Magnesium in PDB 5mfl: Designed Armadillo Repeat Protein (Kr)5_GS10_YIIIM6AII

The structure of Designed Armadillo Repeat Protein (Kr)5_GS10_YIIIM6AII, PDB code: 5mfl 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)	49.56 / 2.50
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	93.100, 93.100, 188.480, 90.00, 90.00, 120.00
R / Rfree (%)	20.6 / 25.5

The structure of Designed Armadillo Repeat Protein (Kr)5_GS10_YIIIM6AII also contains other interesting chemical elements:

Calcium

(Ca)

11 atoms

The binding sites of Magnesium atom in the Designed Armadillo Repeat Protein (Kr)5_GS10_YIIIM6AII (pdb code 5mfl). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Designed Armadillo Repeat Protein (Kr)5_GS10_YIIIM6AII, PDB code: 5mfl:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Designed Armadillo Repeat Protein (Kr)5_GS10_YIIIM6AII


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Designed Armadillo Repeat Protein (Kr)5_GS10_YIIIM6AII within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg405 b:80.1 occ:1.00 OE1 A:GLN71 3.1 0.2 1.0 OE1 B:GLN197 3.1 98.2 1.0 ND2 A:ASN108 3.1 81.9 1.0 OD1 A:ASN108 3.2 79.4 1.0 ND2 B:ASN234 3.2 77.6 1.0 CG A:ASN108 3.5 87.9 1.0 OD1 B:ASN234 3.6 78.9 1.0 CG B:ASN234 3.9 88.8 1.0 CB A:GLU67 4.0 83.0 1.0 CG A:GLU67 4.1 92.2 1.0 CD B:GLN197 4.1 1.0 1.0 CB A:GLN110 4.1 67.8 1.0 CD A:GLN71 4.1 0.9 1.0 CG A:GLN110 4.2 91.4 1.0 CB B:GLU193 4.2 65.3 1.0 CB B:GLN236 4.4 70.7 1.0 CG B:GLU193 4.5 77.1 1.0 NE2 B:GLN197 4.5 92.2 1.0 CD1 A:ILE111 4.7 83.6 1.0 CG1 A:ILE111 4.7 75.6 1.0 CG B:GLN236 4.7 82.2 1.0 CG A:GLN71 4.9 96.5 1.0

Magnesium binding site 2 out of 3 in the Designed Armadillo Repeat Protein (Kr)5_GS10_YIIIM6AII


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Designed Armadillo Repeat Protein (Kr)5_GS10_YIIIM6AII within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg404 b:56.4 occ:1.00 O C:ASP219 1.9 69.2 1.0 OE1 B:GLN60 1.9 86.0 1.0 O B:HOH532 2.5 76.5 1.0 O C:HOH507 2.6 70.0 1.0 O B:HOH529 2.6 46.2 1.0 C C:ASP219 3.1 68.7 1.0 CD B:GLN60 3.1 92.0 1.0 CA C:ASP219 3.7 63.4 1.0 NE2 B:GLN60 3.8 86.4 1.0 OD1 B:ASN21 3.9 97.3 1.0 N C:ALA220 4.2 64.3 1.0 CG B:GLN60 4.3 73.7 1.0 N C:GLY221 4.3 63.8 1.0 CB B:GLN60 4.4 63.2 1.0 C C:ALA220 4.5 66.9 1.0 O C:ILE218 4.5 64.0 1.0 CA C:ALA220 4.6 63.3 1.0 CB C:ASP219 4.6 65.8 1.0 CA C:GLY221 4.8 63.4 1.0 N C:ASP219 4.9 62.5 1.0 O B:HOH513 4.9 60.5 1.0

Magnesium binding site 3 out of 3 in the Designed Armadillo Repeat Protein (Kr)5_GS10_YIIIM6AII


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Designed Armadillo Repeat Protein (Kr)5_GS10_YIIIM6AII within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg405 b:66.8 occ:1.00 OE1 A:GLN197 2.6 67.3 1.0 OE1 B:GLN71 2.7 75.4 1.0 ND2 B:ASN108 2.9 49.9 1.0 ND2 A:ASN234 3.0 44.8 1.0 OD1 B:ASN108 3.5 54.7 1.0 OD1 A:ASN234 3.5 50.8 1.0 CD A:GLN197 3.6 74.8 1.0 CG B:ASN108 3.6 59.9 1.0 CG A:ASN234 3.7 58.5 1.0 CB B:GLU67 3.9 52.2 1.0 CD B:GLN71 4.0 82.5 1.0 CB A:GLN236 4.0 42.8 1.0 NE2 A:GLN197 4.1 70.2 1.0 CB A:GLU193 4.1 43.6 1.0 CB B:GLN110 4.3 47.4 1.0 CG B:GLU67 4.3 59.7 1.0 CG A:GLU193 4.4 52.7 1.0 CG B:GLN110 4.5 64.0 1.0 CG A:GLN236 4.5 54.5 1.0 NE2 B:GLN71 4.8 76.9 1.0 CD1 B:ILE111 4.9 56.7 1.0 CG A:GLN197 4.9 59.1 1.0 CG B:GLN71 4.9 66.9 1.0 CG1 B:ILE111 5.0 51.0 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