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Iron 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
Gadolinium (Gd) 3 atoms

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Iron atom in the Cryptochrome B From Rhodobacter Sphaeroides (pdb code 3zxs). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 12 binding sites of Iron where determined in the Cryptochrome B From Rhodobacter Sphaeroides, PDB code: 3zxs:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 12 in 3zxs

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Iron binding site 1 out of 12 in the Cryptochrome B From Rhodobacter Sphaeroides


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Cryptochrome B From Rhodobacter Sphaeroides within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1510

b:25.1
occ:1.00
FE1 A:SF41510 0.0 25.1 1.0
S4 A:SF41510 2.3 25.4 1.0
SG A:CYS437 2.3 29.2 1.0
S2 A:SF41510 2.3 27.9 1.0
S3 A:SF41510 2.3 24.6 1.0
FE3 A:SF41510 2.7 26.3 1.0
FE2 A:SF41510 2.7 26.6 1.0
FE4 A:SF41510 2.7 26.5 1.0
CB A:CYS437 3.1 34.5 1.0
S1 A:SF41510 3.9 28.3 1.0
N A:ALA345 4.0 32.5 1.0
CB A:TYR439 4.0 32.9 1.0
CD2 A:TYR439 4.5 32.2 1.0
CA A:MET344 4.5 34.9 1.0
CA A:CYS437 4.6 35.0 1.0
CB A:ALA345 4.6 31.2 1.0
SG A:CYS346 4.7 29.6 1.0
C A:MET344 4.7 33.5 1.0
SG A:CYS434 4.7 36.5 1.0
CG A:TYR439 4.8 31.5 1.0
N A:TYR439 4.8 34.2 1.0
SG A:CYS450 4.8 30.8 1.0
CA A:TYR439 4.9 33.7 1.0
CA A:ALA345 4.9 31.5 1.0
O A:TYR439 4.9 33.7 1.0
CA A:CYS434 4.9 38.0 1.0
N A:CYS346 4.9 30.0 1.0

Iron binding site 2 out of 12 in 3zxs

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Iron binding site 2 out of 12 in the Cryptochrome B From Rhodobacter Sphaeroides


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Cryptochrome B From Rhodobacter Sphaeroides within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1510

b:26.6
occ:1.00
FE2 A:SF41510 0.0 26.6 1.0
SG A:CYS346 2.2 29.6 1.0
S3 A:SF41510 2.3 24.6 1.0
S4 A:SF41510 2.3 25.4 1.0
S1 A:SF41510 2.3 28.3 1.0
FE4 A:SF41510 2.7 26.5 1.0
FE3 A:SF41510 2.7 26.3 1.0
FE1 A:SF41510 2.7 25.1 1.0
CB A:CYS346 3.4 29.7 1.0
S2 A:SF41510 3.9 27.9 1.0
N A:CYS346 3.9 30.0 1.0
CA A:CYS346 4.3 29.5 1.0
CE1 A:PHE452 4.3 33.3 1.0
CG2 A:ILE427 4.4 26.2 1.0
N A:ALA345 4.5 32.5 1.0
CD1 A:PHE452 4.5 31.8 1.0
CD1 A:ILE427 4.6 26.3 1.0
SG A:CYS434 4.6 36.5 1.0
SG A:CYS450 4.7 30.8 1.0
SG A:CYS437 4.7 29.2 1.0
CB A:MET344 4.9 35.1 1.0
C A:MET344 4.9 33.5 1.0
C A:ALA345 5.0 30.4 1.0

Iron binding site 3 out of 12 in 3zxs

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Iron binding site 3 out of 12 in the Cryptochrome B From Rhodobacter Sphaeroides


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Cryptochrome B From Rhodobacter Sphaeroides within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1510

b:26.3
occ:1.00
FE3 A:SF41510 0.0 26.3 1.0
SG A:CYS450 2.2 30.8 1.0
S4 A:SF41510 2.3 25.4 1.0
S2 A:SF41510 2.3 27.9 1.0
S1 A:SF41510 2.3 28.3 1.0
FE4 A:SF41510 2.7 26.5 1.0
FE2 A:SF41510 2.7 26.6 1.0
FE1 A:SF41510 2.7 25.1 1.0
CB A:CYS450 3.3 33.6 1.0
S3 A:SF41510 3.9 24.6 1.0
CA A:CYS450 4.1 33.5 1.0
CD1 A:PHE452 4.3 31.8 1.0
CG2 A:VAL441 4.5 38.8 1.0
CD A:PRO451 4.6 30.5 1.0
SG A:CYS434 4.7 36.5 1.0
SG A:CYS346 4.7 29.6 1.0
CB A:TYR439 4.7 32.9 1.0
N A:PRO451 4.8 30.9 1.0
C A:CYS450 4.8 32.5 1.0
SG A:CYS437 4.9 29.2 1.0
CA A:GLY424 4.9 32.8 1.0
CB A:VAL441 4.9 39.4 1.0
CE1 A:PHE452 4.9 33.3 1.0

Iron binding site 4 out of 12 in 3zxs

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Iron binding site 4 out of 12 in the Cryptochrome B From Rhodobacter Sphaeroides


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Cryptochrome B From Rhodobacter Sphaeroides within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1510

b:26.5
occ:1.00
FE4 A:SF41510 0.0 26.5 1.0
SG A:CYS434 2.2 36.5 1.0
S1 A:SF41510 2.3 28.3 1.0
S3 A:SF41510 2.3 24.6 1.0
S2 A:SF41510 2.3 27.9 1.0
FE2 A:SF41510 2.7 26.6 1.0
FE3 A:SF41510 2.7 26.3 1.0
FE1 A:SF41510 2.7 25.1 1.0
CB A:CYS434 3.4 38.5 1.0
CA A:CYS434 3.8 38.0 1.0
S4 A:SF41510 3.8 25.4 1.0
CG2 A:VAL441 4.3 38.8 1.0
N A:CYS434 4.4 36.9 1.0
CG2 A:ILE427 4.4 26.2 1.0
CB A:VAL441 4.4 39.4 1.0
SG A:CYS450 4.6 30.8 1.0
SG A:CYS346 4.7 29.6 1.0
SG A:CYS437 4.7 29.2 1.0
CB A:CYS437 4.7 34.5 1.0
C A:TYR433 4.9 35.9 1.0
CB A:TYR433 5.0 34.1 1.0
CB A:ILE427 5.0 29.1 1.0

Iron binding site 5 out of 12 in 3zxs

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Iron binding site 5 out of 12 in the Cryptochrome B From Rhodobacter Sphaeroides


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Cryptochrome B From Rhodobacter Sphaeroides within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1510

b:27.0
occ:1.00
FE1 B:SF41510 0.0 27.0 1.0
S2 B:SF41510 2.3 26.5 1.0
S3 B:SF41510 2.3 26.0 1.0
S4 B:SF41510 2.3 24.9 1.0
SG B:CYS437 2.3 31.4 1.0
FE4 B:SF41510 2.7 27.9 1.0
FE2 B:SF41510 2.7 25.2 1.0
FE3 B:SF41510 2.7 26.8 1.0
CB B:CYS437 3.3 37.1 1.0
S1 B:SF41510 3.9 27.6 1.0
N B:ALA345 4.0 33.5 1.0
CB B:TYR439 4.3 32.4 1.0
SG B:CYS346 4.6 29.0 1.0
CA B:MET344 4.6 35.4 1.0
CD2 B:TYR439 4.6 30.1 1.0
SG B:CYS434 4.6 35.6 1.0
CB B:ALA345 4.7 32.6 1.0
C B:MET344 4.7 34.1 1.0
CA B:CYS437 4.7 37.7 1.0
O B:TYR439 4.8 33.4 1.0
SG B:CYS450 4.8 29.1 1.0
N B:TYR439 4.8 33.9 1.0
CA B:CYS434 4.8 40.0 1.0
CA B:ALA345 4.9 32.8 1.0
N B:CYS346 4.9 30.7 1.0
CA B:TYR439 4.9 33.4 1.0
CG B:TYR439 5.0 29.5 1.0

Iron binding site 6 out of 12 in 3zxs

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Iron binding site 6 out of 12 in the Cryptochrome B From Rhodobacter Sphaeroides


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Cryptochrome B From Rhodobacter Sphaeroides within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1510

b:25.2
occ:1.00
FE2 B:SF41510 0.0 25.2 1.0
SG B:CYS346 2.2 29.0 1.0
S4 B:SF41510 2.3 24.9 1.0
S3 B:SF41510 2.3 26.0 1.0
S1 B:SF41510 2.3 27.6 1.0
FE1 B:SF41510 2.7 27.0 1.0
FE3 B:SF41510 2.7 26.8 1.0
FE4 B:SF41510 2.7 27.9 1.0
CB B:CYS346 3.5 29.8 1.0
S2 B:SF41510 3.9 26.5 1.0
N B:CYS346 3.9 30.7 1.0
CE1 B:PHE452 4.2 34.5 1.0
CA B:CYS346 4.3 29.9 1.0
CD1 B:PHE452 4.4 34.7 1.0
CG2 B:ILE427 4.4 25.6 1.0
N B:ALA345 4.6 33.5 1.0
SG B:CYS450 4.6 29.1 1.0
SG B:CYS434 4.7 35.6 1.0
CD1 B:ILE427 4.7 27.4 1.0
SG B:CYS437 4.8 31.4 1.0
CB B:MET344 4.9 35.3 1.0
C B:MET344 4.9 34.1 1.0

Iron binding site 7 out of 12 in 3zxs

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Iron binding site 7 out of 12 in the Cryptochrome B From Rhodobacter Sphaeroides


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Cryptochrome B From Rhodobacter Sphaeroides within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1510

b:26.8
occ:1.00
FE3 B:SF41510 0.0 26.8 1.0
SG B:CYS450 2.2 29.1 1.0
S2 B:SF41510 2.3 26.5 1.0
S1 B:SF41510 2.3 27.6 1.0
S4 B:SF41510 2.3 24.9 1.0
FE4 B:SF41510 2.7 27.9 1.0
FE2 B:SF41510 2.7 25.2 1.0
FE1 B:SF41510 2.7 27.0 1.0
CB B:CYS450 3.3 32.2 1.0
S3 B:SF41510 3.9 26.0 1.0
CA B:CYS450 4.2 32.2 1.0
CD1 B:PHE452 4.3 34.7 1.0
CG2 B:VAL441 4.4 39.8 1.0
SG B:CYS434 4.6 35.6 1.0
CD B:PRO451 4.7 29.9 1.0
SG B:CYS346 4.7 29.0 1.0
CB B:VAL441 4.8 40.7 1.0
C B:CYS450 4.8 31.8 1.0
CA B:GLY424 4.9 31.6 1.0
CB B:TYR439 4.9 32.4 1.0
N B:PRO451 4.9 30.1 1.0
SG B:CYS437 4.9 31.4 1.0
CA B:VAL441 5.0 40.4 1.0
CE1 B:PHE452 5.0 34.5 1.0

Iron binding site 8 out of 12 in 3zxs

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Iron binding site 8 out of 12 in the Cryptochrome B From Rhodobacter Sphaeroides


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Cryptochrome B From Rhodobacter Sphaeroides within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1510

b:27.9
occ:1.00
FE4 B:SF41510 0.0 27.9 1.0
SG B:CYS434 2.2 35.6 1.0
S1 B:SF41510 2.3 27.6 1.0
S3 B:SF41510 2.3 26.0 1.0
S2 B:SF41510 2.3 26.5 1.0
FE3 B:SF41510 2.7 26.8 1.0
FE1 B:SF41510 2.7 27.0 1.0
FE2 B:SF41510 2.7 25.2 1.0
CB B:CYS434 3.3 40.0 1.0
CA B:CYS434 3.7 40.0 1.0
S4 B:SF41510 3.8 24.9 1.0
N B:CYS434 4.2 39.2 1.0
CG2 B:VAL441 4.2 39.8 1.0
CB B:VAL441 4.4 40.7 1.0
CG2 B:ILE427 4.5 25.6 1.0
SG B:CYS450 4.6 29.1 1.0
SG B:CYS346 4.7 29.0 1.0
SG B:CYS437 4.7 31.4 1.0
CB B:CYS437 4.8 37.1 1.0
C B:TYR433 4.9 38.0 1.0
CB B:TYR433 5.0 36.4 1.0

Iron binding site 9 out of 12 in 3zxs

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Iron binding site 9 out of 12 in the Cryptochrome B From Rhodobacter Sphaeroides


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Cryptochrome B From Rhodobacter Sphaeroides within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe1510

b:37.4
occ:1.00
FE1 C:SF41510 0.0 37.4 1.0
SG C:CYS434 2.2 48.8 1.0
S4 C:SF41510 2.3 32.5 1.0
S2 C:SF41510 2.3 39.1 1.0
S3 C:SF41510 2.3 36.6 1.0
FE4 C:SF41510 2.6 37.7 1.0
FE2 C:SF41510 2.6 37.5 1.0
FE3 C:SF41510 2.7 38.2 1.0
CB C:CYS434 3.4 49.0 1.0
CA C:CYS434 3.8 49.1 1.0
S1 C:SF41510 3.8 36.0 1.0
N C:CYS434 4.2 48.2 1.0
CG2 C:VAL441 4.3 47.7 1.0
CB C:VAL441 4.4 49.3 1.0
CG2 C:ILE427 4.4 35.6 1.0
SG C:CYS450 4.5 41.0 1.0
SG C:CYS346 4.6 39.8 1.0
SG C:CYS437 4.7 41.4 1.0
CB C:CYS437 4.9 45.7 1.0
C C:TYR433 5.0 47.0 1.0
CB C:ILE427 5.0 37.9 1.0

Iron binding site 10 out of 12 in 3zxs

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Iron binding site 10 out of 12 in the Cryptochrome B From Rhodobacter Sphaeroides


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Cryptochrome B From Rhodobacter Sphaeroides within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe1510

b:37.5
occ:1.00
FE2 C:SF41510 0.0 37.5 1.0
SG C:CYS346 2.2 39.8 1.0
S1 C:SF41510 2.3 36.0 1.0
S3 C:SF41510 2.3 36.6 1.0
S4 C:SF41510 2.3 32.5 1.0
FE1 C:SF41510 2.6 37.4 1.0
FE3 C:SF41510 2.7 38.2 1.0
FE4 C:SF41510 2.8 37.7 1.0
CB C:CYS346 3.4 35.5 1.0
S2 C:SF41510 3.9 39.1 1.0
N C:CYS346 3.9 35.6 1.0
CE1 C:PHE452 4.2 39.2 1.0
CA C:CYS346 4.3 35.5 1.0
CD1 C:PHE452 4.4 38.8 1.0
N C:ALA345 4.5 38.0 1.0
CG2 C:ILE427 4.5 35.6 1.0
SG C:CYS450 4.6 41.0 1.0
CD1 C:ILE427 4.6 35.7 1.0
SG C:CYS434 4.7 48.8 1.0
SG C:CYS437 4.7 41.4 1.0
CB C:MET344 4.8 39.4 1.0
C C:MET344 4.9 38.5 1.0
CA C:MET344 5.0 39.7 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 15:27:38 2020

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