Magnesium in PDB 3zxs: Cryptochrome B From Rhodobacter Sphaeroides

The structure of Cryptochrome B From Rhodobacter Sphaeroides, PDB code: 3zxs was solved by Y.Geisselbrecht, S.Fruhwirth, A.J.Pierik, G.Klug, L.-O.Essen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.95 / 2.70
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	137.840, 137.840, 521.940, 90.00, 90.00, 120.00
R / Rfree (%)	19.774 / 22.837

The structure of Cryptochrome B From Rhodobacter Sphaeroides also contains other interesting chemical elements:

Iron	(Fe)	12 atoms
Gadolinium	(Gd)	3 atoms

The binding sites of Magnesium atom in the Cryptochrome B From Rhodobacter Sphaeroides (pdb code 3zxs). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Cryptochrome B From Rhodobacter Sphaeroides, PDB code: 3zxs:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Cryptochrome B From Rhodobacter Sphaeroides


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cryptochrome B From Rhodobacter Sphaeroides within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1512 b:54.5 occ:1.00 OD1 A:ASP250 3.0 39.3 1.0 OD2 A:ASP250 3.1 38.4 1.0 OD2 A:ASP175 3.3 67.0 1.0 CG A:ASP250 3.5 35.0 1.0 OD1 A:ASP175 3.6 65.0 1.0 CG A:ASP175 3.9 64.2 1.0 O A:ASN178 4.8 64.5 1.0 NE2 A:GLN249 4.9 34.9 1.0 CD A:GLN249 5.0 36.0 1.0 CB A:ASP250 5.0 34.4 1.0

Magnesium binding site 2 out of 3 in the Cryptochrome B From Rhodobacter Sphaeroides


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cryptochrome B From Rhodobacter Sphaeroides within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1512 b:54.6 occ:1.00 OD2 B:ASP250 2.9 39.0 1.0 OD1 B:ASP250 3.0 39.8 1.0 OD1 B:ASP175 3.2 66.1 1.0 CG B:ASP250 3.3 35.8 1.0 OD2 B:ASP175 3.6 67.2 1.0 CG B:ASP175 3.8 64.8 1.0 O B:HOH2051 4.6 42.3 1.0 NE B:ARG179 4.8 75.6 1.0 O B:ASN178 4.8 67.0 1.0 CB B:ASP250 4.9 34.8 1.0 CG B:ARG179 4.9 70.9 1.0 CD B:GLN249 4.9 35.2 1.0 OE1 B:GLN249 4.9 38.6 1.0 NE2 B:GLN249 5.0 34.8 1.0

Magnesium binding site 3 out of 3 in the Cryptochrome B From Rhodobacter Sphaeroides


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Cryptochrome B From Rhodobacter Sphaeroides within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1512 b:61.5 occ:1.00 OD2 C:ASP250 2.9 44.4 1.0 OD1 C:ASP175 3.0 70.7 1.0 OD1 C:ASP250 3.2 44.8 1.0 CG C:ASP250 3.5 40.8 1.0 CG C:ASP175 4.0 69.4 1.0 OD2 C:ASP175 4.2 71.4 1.0 NE2 C:GLN249 4.3 41.6 1.0 O C:ASN178 4.3 73.6 1.0 CD C:GLN249 4.4 41.2 1.0 OE1 C:GLN249 4.5 43.9 1.0 CG C:GLN249 4.9 39.4 1.0 CB C:ASP250 5.0 40.4 1.0 O C:HOH2080 5.0 40.1 1.0

Y.Geisselbrecht, S.Fruhwirth, C.Schroeder, A.J.Pierik, G.Klug, L.-O.Essen. Cryb From Rhodobacter Sphaeroides: A Unique Class of Cryptochromes with New Cofactors. Embo Rep. V. 13 223 2012.
ISSN: ISSN 1469-221X
PubMed: 22290493
DOI: 10.1038/EMBOR.2012.2