Calcium in PDB 6m5m: Spl-1 - Glcnac Complex

The structure of Spl-1 - Glcnac Complex, PDB code: 6m5m 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)	38.23 / 1.70
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	44.460, 44.460, 303.613, 90.00, 90.00, 120.00
R / Rfree (%)	20.3 / 21.6

The binding sites of Calcium atom in the Spl-1 - Glcnac Complex (pdb code 6m5m). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Spl-1 - Glcnac Complex, PDB code: 6m5m:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Spl-1 - Glcnac Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Spl-1 - Glcnac Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca201 b:38.2 occ:1.00 O A:HOH310 2.1 38.8 1.0 O A:THR43 2.3 40.7 1.0 OE1 A:GLU49 2.4 35.8 1.0 OE2 A:GLU132 2.5 39.1 1.0 OE1 A:GLU45 2.5 44.8 1.0 OE2 A:GLU49 2.6 38.8 1.0 O A:HOH355 2.7 37.6 1.0 OE1 A:GLU132 2.7 36.1 1.0 CD A:GLU49 2.8 40.8 1.0 CD A:GLU132 2.9 37.7 1.0 C A:THR43 3.5 37.8 1.0 CD A:GLU45 3.6 55.0 1.0 OG1 A:THR43 3.6 39.4 1.0 O A:HOH301 3.9 37.1 1.0 OE2 A:GLU45 4.0 49.8 1.0 OH A:TYR18 4.3 42.2 1.0 CG A:GLU49 4.3 45.0 1.0 CA A:THR43 4.3 37.0 1.0 N A:THR43 4.4 33.8 1.0 N A:VAL44 4.4 40.6 1.0 CG A:GLU132 4.5 36.4 1.0 CA A:VAL44 4.5 43.5 1.0 CB A:THR43 4.5 38.9 1.0 N A:GLU45 4.5 47.7 1.0 O A:HOH326 4.6 37.8 1.0 O A:HOH340 4.6 37.0 1.0 CG2 A:VAL42 4.7 34.5 1.0 OG A:SER16 4.8 40.9 1.0 CG A:GLU45 4.9 50.3 1.0

Calcium binding site 2 out of 4 in the Spl-1 - Glcnac Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Spl-1 - Glcnac Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca203 b:44.4 occ:1.00 O A:HOH312 2.2 44.8 1.0 O A:ASP118 2.3 37.3 1.0 OE1 A:GLN120 2.4 44.9 1.0 OD2 A:ASP118 2.4 41.2 1.0 O A:HOH328 2.4 39.5 1.0 O A:HOH351 2.4 41.0 1.0 OD1 A:ASP98 2.5 45.6 1.0 CG A:ASP118 3.1 41.1 1.0 C A:ASP118 3.3 32.9 1.0 CD A:GLN120 3.4 40.2 1.0 CG A:ASP98 3.4 49.7 1.0 OD1 A:ASP118 3.6 36.8 1.0 OD2 A:ASP98 3.7 48.1 1.0 NE2 A:GLN120 3.8 39.3 1.0 CB A:ASP118 4.0 44.4 1.0 N A:HIS119 4.0 35.7 1.0 CA A:HIS119 4.2 34.9 1.0 CA A:ASP118 4.2 41.7 1.0 O3 A:NAG202 4.4 34.9 1.0 O4 A:NAG202 4.5 36.9 1.0 CB A:ALA99 4.6 49.6 1.0 OD1 A:ASN117 4.6 40.2 1.0 C A:HIS119 4.6 41.3 1.0 N A:GLN120 4.6 41.1 1.0 N A:ALA99 4.7 47.9 1.0 N A:ASP118 4.7 39.6 1.0 CG A:GLN120 4.7 42.6 1.0 CB A:ASP98 4.8 55.8 1.0 N A:ASP98 4.8 55.4 1.0 C A:ASP98 5.0 53.7 1.0 ND2 A:ASN117 5.0 40.0 1.0

Calcium binding site 3 out of 4 in the Spl-1 - Glcnac Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Spl-1 - Glcnac Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca201 b:37.0 occ:1.00 OE2 B:GLU50 2.2 35.6 1.0 O B:THR44 2.3 31.8 1.0 O B:HOH352 2.3 39.8 1.0 O B:HOH338 2.4 40.1 1.0 OE2 B:GLU133 2.4 37.1 1.0 OE1 B:GLU46 2.4 40.5 1.0 OE1 B:GLU133 2.9 38.5 1.0 CD B:GLU133 2.9 37.4 1.0 CD B:GLU50 2.9 38.1 1.0 OE1 B:GLU50 3.0 36.0 1.0 CD B:GLU46 3.4 43.2 1.0 C B:THR44 3.5 35.4 1.0 OG1 B:THR44 3.7 40.5 1.0 OE2 B:GLU46 3.7 48.5 1.0 OH B:TYR19 4.2 35.8 1.0 O B:HOH304 4.3 50.7 1.0 CA B:THR44 4.4 34.9 1.0 OG B:SER17 4.4 37.3 1.0 N B:VAL45 4.4 34.6 1.0 N B:THR44 4.4 33.9 1.0 CG B:GLU133 4.4 35.4 1.0 CG B:GLU50 4.4 36.6 1.0 CA B:VAL45 4.5 35.9 1.0 CB B:THR44 4.6 42.5 1.0 N B:GLU46 4.7 36.5 1.0 CG2 B:VAL43 4.8 34.7 1.0 CG B:GLU46 4.8 40.8 1.0 O B:HOH321 4.8 35.1 1.0 O B:HOH313 4.9 39.0 1.0 OD2 B:ASP135 4.9 51.3 1.0

Calcium binding site 4 out of 4 in the Spl-1 - Glcnac Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Spl-1 - Glcnac Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca203 b:73.9 occ:1.00 O B:ASP119 2.1 28.5 1.0 OD2 B:ASP99 2.3 33.1 1.0 O B:HOH350 2.4 38.2 1.0 OD1 B:ASN118 2.5 30.3 1.0 OD1 B:ASP119 3.0 29.6 1.0 C B:ASP119 3.3 30.0 1.0 CG B:ASN118 3.3 35.5 1.0 CG B:ASP99 3.4 33.7 1.0 ND2 B:ASN101 3.5 30.0 1.0 O3 B:NAG202 3.5 34.7 1.0 N B:ASP119 3.6 28.2 1.0 ND2 B:ASN118 3.7 31.3 1.0 CB B:ASP99 3.7 29.3 1.0 O4 B:NAG202 3.8 32.7 1.0 NZ B:LYS97 3.8 34.1 1.0 CG B:ASP119 3.9 32.0 1.0 CA B:ASP119 3.9 29.2 1.0 C4 B:NAG202 4.1 34.0 1.0 N B:HIS120 4.3 27.0 1.0 CD B:LYS97 4.4 31.8 1.0 CE B:LYS97 4.4 31.0 1.0 O B:HOH348 4.4 32.0 1.0 CB B:ASP119 4.4 29.6 1.0 OD1 B:ASP99 4.5 33.7 1.0 C3 B:NAG202 4.5 32.2 1.0 N B:ASP99 4.5 30.1 1.0 CA B:HIS120 4.6 26.1 1.0 C B:ASN118 4.6 31.3 1.0 CB B:ASN118 4.6 32.7 1.0 CG B:ASN101 4.7 33.1 1.0 OD2 B:ASP119 4.7 33.0 1.0 CA B:ASP99 4.7 29.1 1.0 CA B:ASN118 4.9 30.8 1.0

H.Unno, S.Higuchi, S.Goda, T.Hatakeyama. Novel Carbohydrate Recognition Mode of the Invertebrate C-Type Lectin Spl-1 From Saxidomus Purpuratus Revealed By the Glcnac-Complex Crystal in the Presence of CA2+ To Be Published.