Manganese 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:

Calcium	(Ca)	4 atoms
Zinc	(Zn)	2 atoms

The binding sites of Manganese 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 Manganese atom.
In total 2 binding sites of Manganese where determined in the Pro-Concanavalin A: Precursor of Circularly Permuted Concanavalin A, PDB code: 6xt6:
Jump to Manganese binding site number: 1; 2;

Manganese 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 Manganese with other atoms in the Mn 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:Mn301 b:23.1 occ:1.00 O A:HOH411 1.9 21.1 1.0 OE2 A:GLU142 1.9 25.4 1.0 O A:HOH414 2.1 28.5 1.0 NE2 A:HIS158 2.2 27.9 1.0 OD2 A:ASP144 2.2 22.6 1.0 OD1 A:ASP153 2.2 28.4 1.0 CD A:GLU142 3.0 26.4 1.0 CG A:ASP153 3.0 28.0 1.0 CE1 A:HIS158 3.1 29.0 1.0 CG A:ASP144 3.2 22.6 1.0 CD2 A:HIS158 3.2 27.3 1.0 OE1 A:GLU142 3.4 26.1 1.0 CB A:ASP144 3.5 22.7 1.0 OD2 A:ASP153 3.5 24.6 1.0 O A:HOH426 3.7 21.4 1.0 OG A:SER168 4.1 26.4 1.0 CA A:CA302 4.1 23.4 1.0 CB A:ASP153 4.2 27.9 1.0 ND1 A:HIS158 4.2 27.1 1.0 CG A:HIS158 4.3 26.9 1.0 OD1 A:ASP144 4.3 20.2 1.0 CG A:GLU142 4.3 24.7 1.0 CA A:ASP153 4.5 29.7 1.0 O A:VAL166 4.8 28.6 1.0 CA A:ASP144 5.0 24.2 1.0

Manganese 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 Manganese with other atoms in the Mn 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:Mn301 b:21.2 occ:1.00 O B:HOH402 1.9 28.7 1.0 NE2 B:HIS158 2.0 25.1 1.0 OD2 B:ASP144 2.0 21.4 1.0 O B:HOH408 2.1 37.3 1.0 OE2 B:GLU142 2.1 30.3 1.0 OD1 B:ASP153 2.2 27.6 1.0 CE1 B:HIS158 2.9 24.4 1.0 CG B:ASP153 3.0 27.5 1.0 CG B:ASP144 3.1 22.7 1.0 CD B:GLU142 3.1 29.2 1.0 CD2 B:HIS158 3.1 25.1 1.0 OE1 B:GLU142 3.5 29.1 1.0 CB B:ASP144 3.5 23.7 1.0 OD2 B:ASP153 3.5 25.3 1.0 OG B:SER168 4.0 26.9 1.0 ND1 B:HIS158 4.0 24.0 1.0 O B:HOH416 4.1 26.1 1.0 CB B:ASP153 4.1 28.1 1.0 CG B:HIS158 4.2 23.3 1.0 OD1 B:ASP144 4.2 23.7 1.0 CA B:CA302 4.2 26.8 1.0 CA B:ASP153 4.4 27.9 1.0 CG B:GLU142 4.4 29.0 1.0 O B:VAL166 4.8 26.9 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