Calcium in PDB 6a56: Ajlec From the Sea Anemone Anthopleura Japonica

The structure of Ajlec From the Sea Anemone Anthopleura Japonica, PDB code: 6a56 was solved by H.Unno, T.Hatakeyama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	22.08 / 1.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	38.079, 79.732, 106.000, 90.00, 90.00, 90.00
R / Rfree (%)	14.2 / 17.6

The binding sites of Calcium atom in the Ajlec From the Sea Anemone Anthopleura Japonica (pdb code 6a56). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Ajlec From the Sea Anemone Anthopleura Japonica, PDB code: 6a56:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Ajlec From the Sea Anemone Anthopleura Japonica


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Ajlec From the Sea Anemone Anthopleura Japonica within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca202 b:9.8 occ:1.00 O A:MET147 2.3 10.3 1.0 OD1 A:ASN151 2.3 11.1 1.0 OD1 A:ASP150 2.4 10.3 1.0 O A:CYS48 2.4 9.8 1.0 O2 A:LAT201 2.5 10.6 1.0 OE1 A:GLU141 2.5 9.3 1.0 O3 A:LAT201 2.5 10.4 1.0 C2 A:LAT201 3.3 10.8 1.0 C3 A:LAT201 3.4 11.3 1.0 CG A:ASP150 3.4 10.4 1.0 C A:CYS48 3.4 10.9 1.0 CG A:ASN151 3.4 9.5 1.0 CD A:GLU141 3.4 9.1 1.0 C A:MET147 3.5 10.7 1.0 OE2 A:GLU141 3.7 9.8 1.0 OD2 A:ASP150 3.8 11.8 1.0 CA A:CYS48 3.8 10.7 1.0 CB A:CYS48 3.9 10.2 1.0 ND2 A:ASN151 3.9 9.8 1.0 CB A:MET147 4.0 10.8 1.0 CA A:MET147 4.4 10.9 1.0 N A:GLU148 4.4 10.5 1.0 CA A:GLU148 4.4 11.7 1.0 N A:ASN151 4.5 9.9 1.0 C A:ASP150 4.6 10.0 1.0 N A:GLN49 4.6 9.8 1.0 O A:HOH458 4.6 23.6 1.0 CB A:ASP150 4.6 10.4 1.0 CB A:ASN151 4.7 8.9 1.0 C A:GLU148 4.7 11.6 1.0 C1 A:LAT201 4.8 10.3 1.0 C4 A:LAT201 4.8 9.9 1.0 N A:ASP150 4.8 10.2 1.0 SG A:CYS48 4.8 10.3 1.0 CG A:GLU141 4.8 9.4 1.0 CA A:ASN151 4.9 10.5 1.0 CA A:ASP150 4.9 10.4 1.0 O A:THR146 4.9 10.8 1.0 O A:ASP150 4.9 11.5 1.0 CA A:GLN49 5.0 10.8 1.0 O A:GLU148 5.0 11.9 1.0

Calcium binding site 2 out of 4 in the Ajlec From the Sea Anemone Anthopleura Japonica


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Ajlec From the Sea Anemone Anthopleura Japonica within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca203 b:13.3 occ:1.00 O A:HOH368 2.3 16.1 1.0 OE2 A:GLU148 2.3 18.3 1.0 OD1 A:ASN145 2.3 13.4 1.0 OD1 A:ASP142 2.3 11.5 1.0 OD1 A:ASN21 2.3 13.8 1.0 O A:ASP142 2.4 11.4 1.0 CD A:GLU148 3.2 16.0 1.0 C A:ASP142 3.3 10.7 1.0 OE1 A:GLU148 3.3 17.4 1.0 CG A:ASN21 3.4 13.2 1.0 CG A:ASN145 3.5 14.1 1.0 CG A:ASP142 3.5 10.2 1.0 CA A:ASP142 3.6 11.2 1.0 N A:ASN21 3.8 11.7 1.0 O A:HOH413 3.8 17.1 1.0 CB A:ASP142 4.1 11.1 1.0 ND2 A:ASN21 4.2 17.1 1.0 CA A:ASN21 4.2 10.8 1.0 CA A:ASN145 4.3 12.0 1.0 ND2 A:ASN145 4.3 16.7 1.0 O A:HOH408 4.3 23.4 1.0 N A:GLY20 4.4 11.7 1.0 CB A:ASN21 4.4 13.4 1.0 CB A:ASN145 4.4 12.4 1.0 N A:ASN145 4.5 12.1 1.0 OD2 A:ASP142 4.5 11.5 1.0 N A:LEU143 4.5 10.5 1.0 CG A:GLU148 4.6 14.2 1.0 O A:GLU141 4.7 10.1 1.0 C A:GLY20 4.7 15.1 1.0 CZ3 A:TRP138 4.8 11.6 1.0 O A:HOH471 4.8 25.0 1.0 CA A:GLY20 4.9 12.6 1.0 N A:ASP142 4.9 11.3 1.0

Calcium binding site 3 out of 4 in the Ajlec From the Sea Anemone Anthopleura Japonica


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Ajlec From the Sea Anemone Anthopleura Japonica within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca203 b:15.2 occ:1.00 O B:MET147 2.3 14.7 1.0 OD1 B:ASP150 2.3 19.1 1.0 OD1 B:ASN151 2.3 15.4 1.0 O B:CYS48 2.4 16.9 1.0 O2 B:LAT201 2.4 17.2 1.0 O3 B:LAT201 2.4 16.8 1.0 OE1 B:GLU141 2.5 12.6 1.0 C2 B:LAT201 3.3 18.2 1.0 C3 B:LAT201 3.4 18.0 1.0 CG B:ASP150 3.4 18.8 1.0 C B:CYS48 3.4 17.4 1.0 CG B:ASN151 3.4 15.0 1.0 CD B:GLU141 3.4 12.1 1.0 C B:MET147 3.5 14.6 1.0 OE2 B:GLU141 3.7 13.5 1.0 OD2 B:ASP150 3.7 19.7 1.0 CA B:CYS48 3.8 16.8 1.0 CB B:CYS48 3.9 16.2 1.0 ND2 B:ASN151 3.9 14.4 1.0 CB B:MET147 4.0 14.2 1.0 CA B:MET147 4.4 15.5 1.0 CA B:GLU148 4.5 14.7 1.0 N B:GLU148 4.5 14.9 1.0 N B:ASN151 4.5 18.3 1.0 N B:GLN49 4.6 18.0 1.0 C B:ASP150 4.6 19.6 1.0 CB B:ASP150 4.6 19.1 1.0 CB B:ASN151 4.7 16.3 1.0 C B:GLU148 4.7 16.4 1.0 C1 B:LAT201 4.7 18.5 1.0 C4 B:LAT201 4.7 16.4 1.0 N B:ASP150 4.8 19.0 1.0 CG B:GLU141 4.8 10.8 1.0 SG B:CYS48 4.8 17.6 1.0 CA B:ASN151 4.8 18.1 1.0 O B:THR146 4.8 13.9 1.0 CA B:ASP150 4.9 19.0 1.0 CA B:GLN49 4.9 19.2 1.0 O B:ASP150 5.0 19.9 1.0

Calcium binding site 4 out of 4 in the Ajlec From the Sea Anemone Anthopleura Japonica


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Ajlec From the Sea Anemone Anthopleura Japonica within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca204 b:15.1 occ:1.00 OD1 B:ASN145 2.3 15.4 1.0 OE1 B:GLU148 2.3 18.6 1.0 OD1 B:ASN21 2.3 14.4 1.0 O B:ASP142 2.3 13.4 1.0 OD1 B:ASP142 2.4 12.4 1.0 O B:HOH341 2.4 18.2 1.0 CD B:GLU148 3.2 18.5 1.0 C B:ASP142 3.3 12.4 1.0 OE2 B:GLU148 3.3 20.5 1.0 CG B:ASN21 3.4 14.3 1.0 CG B:ASN145 3.4 14.4 1.0 CG B:ASP142 3.5 11.0 1.0 CA B:ASP142 3.6 12.6 1.0 N B:ASN21 3.8 13.5 1.0 O B:HOH402 3.8 16.7 1.0 CB B:ASP142 4.1 10.1 1.0 ND2 B:ASN21 4.1 17.5 1.0 CA B:ASN21 4.2 14.1 1.0 ND2 B:ASN145 4.2 17.3 1.0 O B:HOH421 4.2 21.6 1.0 CA B:ASN145 4.3 13.3 1.0 N B:GLY20 4.4 14.4 1.0 CB B:ASN21 4.4 13.6 1.0 CB B:ASN145 4.4 14.1 1.0 N B:ASN145 4.4 11.2 1.0 N B:LEU143 4.5 11.2 1.0 OD2 B:ASP142 4.5 11.2 1.0 CG B:GLU148 4.6 18.3 1.0 C B:GLY20 4.7 15.1 1.0 O B:GLU141 4.7 12.8 1.0 CZ3 B:TRP138 4.8 10.7 1.0 CA B:GLY20 4.9 16.6 1.0 N B:ASP142 4.9 11.1 1.0 O B:HOH444 5.0 22.5 1.0

H.Unno, A.Nakamura, S.Mori, S.Goda, K.Yamaguchi, K.Hiemori, H.Tateno, T.Hatakeyama. Identification, Characterization, and X-Ray Crystallographic Analysis of A Novel Type of Lectin Ajlec From the Sea Anemone Anthopleura Japonica. Sci Rep V. 8 11516 2018.
ISSN: ESSN 2045-2322
PubMed: 30068923
DOI: 10.1038/S41598-018-29498-0