 54.4 1.0
C F:ASN228 3.2 44.2 1.0
CG F:ASP226 3.2 38.6 1.0
OD2 F:ASP226 3.6 37.6 1.0
N F:ASN228 3.8 43.3 1.0
C F:GLY230 3.8 41.3 1.0
C F:THR229 4.0 44.1 1.0
CA F:ASN228 4.0 44.0 1.0
O F:ASP226 4.1 39.1 1.0
N F:THR229 4.1 44.5 1.0
N F:GLY230 4.1 43.3 1.0
O F:THR229 4.2 44.6 1.0
C F:ASP226 4.2 39.0 1.0
CA F:THR229 4.2 44.6 1.0
CB F:ASN228 4.3 44.1 1.0
CB F:ASP226 4.5 38.3 1.0
CA F:GLY230 4.5 42.1 1.0
CB F:ASP224 4.6 38.3 1.0
N F:ASP226 4.6 37.6 1.0
CA F:ASP226 4.6 38.3 1.0
N F:LEU227 4.6 40.1 1.0
C F:LEU227 4.7 42.1 1.0
N F:ASN231 4.8 39.7 1.0
CA F:LEU227 5.0 41.5 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 13:16:45 2024

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