Calcium in PDB 1byf: Structure of TC14; A C-Type Lectin From the Tunicate Polyandrocarpa Misakiensis

The structure of Structure of TC14; A C-Type Lectin From the Tunicate Polyandrocarpa Misakiensis, PDB code: 1byf was solved by S.F.Poget, G.B.Legge, M.Bycroft, R.L.Williams, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.00 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	54.180, 66.450, 85.900, 90.00, 90.00, 90.00
R / Rfree (%)	20.7 / 25

The structure of Structure of TC14; A C-Type Lectin From the Tunicate Polyandrocarpa Misakiensis also contains other interesting chemical elements:

Zinc

(Zn)

7 atoms

The binding sites of Calcium atom in the Structure of TC14; A C-Type Lectin From the Tunicate Polyandrocarpa Misakiensis (pdb code 1byf). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Structure of TC14; A C-Type Lectin From the Tunicate Polyandrocarpa Misakiensis, PDB code: 1byf:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Structure of TC14; A C-Type Lectin From the Tunicate Polyandrocarpa Misakiensis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of TC14; A C-Type Lectin From the Tunicate Polyandrocarpa Misakiensis within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca201 b:21.0 occ:1.00 OE1 A:GLU86 2.2 20.1 1.0 OD1 A:ASP107 2.2 16.0 1.0 OD1 A:ASP108 2.3 17.6 1.0 O2 A:GOL305 2.3 30.8 1.0 OD1 A:ASN89 2.5 19.6 1.0 O A:ASP108 2.5 15.9 1.0 O3 A:GOL305 2.5 29.6 1.0 CD A:GLU86 3.1 20.6 1.0 C2 A:GOL305 3.1 31.1 1.0 C3 A:GOL305 3.2 30.1 1.0 CG A:ASP107 3.3 16.7 1.0 CG A:ASP108 3.3 17.6 1.0 C A:ASP108 3.5 16.3 1.0 CG A:ASN89 3.6 20.4 1.0 N A:ASP108 3.6 15.7 1.0 OE2 A:GLU86 3.7 20.6 1.0 OG A:SER88 3.7 19.4 1.0 OD2 A:ASP107 3.7 16.2 1.0 CA A:ASP108 4.0 15.7 1.0 OD2 A:ASP108 4.1 17.9 1.0 N A:SER88 4.1 19.9 1.0 CG A:GLU86 4.2 20.4 1.0 CB A:ASP108 4.2 17.0 1.0 N A:ASN89 4.3 20.1 1.0 ND2 A:ASN89 4.4 19.8 1.0 O A:HOH317 4.4 17.0 1.0 O A:HOH386 4.5 29.6 1.0 C A:ASP107 4.5 15.4 1.0 C1 A:GOL305 4.5 32.6 1.0 CB A:ASP107 4.5 15.6 1.0 CB A:ASN89 4.6 20.0 1.0 CB A:GLU86 4.6 20.3 1.0 N A:VAL109 4.7 16.6 1.0 CA A:ASP107 4.8 15.1 1.0 CB A:SER88 4.8 20.2 1.0 CA A:SER88 4.8 19.8 1.0 C A:SER88 4.8 20.1 1.0 CA A:ASN89 5.0 20.0 1.0 CA A:PRO87 5.0 20.0 1.0

Calcium binding site 2 out of 4 in the Structure of TC14; A C-Type Lectin From the Tunicate Polyandrocarpa Misakiensis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of TC14; A C-Type Lectin From the Tunicate Polyandrocarpa Misakiensis within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca202 b:29.1 occ:1.00 O A:HOH423 1.9 28.2 1.0 O A:HOH422 2.0 32.1 1.0 O A:HOH424 2.0 27.7 1.0 O A:HOH421 2.0 38.2 1.0 O A:HOH425 2.1 36.5 1.0 O A:HOH420 2.2 33.6 1.0 O A:HOH356 4.1 41.1 1.0 O A:HOH306 4.1 32.5 1.0 O A:TRP82 4.2 22.0 1.0 O A:SER79 4.3 23.9 1.0 O A:HOH380 4.3 46.1 1.0 O A:HOH377 4.3 45.0 1.0 O A:SER83 4.5 22.0 1.0 CB A:TRP82 4.8 21.0 1.0 C A:TRP82 5.0 21.4 1.0

Calcium binding site 3 out of 4 in the Structure of TC14; A C-Type Lectin From the Tunicate Polyandrocarpa Misakiensis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of TC14; A C-Type Lectin From the Tunicate Polyandrocarpa Misakiensis within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca201 b:12.6 occ:1.00 OD1 B:ASP108 2.3 13.6 1.0 OD1 B:ASN89 2.4 16.1 1.0 OD1 B:ASP107 2.4 13.1 1.0 O3 B:GOL305 2.4 19.1 1.0 OE1 B:GLU86 2.4 14.3 1.0 O B:ASP108 2.4 15.3 1.0 O2 B:GOL305 2.4 19.7 1.0 CD B:GLU86 3.2 15.8 1.0 C3 B:GOL305 3.3 20.1 1.0 C2 B:GOL305 3.3 20.8 1.0 CG B:ASP107 3.4 13.6 1.0 CG B:ASP108 3.4 14.3 1.0 CG B:ASN89 3.5 16.9 1.0 C B:ASP108 3.5 16.1 1.0 N B:ASP108 3.6 15.4 1.0 OE2 B:GLU86 3.7 14.1 1.0 OD2 B:ASP107 3.7 12.2 1.0 OG B:SER88 3.8 16.6 1.0 CA B:ASP108 4.0 15.4 1.0 ND2 B:ASN89 4.1 16.1 1.0 OD2 B:ASP108 4.1 13.7 1.0 CB B:ASP108 4.2 14.5 1.0 N B:SER88 4.3 19.7 1.0 CG B:GLU86 4.3 16.1 1.0 N B:ASN89 4.3 19.8 1.0 O B:HOH326 4.4 13.8 1.0 O B:HOH315 4.4 23.7 1.0 C B:ASP107 4.5 15.3 1.0 CB B:ASN89 4.6 17.7 1.0 CB B:ASP107 4.6 13.4 1.0 C1 B:GOL305 4.6 22.8 1.0 N B:VAL109 4.7 16.3 1.0 CB B:GLU86 4.8 18.2 1.0 CA B:ASP107 4.8 14.8 1.0 C B:SER88 4.9 19.8 1.0 CB B:SER88 4.9 18.4 1.0 CA B:SER88 4.9 19.7 1.0 CG1 B:VAL109 4.9 16.7 1.0 CA B:ASN89 5.0 19.7 1.0

Calcium binding site 4 out of 4 in the Structure of TC14; A C-Type Lectin From the Tunicate Polyandrocarpa Misakiensis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of TC14; A C-Type Lectin From the Tunicate Polyandrocarpa Misakiensis within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca202 b:20.4 occ:1.00 O B:HOH457 1.9 24.0 1.0 O B:HOH455 2.0 21.0 1.0 O B:HOH456 2.0 23.3 1.0 O B:HOH454 2.1 35.1 1.0 O B:HOH458 2.1 47.5 1.0 O B:HOH391 2.3 35.1 1.0 O B:HOH330 4.0 14.6 1.0 O B:TRP82 4.1 12.3 1.0 O B:HOH392 4.1 33.8 1.0 O B:HOH393 4.1 24.9 1.0 O B:HOH372 4.1 25.9 1.0 O B:HOH334 4.1 24.6 1.0 O B:SER79 4.4 23.3 1.0 O B:SER83 4.4 12.5 1.0 CB B:TRP82 4.7 12.9 1.0 C B:TRP82 4.8 12.6 1.0 O B:HOH324 4.9 23.9 1.0 CA B:PRO84 4.9 15.3 1.0 C B:SER83 5.0 13.2 1.0

S.F.Poget, G.B.Legge, M.R.Proctor, P.J.Butler, M.Bycroft, R.L.Williams. The Structure of A Tunicate C-Type Lectin From Polyandrocarpa Misakiensis Complexed with D -Galactose. J.Mol.Biol. V. 290 867 1999.
ISSN: ISSN 0022-2836
PubMed: 10398588
DOI: 10.1006/JMBI.1999.2910