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Iron in PDB 1yk5: Pyrococcus Abyssi Rubredoxin

Protein crystallography data

The structure of Pyrococcus Abyssi Rubredoxin, PDB code: 1yk5 was solved by H.Bonisch, C.L.Schmidt, P.Bianco, R.Ladenstein, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.37 / 1.79
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 54.301, 59.513, 80.740, 90.00, 90.00, 90.00
R / Rfree (%) 15.8 / 19.1

Iron Binding Sites:

The binding sites of Iron atom in the Pyrococcus Abyssi Rubredoxin (pdb code 1yk5). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Pyrococcus Abyssi Rubredoxin, PDB code: 1yk5:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 1yk5

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Iron binding site 1 out of 4 in the Pyrococcus Abyssi Rubredoxin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Pyrococcus Abyssi Rubredoxin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe54

b:18.5
occ:1.00
 SG A:CYS42 2.2 19.3 1.0
SG A:CYS9 2.2 16.9 1.0
SG A:CYS6 2.3 16.6 1.0
SG A:CYS39 2.3 17.8 1.0
CB A:CYS39 3.1 19.8 1.0
CB A:CYS6 3.3 16.7 1.0
CB A:CYS9 3.3 16.3 1.0
CB A:CYS42 3.3 21.5 1.0
N A:CYS9 3.8 16.6 1.0
N A:CYS42 3.9 21.3 1.0
CA A:CYS9 4.1 15.7 1.0
CA A:CYS42 4.2 21.4 1.0
CB A:TYR11 4.4 16.1 1.0
CB A:ALA44 4.5 23.1 1.0
CA A:CYS39 4.6 20.0 1.0
CB A:ILE8 4.6 17.0 1.0
C A:CYS9 4.7 15.1 1.0
CA A:CYS6 4.7 15.0 1.0
C A:ILE8 4.8 16.9 1.0
N A:TYR11 4.8 14.7 1.0
C A:CYS42 4.8 22.4 1.0
N A:GLY10 4.8 15.2 1.0
N A:ALA44 4.9 21.6 1.0
CB A:LEU41 4.9 24.1 1.0
C A:LEU41 4.9 23.3 1.0
N A:GLY43 4.9 22.6 1.0

Iron binding site 2 out of 4 in 1yk5

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Iron binding site 2 out of 4 in the Pyrococcus Abyssi Rubredoxin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Pyrococcus Abyssi Rubredoxin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe54

b:16.4
occ:1.00
 SG B:CYS42 2.2 16.7 1.0
SG B:CYS9 2.3 15.2 1.0
SG B:CYS39 2.3 14.7 1.0
SG B:CYS6 2.3 15.0 1.0
CB B:CYS39 3.1 16.2 1.0
CB B:CYS6 3.2 13.1 1.0
CB B:CYS42 3.3 18.2 1.0
CB B:CYS9 3.4 14.1 1.0
N B:CYS9 3.8 14.1 1.0
N B:CYS42 3.9 18.5 1.0
CA B:CYS9 4.1 13.9 1.0
CA B:CYS42 4.1 18.7 1.0
CB B:TYR11 4.4 14.8 1.0
CB B:ALA44 4.4 20.1 1.0
CB B:ILE8 4.6 16.5 1.0
CA B:CYS39 4.6 16.6 1.0
C B:CYS9 4.6 12.5 1.0
CA B:CYS6 4.7 13.5 1.0
C B:ILE8 4.8 17.0 1.0
C B:CYS42 4.8 19.1 1.0
N B:ALA44 4.8 19.9 1.0
N B:TYR11 4.8 13.4 1.0
N B:GLY10 4.8 12.0 1.0
N B:GLY43 4.9 17.8 1.0
CB B:LEU41 4.9 21.1 1.0
C B:LEU41 4.9 21.2 1.0

Iron binding site 3 out of 4 in 1yk5

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Iron binding site 3 out of 4 in the Pyrococcus Abyssi Rubredoxin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Pyrococcus Abyssi Rubredoxin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe54

b:17.3
occ:1.00
 SG C:CYS9 2.2 15.3 1.0
SG C:CYS6 2.2 13.8 1.0
SG C:CYS39 2.3 15.8 1.0
SG C:CYS42 2.3 17.4 1.0
CB C:CYS39 3.2 16.4 1.0
CB C:CYS6 3.2 11.9 1.0
CB C:CYS9 3.3 15.2 1.0
CB C:CYS42 3.4 19.6 1.0
N C:CYS9 3.8 14.7 1.0
N C:CYS42 3.9 20.9 1.0
CA C:CYS9 4.1 13.8 1.0
CA C:CYS42 4.2 20.4 1.0
CB C:TYR11 4.4 14.6 1.0
CB C:ALA44 4.4 18.0 1.0
CB C:ILE8 4.5 15.5 1.0
CA C:CYS39 4.6 15.5 1.0
CA C:CYS6 4.7 13.1 1.0
C C:CYS9 4.7 14.5 1.0
C C:ILE8 4.8 15.0 1.0
C C:CYS42 4.8 19.6 1.0
N C:GLY10 4.8 13.4 1.0
N C:TYR11 4.8 13.6 1.0
N C:ALA44 4.9 17.5 1.0
N C:GLY43 4.9 19.4 1.0
C C:LEU41 4.9 23.1 1.0
CB C:LEU41 4.9 23.8 1.0

Iron binding site 4 out of 4 in 1yk5

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Iron binding site 4 out of 4 in the Pyrococcus Abyssi Rubredoxin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Pyrococcus Abyssi Rubredoxin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe54

b:18.6
occ:1.00
 SG D:CYS9 2.2 16.9 1.0
SG D:CYS39 2.3 18.9 1.0
SG D:CYS42 2.3 20.7 1.0
SG D:CYS6 2.3 16.6 1.0
CB D:CYS39 3.1 20.1 1.0
CB D:CYS6 3.2 15.6 1.0
CB D:CYS9 3.3 14.8 1.0
CB D:CYS42 3.4 23.1 1.0
N D:CYS42 3.8 22.8 1.0
N D:CYS9 3.8 14.5 1.0
CA D:CYS9 4.1 14.5 1.0
CA D:CYS42 4.1 22.7 1.0
CB D:TYR11 4.4 14.9 1.0
CB D:ALA44 4.5 23.3 1.0
CB D:ILE8 4.6 14.2 1.0
CA D:CYS39 4.6 20.9 1.0
CA D:CYS6 4.6 14.8 1.0
C D:CYS9 4.7 13.8 1.0
C D:CYS42 4.8 22.9 1.0
N D:ALA44 4.8 21.5 1.0
N D:TYR11 4.8 14.5 1.0
N D:GLY10 4.8 14.1 1.0
C D:ILE8 4.8 14.0 1.0
C D:LEU41 4.8 24.6 1.0
N D:GLY43 4.9 22.3 1.0
CB D:LEU41 4.9 26.0 1.0

Reference:

H.Bonisch, C.L.Schmidt, P.Bianco, R.Ladenstein. Ultrahigh-Resolution Study on Pyrococcus Abyssi Rubredoxin. I. 0.69 A X-Ray Structure of Mutant W4L/R5S. Acta Crystallogr.,Sect.D V. 61 990 2005.
ISSN: ISSN 0907-4449
PubMed: 15983423
DOI: 10.1107/S090744490501293X
Page generated: Wed Jul 16 22:45:35 2025

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