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Magnesium in PDB 3zxs: Cryptochrome B From Rhodobacter Sphaeroides

Protein crystallography data

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

Other elements in 3zxs:

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

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

Magnesium Binding Sites:

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 3zxs

Go back to Magnesium Binding Sites List in 3zxs
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 3zxs

Go back to Magnesium Binding Sites List in 3zxs
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 3zxs

Go back to Magnesium Binding Sites List in 3zxs
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

Reference:

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
Page generated: Mon Dec 14 09:04:56 2020

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