Zinc in PDB 6xt6: Pro-Concanavalin A: Precursor of Circularly Permuted Concanavalin A

The structure of Pro-Concanavalin A: Precursor of Circularly Permuted Concanavalin A, PDB code: 6xt6 was solved by S.G.Nonis, J.Haywood, J.W.Schmidberger, C.S.Bond, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.89 / 2.10
Space group	I 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	59.939, 90.420, 86.863, 90.00, 91.13, 90.00
R / Rfree (%)	19.1 / 24.4

The structure of Pro-Concanavalin A: Precursor of Circularly Permuted Concanavalin A also contains other interesting chemical elements:

Manganese	(Mn)	2 atoms
Calcium	(Ca)	4 atoms

The binding sites of Zinc atom in the Pro-Concanavalin A: Precursor of Circularly Permuted Concanavalin A (pdb code 6xt6). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Pro-Concanavalin A: Precursor of Circularly Permuted Concanavalin A, PDB code: 6xt6:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Pro-Concanavalin A: Precursor of Circularly Permuted Concanavalin A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Pro-Concanavalin A: Precursor of Circularly Permuted Concanavalin A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:48.6 occ:1.00 OD2 A:ASP216 1.9 45.6 1.0 OD2 A:ASP214 2.2 42.8 1.0 O A:HOH416 2.3 50.8 1.0 OD1 A:ASP214 2.5 33.2 1.0 CG A:ASP214 2.6 33.3 1.0 CG A:ASP216 2.6 38.4 1.0 OD1 A:ASP216 2.8 36.1 1.0 CE A:LYS193 3.6 47.1 1.0 CD A:LYS193 3.9 42.1 1.0 CB A:ASP214 4.0 32.5 1.0 O A:HOH433 4.1 38.8 1.0 CB A:ASP216 4.1 34.5 1.0 NZ A:LYS193 4.2 47.6 1.0 CG1 A:VAL70 4.8 28.1 1.0 CA A:ASP214 4.8 28.9 1.0 O A:SER190 4.9 28.2 1.0 N A:ASP216 4.9 32.5 1.0 OD1 A:ASN217 5.0 47.0 1.0 CA A:ASP216 5.0 34.3 1.0

Zinc binding site 2 out of 2 in the Pro-Concanavalin A: Precursor of Circularly Permuted Concanavalin A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Pro-Concanavalin A: Precursor of Circularly Permuted Concanavalin A within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn303 b:30.4 occ:1.00 O B:HOH413 1.7 19.8 1.0 OD2 B:ASP214 1.9 32.2 1.0 OD2 B:ASP216 2.0 25.2 1.0 CG B:ASP216 2.5 26.4 1.0 OD1 B:ASP216 2.6 27.4 1.0 CG B:ASP214 2.8 29.9 1.0 OD1 B:ASP214 3.1 30.7 1.0 NZ B:LYS193 3.8 44.0 1.0 CB B:ASP216 4.0 29.8 1.0 O B:ALA68 4.1 27.9 1.0 CB B:ASP214 4.1 27.3 1.0 CB B:ALA68 4.1 30.0 1.0 OD2 B:ASP256 4.3 40.8 1.0 CG2 B:VAL70 4.4 28.6 1.0 CA B:ALA68 4.6 29.7 1.0 OD1 B:ASN217 4.6 45.4 1.0 C B:ALA68 4.8 30.2 1.0 CD B:LYS193 4.9 35.4 1.0 CE B:LYS193 4.9 38.3 1.0 CA B:ASP216 5.0 28.8 1.0

S.G.Nonis, J.Haywood, J.W.Schmidberger, C.S.Bond, J.S.Mylne. Structural Basis For A Natural Circular Permutation in Proteins Biorxiv 2020.
DOI: 10.1101/2020.10.28.360099