Calcium in PDB 5mfn: Designed Armadillo Repeat Protein YIIIM5AII

The structure of Designed Armadillo Repeat Protein YIIIM5AII, PDB code: 5mfn was solved by S.Hansen, P.Ernst, C.Reichen, C.Ewald, P.Mittl, A.Plueckthun, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.66 / 2.80
Space group	P 63 2 2
Cell size a, b, c (Å), α, β, γ (°)	142.550, 142.550, 142.120, 90.00, 90.00, 120.00
R / Rfree (%)	20 / 24.6

The binding sites of Calcium atom in the Designed Armadillo Repeat Protein YIIIM5AII (pdb code 5mfn). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Designed Armadillo Repeat Protein YIIIM5AII, PDB code: 5mfn:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Designed Armadillo Repeat Protein YIIIM5AII


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Designed Armadillo Repeat Protein YIIIM5AII within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:0.6 occ:1.00 O B:PRO149 2.4 97.7 1.0 OE2 A:GLU67 2.5 0.8 1.0 OE1 B:GLU151 2.6 0.7 1.0 O A:PRO65 3.3 92.2 1.0 CD A:GLU67 3.4 0.2 1.0 CD B:GLU151 3.4 0.5 1.0 C B:PRO149 3.6 96.2 1.0 OE1 A:GLU67 3.6 93.3 1.0 OE2 B:GLU151 3.7 0.2 1.0 CA B:ASN150 4.1 87.5 1.0 N B:ASN150 4.2 88.5 1.0 C A:PRO65 4.3 94.7 1.0 N B:GLU151 4.4 95.0 1.0 CA A:ASN66 4.6 93.7 1.0 N A:GLU67 4.6 91.2 1.0 CA B:PRO149 4.7 94.4 1.0 CB B:PRO149 4.7 94.8 1.0 C B:ASN150 4.8 96.8 1.0 CG B:GLU151 4.8 0.8 1.0 CG A:GLU67 4.9 95.2 1.0 N A:ASN66 4.9 93.8 1.0

Calcium binding site 2 out of 3 in the Designed Armadillo Repeat Protein YIIIM5AII


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Designed Armadillo Repeat Protein YIIIM5AII within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca301 b:0.7 occ:1.00 OE2 B:GLU67 2.4 73.9 1.0 OE1 A:GLU151 2.6 94.0 1.0 O A:PRO149 2.7 88.0 1.0 O B:PRO65 2.9 76.5 1.0 CD B:GLU67 3.3 91.4 1.0 CD A:GLU151 3.5 98.6 1.0 OE1 B:GLU67 3.5 77.5 1.0 C A:PRO149 3.7 85.5 1.0 OE2 A:GLU151 3.8 0.6 1.0 C B:PRO65 3.9 76.6 1.0 CA A:ASN150 4.1 78.7 1.0 CA B:ASN66 4.3 74.1 1.0 N A:ASN150 4.3 79.9 1.0 N B:GLU67 4.4 76.2 1.0 N A:GLU151 4.4 78.0 1.0 N B:ASN66 4.5 74.0 1.0 CG B:GLU67 4.7 85.0 1.0 C A:ASN150 4.8 82.4 1.0 CG A:GLU151 4.9 82.0 1.0 C B:ASN66 4.9 79.9 1.0 CA A:PRO149 4.9 78.7 1.0 CB A:PRO149 5.0 78.9 1.0

Calcium binding site 3 out of 3 in the Designed Armadillo Repeat Protein YIIIM5AII


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Designed Armadillo Repeat Protein YIIIM5AII within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca302 b:0.8 occ:1.00 OE1 B:GLU109 2.3 0.1 1.0 O B:PRO107 2.6 85.0 1.0 OE1 A:GLU109 2.6 0.2 1.0 O A:PRO107 2.8 78.0 1.0 CD B:GLU109 3.2 0.9 1.0 OE2 B:GLU109 3.4 0.8 1.0 CD A:GLU109 3.6 0.1 1.0 C B:PRO107 3.7 84.1 1.0 C A:PRO107 3.8 77.3 1.0 OE2 A:GLU109 3.9 0.4 1.0 N B:GLU109 4.4 76.6 1.0 CA A:ASN108 4.5 72.3 1.0 CA B:ASN108 4.5 76.0 1.0 N B:ASN108 4.5 77.7 1.0 CG B:GLU109 4.5 81.4 1.0 N A:ASN108 4.5 72.8 1.0 N A:GLU109 4.6 72.4 1.0 CA B:PRO107 4.7 80.5 1.0 CB B:PRO107 4.7 80.2 1.0 CB A:PRO107 4.8 71.8 1.0 CA A:PRO107 4.9 71.2 1.0 CG A:GLU109 4.9 78.9 1.0

S.Hansen, P.Ernst, S.L.B.Konig, C.Reichen, C.Ewald, D.Nettels, P.R.E.Mittl, B.Schuler, A.Pluckthun. Curvature of Designed Armadillo Repeat Proteins Allows Modular Peptide Binding. J. Struct. Biol. V. 201 108 2018.
ISSN: ESSN 1095-8657
PubMed: 28864298
DOI: 10.1016/J.JSB.2017.08.009