Magnesium in PDB 4db8: Designed Armadillo-Repeat Protein

The structure of Designed Armadillo-Repeat Protein, PDB code: 4db8 was solved by C.Madhurantakam, G.Varadamsetty, M.G.Grutter, A.Pluckthun, P.R.E.Mittl, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 2.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	58.002, 113.643, 85.592, 90.00, 106.83, 90.00
R / Rfree (%)	23.2 / 29.9

The binding sites of Magnesium atom in the Designed Armadillo-Repeat Protein (pdb code 4db8). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Designed Armadillo-Repeat Protein, PDB code: 4db8:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Designed Armadillo-Repeat Protein


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:30.0 occ:1.00 CD A:LYS214 3.5 40.9 1.0 O A:HOH410 3.6 30.0 1.0 CB A:LYS214 3.9 43.0 1.0 O A:HOH421 4.1 30.0 1.0 CG A:LYS214 4.3 42.2 1.0 OD1 A:ASN211 4.3 44.1 1.0 CG A:ASN211 4.4 43.3 1.0 CA A:ASN211 4.5 42.8 1.0 O A:LEU248 4.7 70.1 1.0 O A:ASN211 4.7 42.7 1.0 CB A:ASN211 4.7 42.6 1.0 CE A:LYS214 4.7 40.9 1.0 ND2 A:ASN211 4.8 42.7 1.0 C A:GLN249 4.8 69.7 1.0

Magnesium binding site 2 out of 4 in the Designed Armadillo-Repeat Protein


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:30.0 occ:1.00 CB B:GLU170 3.4 35.3 1.0 CA B:GLY168 3.5 32.9 1.0 N B:GLU170 3.6 34.8 1.0 C B:GLY168 3.7 33.5 1.0 CG B:GLN171 3.9 35.5 1.0 N B:ASN169 4.0 34.0 1.0 CA B:GLU170 4.0 35.1 1.0 N B:GLN171 4.1 34.5 1.0 N B:GLY168 4.2 32.2 1.0 CG B:GLU170 4.3 37.2 1.0 O B:GLY168 4.3 33.3 1.0 OE1 B:GLU170 4.3 40.6 1.0 CD B:GLN171 4.4 36.4 1.0 OE1 B:GLN171 4.4 36.9 1.0 C B:GLU170 4.5 34.9 1.0 CD B:GLU170 4.6 40.2 1.0 C B:ASN169 4.7 34.4 1.0 CB B:GLN171 4.8 34.4 1.0 CA B:ASN169 4.9 34.3 1.0

Magnesium binding site 3 out of 4 in the Designed Armadillo-Repeat Protein


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg302 b:30.0 occ:1.00 CD1 B:TRP75 3.3 36.2 1.0 CG B:GLU114 3.5 33.9 1.0 O B:GLN71 3.5 31.1 1.0 CB B:TRP75 3.8 31.0 1.0 CB B:GLU114 3.9 33.7 1.0 CG B:TRP75 3.9 34.2 1.0 CA B:TRP75 4.2 30.4 1.0 N B:TRP75 4.2 29.9 1.0 CD B:GLU114 4.3 34.3 1.0 C B:GLN71 4.4 31.2 1.0 NE1 B:TRP75 4.5 38.1 1.0 CA B:GLN71 4.5 31.4 1.0 CB B:GLN71 4.6 31.4 1.0 CD1 B:LEU74 4.6 29.3 1.0 CB B:LEU74 4.7 29.3 1.0 NE2 B:GLN71 4.7 35.5 1.0 OE1 B:GLU114 4.8 34.7 1.0 OE2 B:GLU114 4.8 34.9 1.0 C B:LEU74 4.9 29.6 1.0

Magnesium binding site 4 out of 4 in the Designed Armadillo-Repeat Protein


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Designed Armadillo-Repeat Protein within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg301 b:36.9 occ:1.00 OE1 D:GLN37 4.1 30.3 1.0 CB D:SER40 4.2 25.5 1.0 N D:GLN37 4.3 23.9 1.0 C D:SER36 4.3 23.6 1.0 O D:SER36 4.3 23.5 1.0 CB D:SER36 4.3 23.4 1.0 CA D:GLN37 4.4 24.4 1.0 OG D:SER40 4.5 26.2 1.0 CD D:GLN37 4.6 29.1 1.0 NE2 D:GLN37 4.9 29.3 1.0 CH2 A:TRP75 4.9 30.8 1.0 CA D:SER36 5.0 23.7 1.0

C.Madhurantakam, G.Varadamsetty, M.G.Grutter, A.Pluckthun, P.R.Mittl. Structure-Based Optimization of Designed Armadillo-Repeat Proteins. Protein Sci. V. 21 1015 2012.
ISSN: ISSN 0961-8368
PubMed: 22544642
DOI: 10.1002/PRO.2085