Calcium 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
Zinc	(Zn)	2 atoms

The binding sites of Calcium 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 Calcium atom.
In total 4 binding sites of Calcium where determined in the Pro-Concanavalin A: Precursor of Circularly Permuted Concanavalin A, PDB code: 6xt6:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Pro-Concanavalin A: Precursor of Circularly Permuted Concanavalin A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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:Ca302 b:23.4 occ:1.00 OD2 A:ASP153 2.3 24.6 1.0 O A:TYR146 2.3 28.7 1.0 O A:HOH426 2.3 21.4 1.0 OD1 A:ASN148 2.4 25.4 1.0 OD2 A:ASP144 2.4 22.6 1.0 O A:HOH420 2.4 23.7 1.0 OD1 A:ASP144 2.6 20.2 1.0 CG A:ASP144 2.8 22.6 1.0 CG A:ASP153 3.4 28.0 1.0 C A:TYR146 3.5 27.6 1.0 CG A:ASN148 3.6 27.1 1.0 OD1 A:ASP153 3.9 28.4 1.0 N A:ASN148 3.9 29.6 1.0 MN A:MN301 4.1 23.1 1.0 CB A:ASN148 4.2 28.0 1.0 CB A:ASP144 4.3 22.7 1.0 O A:HOH414 4.4 28.5 1.0 CA A:TYR146 4.4 26.8 1.0 N A:PRO147 4.5 30.1 1.0 CA A:PRO147 4.5 29.6 1.0 O A:ASP90 4.5 27.4 1.0 CE1 A:HIS158 4.5 29.0 1.0 N A:TYR146 4.5 24.8 1.0 C A:PRO147 4.6 28.2 1.0 ND2 A:ASN148 4.6 23.0 1.0 CB A:TYR146 4.6 27.7 1.0 OD1 A:ASP90 4.6 28.1 1.0 CB A:ASP153 4.7 27.9 1.0 CA A:ASN148 4.7 29.1 1.0 O A:ARG110 4.8 32.7 1.0 CA A:ARG110 4.8 31.4 1.0 NE2 A:HIS158 4.9 27.9 1.0 CB A:ARG110 4.9 34.9 1.0 CD1 A:TYR146 5.0 29.0 1.0

Calcium binding site 2 out of 4 in the Pro-Concanavalin A: Precursor of Circularly Permuted Concanavalin A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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 A:Ca304 b:30.4 occ:1.00 OE2 A:GLU221 2.0 37.4 1.0 O B:HOH414 2.1 31.9 1.0 O A:HOH403 2.1 23.1 1.0 O A:HOH408 2.1 35.6 1.0 O A:HOH401 2.2 42.4 1.0 OE2 A:GLU65 2.3 45.5 1.0 CD A:GLU221 3.1 31.8 1.0 CD A:GLU65 3.2 47.2 1.0 OE1 A:GLU65 3.5 47.9 1.0 OE1 A:GLU221 3.6 36.1 1.0 NE2 A:HIS62 3.9 26.0 1.0 CE1 A:HIS62 4.2 24.6 1.0 O A:GLU65 4.2 42.3 1.0 CG A:GLU221 4.3 30.9 1.0 OG B:SER16 4.5 48.7 1.0 CA A:GLU65 4.5 37.0 1.0 CG A:GLU65 4.5 42.2 1.0 CB B:SER16 4.8 39.6 1.0 C A:GLU65 4.9 37.3 1.0 CB A:GLU65 4.9 38.5 1.0

Calcium binding site 3 out of 4 in the Pro-Concanavalin A: Precursor of Circularly Permuted Concanavalin A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Pro-Concanavalin A: Precursor of Circularly Permuted Concanavalin A within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca302 b:26.8 occ:1.00 O B:TYR146 2.3 26.5 1.0 OD2 B:ASP153 2.4 25.3 1.0 OD1 B:ASN148 2.4 30.2 1.0 O B:HOH415 2.4 23.4 1.0 O B:HOH416 2.5 26.1 1.0 OD1 B:ASP144 2.6 23.7 1.0 OD2 B:ASP144 2.6 21.4 1.0 CG B:ASP144 2.9 22.7 1.0 CG B:ASP153 3.5 27.5 1.0 CG B:ASN148 3.5 26.6 1.0 C B:TYR146 3.6 25.3 1.0 OD1 B:ASP153 3.9 27.6 1.0 N B:ASN148 3.9 26.9 1.0 O B:HOH402 4.0 28.7 1.0 MN B:MN301 4.2 21.2 1.0 CB B:ASN148 4.2 27.6 1.0 CA B:TYR146 4.4 25.3 1.0 CB B:ASP144 4.4 23.7 1.0 N B:PRO147 4.5 27.9 1.0 N B:TYR146 4.5 23.8 1.0 CA B:PRO147 4.5 29.8 1.0 CB B:ARG110 4.5 25.2 1.0 C B:PRO147 4.6 29.5 1.0 ND2 B:ASN148 4.6 26.6 1.0 CB B:TYR146 4.6 24.7 1.0 OD1 B:ASP90 4.6 36.2 1.0 CA B:ARG110 4.6 25.6 1.0 CE1 B:HIS158 4.6 24.4 1.0 O B:ASP90 4.7 28.6 1.0 CB B:ASP153 4.7 28.1 1.0 CA B:ASN148 4.7 25.8 1.0 O B:ARG110 4.7 27.5 1.0 CD2 B:TYR146 4.8 26.5 1.0

Calcium binding site 4 out of 4 in the Pro-Concanavalin A: Precursor of Circularly Permuted Concanavalin A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Pro-Concanavalin A: Precursor of Circularly Permuted Concanavalin A within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca304 b:49.2 occ:1.00 O B:HOH436 2.2 40.2 1.0 OE2 B:GLU253 2.3 62.0 1.0 O B:HOH422 2.4 37.6 1.0 OE1 B:GLU253 2.6 65.5 1.0 CD B:GLU253 2.8 60.3 1.0 CG B:GLU253 4.3 54.7 1.0 NZ B:LYS250 4.5 60.1 1.0 CE B:LYS250 4.7 59.1 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