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Gadolinium 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:

Magnesium (Mg) 3 atoms
Iron (Fe) 12 atoms

Gadolinium Binding Sites:

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

Gadolinium binding site 1 out of 3 in 3zxs

Go back to Gadolinium Binding Sites List in 3zxs
Gadolinium binding site 1 out of 3 in the Cryptochrome B From Rhodobacter Sphaeroides


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 1 of Cryptochrome B From Rhodobacter Sphaeroides within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Gd1513

b:93.2
occ:0.50
OD2 A:ASP379 3.7 35.4 1.0
OD1 A:ASP379 4.1 34.0 1.0
ND2 A:ASN325 4.2 28.8 1.0
O A:HOH2160 4.2 42.4 1.0
CG A:ASP379 4.3 30.5 1.0
O A:HOH2133 4.5 19.0 1.0
O A:ARG323 4.5 35.5 1.0
CB A:ALA381 4.6 27.0 1.0
CB A:ASN325 4.8 32.8 1.0
CG A:ASN325 5.0 31.0 1.0

Gadolinium binding site 2 out of 3 in 3zxs

Go back to Gadolinium Binding Sites List in 3zxs
Gadolinium binding site 2 out of 3 in the Cryptochrome B From Rhodobacter Sphaeroides


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 2 of Cryptochrome B From Rhodobacter Sphaeroides within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Gd1513

b:87.1
occ:0.50
OD2 B:ASP379 3.9 31.5 1.0
OD1 B:ASP379 3.9 32.5 1.0
O B:ARG323 4.3 36.4 1.0
O B:HOH2105 4.3 16.4 0.5
ND2 B:ASN325 4.4 23.9 1.0
CG B:ASP379 4.4 28.6 1.0
CB B:ALA381 4.6 23.7 1.0
CB B:ASN325 4.9 32.3 1.0

Gadolinium binding site 3 out of 3 in 3zxs

Go back to Gadolinium Binding Sites List in 3zxs
Gadolinium binding site 3 out of 3 in the Cryptochrome B From Rhodobacter Sphaeroides


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 3 of Cryptochrome B From Rhodobacter Sphaeroides within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Gd1513

b:98.8
occ:0.50
OD2 C:ASP379 3.6 38.6 1.0
OD1 C:ASP379 3.9 37.4 1.0
ND2 C:ASN325 4.0 33.9 1.0
CG C:ASP379 4.2 33.0 1.0
O C:HOH2069 4.2 29.7 1.0
CB C:ALA381 4.4 28.5 1.0
O C:ARG323 4.5 40.3 1.0
CB C:ASN325 4.8 35.9 1.0
CG C:ASN325 4.9 35.2 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: Sun Dec 13 18:59:36 2020

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