Zinc 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:

Calcium

(Ca)

4 atoms

The binding sites of Zinc 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 Zinc atom.
In total 7 binding sites of Zinc where determined in the Structure of TC14; A C-Type Lectin From the Tunicate Polyandrocarpa Misakiensis, PDB code: 1byf:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in the Structure of TC14; A C-Type Lectin From the Tunicate Polyandrocarpa Misakiensis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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:Zn301 b:24.0 occ:1.00 OD2 A:ASP2 2.0 21.5 1.0 CG A:ASP2 2.8 22.6 1.0 OD1 A:ASP2 3.0 22.3 1.0 O A:HOH348 3.3 2.0 1.0 CB A:ASP2 4.2 23.1 1.0 O B:HOH400 4.7 29.2 1.0 NH2 B:ARG116 4.9 17.8 1.0

Zinc binding site 2 out of 7 in the Structure of TC14; A C-Type Lectin From the Tunicate Polyandrocarpa Misakiensis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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:Zn302 b:30.9 occ:1.00 OD2 A:ASP52 1.9 13.1 1.0 OXT A:ACT127 2.0 32.8 1.0 O A:ACT126 2.1 25.2 1.0 C A:ACT127 2.7 32.5 1.0 OXT A:ACT126 2.7 26.1 1.0 C A:ACT126 2.7 25.9 1.0 O A:ACT127 2.8 32.9 1.0 CG A:ASP52 2.8 13.1 1.0 OD1 A:ASP52 3.0 13.3 1.0 O A:HOH408 3.7 48.9 1.0 NH2 A:ARG115 3.8 27.1 1.0 CD1 A:TRP100 3.9 16.7 1.0 NE1 A:TRP100 4.1 17.1 1.0 CH3 A:ACT127 4.2 32.0 1.0 CB A:ASP52 4.2 12.6 1.0 CH3 A:ACT126 4.2 25.1 1.0 OG A:SER101 4.4 17.4 1.0 OE1 A:GLN98 4.5 16.1 1.0 NE2 A:GLN98 4.7 14.7 1.0 O A:HOH325 4.7 20.4 1.0 CZ A:ARG115 4.9 25.8 1.0

Zinc binding site 3 out of 7 in the Structure of TC14; A C-Type Lectin From the Tunicate Polyandrocarpa Misakiensis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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 A:Zn304 b:30.2 occ:1.00 OD2 A:ASP35 2.1 20.2 1.0 O A:HOH427 2.1 40.7 1.0 O A:HOH426 2.2 29.2 1.0 O A:HOH364 2.6 29.5 1.0 CG A:ASP35 2.9 21.3 1.0 OD1 A:ASP35 3.1 21.9 1.0 N A:ASP2 3.9 23.6 1.0 CB A:ASP35 4.3 21.9 1.0 CE1 A:TYR3 4.7 21.1 1.0 CA A:ASP2 4.9 23.3 1.0

Zinc binding site 4 out of 7 in the Structure of TC14; A C-Type Lectin From the Tunicate Polyandrocarpa Misakiensis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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 A:Zn303 b:59.8 occ:1.00 O B:HOH460 2.1 23.4 1.0 O B:HOH423 3.0 18.3 1.0 O B:HOH398 3.0 7.0 1.0 O A:HOH391 3.4 32.5 1.0 O B:HOH437 3.9 41.6 1.0 O A:HOH378 4.6 47.6 1.0

Zinc binding site 5 out of 7 in the Structure of TC14; A C-Type Lectin From the Tunicate Polyandrocarpa Misakiensis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 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:Zn303 b:27.1 occ:1.00 O B:HOH453 2.0 27.2 1.0 OE2 B:GLU10 2.1 21.6 1.0 CD B:GLU10 2.9 22.0 1.0 OE1 B:GLU10 3.0 21.1 1.0 O A:HOH348 3.1 2.0 1.0 O B:HOH343 4.1 20.3 1.0 CG B:GLU10 4.4 21.2 1.0 O B:HOH440 4.9 46.3 1.0

Zinc binding site 6 out of 7 in the Structure of TC14; A C-Type Lectin From the Tunicate Polyandrocarpa Misakiensis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 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:Zn302 b:20.5 occ:1.00 OD2 B:ASP52 1.9 13.7 1.0 O B:HOH459 1.9 17.0 1.0 OXT B:ACT127 1.9 25.1 1.0 OXT B:ACT126 2.0 15.2 1.0 C B:ACT127 2.7 24.8 1.0 C B:ACT126 2.7 17.0 1.0 O B:ACT126 2.7 17.8 1.0 CG B:ASP52 2.8 13.5 1.0 O B:ACT127 2.8 25.5 1.0 OD1 B:ASP52 2.9 12.5 1.0 O B:HOH378 3.7 34.5 1.0 NH1 B:ARG115 3.8 20.0 1.0 CD1 B:TRP100 4.0 14.2 1.0 NE1 B:TRP100 4.1 14.0 1.0 CH3 B:ACT127 4.1 25.2 1.0 CB B:ASP52 4.1 13.2 1.0 CH3 B:ACT126 4.2 16.0 1.0 OG B:SER101 4.5 15.9 1.0 OE1 B:GLN98 4.5 14.4 1.0 NE2 B:GLN98 4.6 13.0 1.0 O B:HOH337 4.6 13.7 1.0

Zinc binding site 7 out of 7 in the Structure of TC14; A C-Type Lectin From the Tunicate Polyandrocarpa Misakiensis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 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:Zn304 b:30.8 occ:1.00 OD2 B:ASP35 2.0 18.6 1.0 O B:HOH461 2.2 23.3 1.0 O B:HOH462 2.3 29.6 1.0 CG B:ASP35 2.9 18.9 1.0 OD1 B:ASP35 3.1 18.6 1.0 N B:ASP2 3.5 24.4 1.0 CB B:ASP35 4.3 19.0 1.0 CE1 B:TYR3 4.6 18.8 1.0 CA B:ASP2 4.7 23.5 1.0 CG B:MET38 4.7 22.0 1.0 OD1 B:ASP2 4.8 21.9 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