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Calcium in PDB 1wmy: Crystal Structure of C-Type Lectin Cel-I From Cucumaria Echinata

Protein crystallography data

The structure of Crystal Structure of C-Type Lectin Cel-I From Cucumaria Echinata, PDB code: 1wmy was solved by H.Sugawara, M.Kusunoki, G.Kurisu, T.Fujimoto, H.Aoyagi, T.Hatakeyama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 52.70 / 2.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 92.380, 69.940, 76.690, 90.00, 136.46, 90.00
R / Rfree (%) 13.8 / 17.9

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of C-Type Lectin Cel-I From Cucumaria Echinata (pdb code 1wmy). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of C-Type Lectin Cel-I From Cucumaria Echinata, PDB code: 1wmy:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 1wmy

Go back to Calcium Binding Sites List in 1wmy
Calcium binding site 1 out of 6 in the Crystal Structure of C-Type Lectin Cel-I From Cucumaria Echinata


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of C-Type Lectin Cel-I From Cucumaria Echinata within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca201

b:13.1
occ:1.00
 OD2 A:ASP110 2.3 18.3 1.0
O A:GLU109 2.4 16.3 1.0
OE1 A:GLU81 2.4 17.2 1.0
OD2 A:ASP77 2.5 17.9 1.0
OE2 A:GLU81 2.5 21.8 1.0
O A:HOH320 2.5 16.3 1.0
OD1 A:ASP77 2.5 15.1 1.0
OD1 A:ASN104 2.6 14.4 1.0
CD A:GLU81 2.8 21.0 1.0
CG A:ASP77 2.9 17.2 1.0
CG A:ASN104 3.3 21.6 1.0
C A:GLU109 3.4 19.9 1.0
CG A:ASP110 3.4 21.1 1.0
CA A:ASP110 3.7 19.9 1.0
CA A:CA203 3.9 17.3 1.0
N A:ASP110 3.9 19.0 1.0
CB A:ASN104 4.0 20.8 1.0
O A:HOH354 4.1 26.0 1.0
CB A:ASP110 4.1 20.7 1.0
ND2 A:ASN104 4.2 24.3 1.0
CG A:GLU81 4.3 19.1 1.0
OD1 A:ASP110 4.3 22.9 1.0
CZ A:PHE84 4.4 15.5 1.0
CB A:ASP77 4.4 16.2 1.0
CA A:ASN104 4.4 21.6 1.0
O A:HOH322 4.5 21.1 1.0
CA A:GLU109 4.5 20.2 1.0
OD2 A:ASP124 4.6 16.5 1.0
O A:ASP77 4.6 17.4 1.0
N A:GLU109 4.6 21.4 1.0
N A:GLY82 4.7 20.8 1.0
O A:HOH321 4.8 19.8 1.0
C A:ASP110 4.8 19.5 1.0
O A:HOH323 4.9 20.7 1.0
CA A:GLU81 4.9 19.9 1.0
CE2 A:PHE84 5.0 16.0 1.0

Calcium binding site 2 out of 6 in 1wmy

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Calcium binding site 2 out of 6 in the Crystal Structure of C-Type Lectin Cel-I From Cucumaria Echinata


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of C-Type Lectin Cel-I From Cucumaria Echinata within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca202

b:17.4
occ:1.00
 OD1 A:ASP124 2.3 19.3 1.0
OE1 A:GLU109 2.4 19.2 1.0
OD1 A:ASN123 2.5 18.4 1.0
OE1 A:GLN101 2.5 24.2 1.0
OD2 A:ASP103 2.5 19.9 1.0
O4 A:MPD301 2.5 25.5 1.0
O A:ASP124 2.5 18.5 1.0
O2 A:MPD301 2.6 27.6 1.0
CD A:GLU109 3.4 19.6 1.0
CD A:GLN101 3.4 23.1 1.0
CG A:ASP124 3.4 17.8 1.0
CG A:ASP103 3.5 23.2 1.0
CG A:ASN123 3.5 19.8 1.0
C4 A:MPD301 3.5 31.5 1.0
C A:ASP124 3.6 20.4 1.0
OE2 A:GLU109 3.7 22.2 1.0
OD1 A:ASP103 3.8 20.9 1.0
NE2 A:GLN101 3.8 20.7 1.0
C2 A:MPD301 3.8 32.8 1.0
N A:ASP124 3.8 20.5 1.0
ND2 A:ASN123 3.9 23.7 1.0
C3 A:MPD301 3.9 33.9 1.0
OD2 A:ASP124 4.1 16.5 1.0
CA A:ASP124 4.1 18.3 1.0
N A:ASP103 4.4 21.4 1.0
CB A:ASP124 4.4 19.1 1.0
CB A:TRP105 4.6 22.9 1.0
CG A:GLN101 4.6 23.3 1.0
CG A:GLU109 4.7 19.7 1.0
C1 A:MPD301 4.7 40.2 1.0
N A:ASN125 4.7 18.5 1.0
CB A:ASP103 4.7 23.0 1.0
CB A:ASN123 4.8 21.5 1.0
N A:TRP105 4.8 22.4 1.0
C5 A:MPD301 4.8 36.8 1.0
C A:ASN123 4.8 19.7 1.0
N A:ASN104 4.8 22.4 1.0
CB A:GLU109 4.8 20.4 1.0
CM A:MPD301 4.9 34.5 1.0
CA A:ASN123 5.0 21.0 1.0
CA A:ASP103 5.0 22.5 1.0

Calcium binding site 3 out of 6 in 1wmy

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Calcium binding site 3 out of 6 in the Crystal Structure of C-Type Lectin Cel-I From Cucumaria Echinata


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of C-Type Lectin Cel-I From Cucumaria Echinata within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca203

b:17.3
occ:1.00
 O A:HOH321 2.3 19.8 1.0
O A:HOH354 2.3 26.0 1.0
OE2 A:GLU81 2.3 21.8 1.0
O A:HOH376 2.4 31.2 1.0
OD2 A:ASP110 2.4 18.3 1.0
OD1 A:ASP110 2.4 22.9 1.0
CG A:ASP110 2.8 21.1 1.0
CD A:GLU81 3.5 21.0 1.0
CA A:CA201 3.9 13.1 1.0
OD1 A:ASN104 4.1 14.4 1.0
O A:HOH416 4.1 35.5 1.0
O A:ASP77 4.2 17.4 1.0
CB A:GLU81 4.2 20.1 1.0
CG A:GLU81 4.2 19.1 1.0
CB A:ASP110 4.3 20.7 1.0
OE1 A:GLU81 4.4 17.2 1.0
OD1 A:ASP77 4.6 15.1 1.0
ND2 A:ASN104 4.6 24.3 1.0
CG A:ASN104 4.8 21.6 1.0
CA A:GLU81 4.8 19.9 1.0
O A:ASN107 4.9 26.4 1.0
OD2 A:ASP77 4.9 17.9 1.0
CG A:ASP77 5.0 17.2 1.0

Calcium binding site 4 out of 6 in 1wmy

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Calcium binding site 4 out of 6 in the Crystal Structure of C-Type Lectin Cel-I From Cucumaria Echinata


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of C-Type Lectin Cel-I From Cucumaria Echinata within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca201

b:15.3
occ:1.00
 OD1 B:ASP110 2.3 21.6 1.0
O B:HOH322 2.4 22.9 1.0
OE2 B:GLU81 2.4 15.2 1.0
O B:GLU109 2.5 17.7 1.0
OD2 B:ASP77 2.6 16.0 1.0
OE1 B:GLU81 2.6 17.5 1.0
OD1 B:ASP77 2.6 16.2 1.0
OD1 B:ASN104 2.6 23.1 1.0
CD B:GLU81 2.8 17.1 1.0
CG B:ASP77 3.0 19.7 1.0
CG B:ASN104 3.4 22.6 1.0
CG B:ASP110 3.4 20.6 1.0
C B:GLU109 3.4 18.0 1.0
CA B:ASP110 3.8 18.1 1.0
CA B:CA203 3.8 29.9 1.0
O B:HOH355 3.9 42.1 1.0
CB B:ASN104 4.0 19.3 1.0
N B:ASP110 4.0 18.3 1.0
CB B:ASP110 4.1 18.6 1.0
ND2 B:ASN104 4.2 23.8 1.0
CG B:GLU81 4.3 18.3 1.0
O B:HOH324 4.4 34.5 1.0
OD2 B:ASP110 4.4 28.7 1.0
CZ B:PHE84 4.4 15.2 1.0
CB B:ASP77 4.5 17.9 1.0
CA B:ASN104 4.5 19.9 1.0
N B:GLU109 4.5 22.9 1.0
CA B:GLU109 4.6 20.4 1.0
N B:GLY82 4.6 19.6 1.0
OD2 B:ASP124 4.7 17.0 1.0
O B:HOH323 4.7 31.2 1.0
O B:HOH325 4.8 34.6 1.0
CE2 B:PHE84 4.8 15.0 1.0
CA B:GLU81 4.9 19.8 1.0
O B:ASP77 4.9 20.1 1.0
C B:ASP110 5.0 18.5 1.0

Calcium binding site 5 out of 6 in 1wmy

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Calcium binding site 5 out of 6 in the Crystal Structure of C-Type Lectin Cel-I From Cucumaria Echinata


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of C-Type Lectin Cel-I From Cucumaria Echinata within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca202

b:14.8
occ:1.00
 OE1 B:GLU109 2.3 18.0 1.0
OD1 B:ASP124 2.4 14.4 1.0
OD2 B:ASP103 2.4 21.2 1.0
OE1 B:GLN101 2.5 26.6 1.0
OD1 B:ASN123 2.5 24.3 1.0
O2 B:MPD302 2.5 36.1 1.0
O B:ASP124 2.5 16.3 1.0
O4 B:MPD302 2.7 39.5 1.0
CD B:GLU109 3.3 24.0 1.0
CD B:GLN101 3.4 26.9 1.0
C4 B:MPD302 3.4 47.3 1.0
CG B:ASP124 3.4 18.5 1.0
CG B:ASN123 3.5 19.5 1.0
CG B:ASP103 3.5 20.8 1.0
C B:ASP124 3.6 16.8 1.0
C2 B:MPD302 3.8 47.4 1.0
NE2 B:GLN101 3.8 22.5 1.0
OE2 B:GLU109 3.8 21.8 1.0
C3 B:MPD302 3.8 48.0 1.0
OD1 B:ASP103 3.9 20.9 1.0
ND2 B:ASN123 3.9 21.2 1.0
N B:ASP124 3.9 17.5 1.0
OD2 B:ASP124 4.1 17.0 1.0
CA B:ASP124 4.2 17.3 1.0
N B:ASP103 4.3 21.8 1.0
CB B:ASP124 4.4 16.5 1.0
CG B:GLU109 4.6 21.7 1.0
CG B:GLN101 4.7 22.8 1.0
C1 B:MPD302 4.7 46.1 1.0
CB B:TRP105 4.7 26.4 1.0
CB B:GLU109 4.7 18.5 1.0
N B:ASN125 4.8 16.5 1.0
CB B:ASP103 4.8 21.8 1.0
CB B:ASN123 4.8 18.1 1.0
C5 B:MPD302 4.8 50.7 1.0
N B:TRP105 4.8 22.8 1.0
N B:ASN104 4.9 19.6 1.0
CM B:MPD302 4.9 47.8 1.0
C B:ASN123 4.9 17.5 1.0
CA B:ASP103 5.0 21.2 1.0

Calcium binding site 6 out of 6 in 1wmy

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Calcium binding site 6 out of 6 in the Crystal Structure of C-Type Lectin Cel-I From Cucumaria Echinata


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of C-Type Lectin Cel-I From Cucumaria Echinata within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca203

b:29.9
occ:1.00
 O B:HOH323 2.4 31.2 1.0
O B:HOH355 2.4 42.1 1.0
OE2 B:GLU81 2.5 15.2 1.0
O B:HOH421 2.5 40.7 1.0
OD2 B:ASP110 2.6 28.7 1.0
OD1 B:ASP110 2.6 21.6 1.0
CG B:ASP110 2.9 20.6 1.0
CD B:GLU81 3.7 17.1 1.0
CA B:CA201 3.8 15.3 1.0
OD1 B:ASN104 4.2 23.1 1.0
CB B:GLU81 4.2 20.8 1.0
CG B:GLU81 4.3 18.3 1.0
CB B:ASP110 4.4 18.6 1.0
OD1 B:ASP77 4.6 16.2 1.0
O B:ASP77 4.6 20.1 1.0
OE1 B:GLU81 4.6 17.5 1.0
O B:HOH402 4.7 46.5 1.0
CA B:GLU81 4.7 19.8 1.0
O B:ASN107 4.8 30.5 1.0
O B:LYS78 4.9 16.7 1.0
ND2 B:ASN104 4.9 23.8 1.0
OD1 B:ASN107 4.9 47.4 1.0
CG B:ASN104 4.9 22.6 1.0
OD2 B:ASP77 5.0 16.0 1.0

Reference:

H.Sugawara, M.Kusunoki, G.Kurisu, T.Fujimoto, H.Aoyagi, T.Hatakeyama. Characteristic Recognition of N-Acetylgalactosamine By An Invertebrate C-Type Lectin, Cel-I, Revealed By X-Ray Crystallographic Analysis J.Biol.Chem. V. 279 45219 2004.
ISSN: ISSN 0021-9258
PubMed: 15319425
DOI: 10.1074/JBC.M408840200
Page generated: Fri Jul 12 07:12:42 2024

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