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Iron in PDB 6kum: Ferredoxin I From C. Reinhardtii, Low X-Ray Dose

Protein crystallography data

The structure of Ferredoxin I From C. Reinhardtii, Low X-Ray Dose, PDB code: 6kum was solved by Y.Onishi, G.Kurisu, H.Tanaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.74 / 1.40
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 25.878, 32.326, 49.915, 72.38, 78.06, 72.39
R / Rfree (%) 17.1 / 19

Other elements in 6kum:

The structure of Ferredoxin I From C. Reinhardtii, Low X-Ray Dose also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms
Sodium (Na) 1 atom

Iron Binding Sites:

The binding sites of Iron atom in the Ferredoxin I From C. Reinhardtii, Low X-Ray Dose (pdb code 6kum). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Ferredoxin I From C. Reinhardtii, Low X-Ray Dose, PDB code: 6kum:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 6kum

Go back to Iron Binding Sites List in 6kum
Iron binding site 1 out of 4 in the Ferredoxin I From C. Reinhardtii, Low X-Ray Dose


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Ferredoxin I From C. Reinhardtii, Low X-Ray Dose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe101

b:9.2
occ:1.00
FE1 A:FES101 0.0 9.2 1.0
S2 A:FES101 2.1 9.3 1.0
S1 A:FES101 2.2 9.3 1.0
SG A:CYS42 2.3 10.0 1.0
SG A:CYS37 2.3 11.6 1.0
FE2 A:FES101 2.7 8.0 1.0
CB A:CYS42 3.5 10.5 1.0
CB A:CYS37 3.5 11.7 1.0
N A:CYS42 3.7 11.0 1.0
N A:CYS37 3.7 10.9 1.0
N A:ARG38 3.8 14.1 0.5
N A:ARG38 3.8 14.1 0.5
CA A:CYS42 3.9 10.8 1.0
CA A:CYS37 4.0 11.3 1.0
C A:CYS42 4.0 10.0 1.0
O A:CYS42 4.2 9.7 1.0
N A:ALA41 4.3 12.2 1.0
C A:CYS37 4.3 11.1 1.0
OG A:SER36 4.3 10.1 0.8
SG A:CYS75 4.4 8.5 1.0
N A:GLY40 4.4 10.7 1.0
N A:ALA39 4.5 12.5 1.0
C A:ALA41 4.5 12.8 1.0
N A:SER44 4.6 9.3 1.0
SG A:CYS45 4.6 7.3 1.0
N A:SER43 4.6 11.5 1.0
CA A:ARG38 4.7 14.1 0.5
CA A:ARG38 4.7 14.1 0.5
C A:SER36 4.7 9.8 0.8
CB A:SER44 4.7 9.6 1.0
N A:SER36 4.8 8.7 0.8
C A:SER36 4.8 9.9 0.2
N A:SER36 4.8 8.7 0.2
CA A:GLY40 4.9 10.8 1.0
C A:GLY40 4.9 11.4 1.0

Iron binding site 2 out of 4 in 6kum

Go back to Iron Binding Sites List in 6kum
Iron binding site 2 out of 4 in the Ferredoxin I From C. Reinhardtii, Low X-Ray Dose


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Ferredoxin I From C. Reinhardtii, Low X-Ray Dose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe101

b:8.0
occ:1.00
FE2 A:FES101 0.0 8.0 1.0
S2 A:FES101 2.1 9.3 1.0
S1 A:FES101 2.2 9.3 1.0
SG A:CYS45 2.3 7.3 1.0
SG A:CYS75 2.3 8.5 1.0
FE1 A:FES101 2.7 9.2 1.0
CB A:CYS75 3.2 8.0 1.0
CB A:CYS45 3.3 6.8 1.0
N A:CYS75 4.2 7.4 1.0
N A:CYS45 4.3 7.6 1.0
N A:ARG38 4.3 14.1 0.5
CA A:CYS75 4.3 8.0 1.0
N A:ARG38 4.3 14.1 0.5
N A:GLY40 4.3 10.7 1.0
SG A:CYS37 4.4 11.6 1.0
CA A:ARG38 4.4 14.1 0.5
CA A:CYS45 4.4 7.1 1.0
CA A:ARG38 4.4 14.1 0.5
CB A:LEU73 4.5 8.3 1.0
SG A:CYS42 4.6 10.0 1.0
CA A:GLY40 4.7 10.8 1.0
N A:ALA39 4.7 12.5 1.0
O A:CYS42 4.9 9.7 1.0
C A:ARG38 4.9 14.1 0.5
C A:ARG38 4.9 14.2 0.5

Iron binding site 3 out of 4 in 6kum

Go back to Iron Binding Sites List in 6kum
Iron binding site 3 out of 4 in the Ferredoxin I From C. Reinhardtii, Low X-Ray Dose


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Ferredoxin I From C. Reinhardtii, Low X-Ray Dose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe101

b:9.0
occ:1.00
FE1 B:FES101 0.0 9.0 1.0
S2 B:FES101 2.2 9.0 1.0
S1 B:FES101 2.2 8.4 1.0
SG B:CYS42 2.3 9.5 1.0
SG B:CYS37 2.3 10.3 1.0
FE2 B:FES101 2.7 8.1 1.0
CB B:CYS42 3.4 10.0 1.0
CB B:CYS37 3.5 10.2 1.0
N B:CYS37 3.7 9.0 1.0
N B:CYS42 3.7 10.1 1.0
N B:ARG38 3.8 12.1 1.0
CA B:CYS42 3.9 10.2 1.0
CA B:CYS37 4.0 9.8 1.0
C B:CYS42 4.0 9.5 1.0
O B:CYS42 4.1 9.1 1.0
N B:ALA41 4.2 13.0 1.0
C B:CYS37 4.3 9.9 1.0
OG B:SER36 4.3 10.3 1.0
SG B:CYS75 4.4 8.2 1.0
N B:GLY40 4.5 13.5 1.0
N B:ALA39 4.5 13.7 1.0
C B:ALA41 4.5 13.0 1.0
N B:SER44 4.6 8.8 1.0
SG B:CYS45 4.6 7.7 1.0
CA B:ARG38 4.7 12.3 1.0
N B:SER43 4.7 11.7 1.0
C B:SER36 4.7 10.4 1.0
CB B:SER44 4.8 9.0 1.0
N B:SER36 4.8 9.8 1.0
C B:GLY40 5.0 11.6 1.0
CA B:ALA41 5.0 13.2 1.0
CA B:GLY40 5.0 12.2 1.0

Iron binding site 4 out of 4 in 6kum

Go back to Iron Binding Sites List in 6kum
Iron binding site 4 out of 4 in the Ferredoxin I From C. Reinhardtii, Low X-Ray Dose


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Ferredoxin I From C. Reinhardtii, Low X-Ray Dose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe101

b:8.1
occ:1.00
FE2 B:FES101 0.0 8.1 1.0
S2 B:FES101 2.1 9.0 1.0
S1 B:FES101 2.2 8.4 1.0
SG B:CYS75 2.3 8.2 1.0
SG B:CYS45 2.3 7.7 1.0
FE1 B:FES101 2.7 9.0 1.0
CB B:CYS75 3.2 8.2 1.0
CB B:CYS45 3.3 7.6 1.0
N B:CYS75 4.2 8.3 1.0
N B:CYS45 4.3 8.6 1.0
CA B:CYS75 4.3 8.1 1.0
N B:GLY40 4.3 13.5 1.0
N B:ARG38 4.3 12.1 1.0
SG B:CYS37 4.4 10.3 1.0
CA B:CYS45 4.4 8.0 1.0
CA B:ARG38 4.4 12.3 1.0
CB B:LEU73 4.5 7.5 1.0
SG B:CYS42 4.6 9.5 1.0
CA B:GLY40 4.7 12.2 1.0
N B:ALA39 4.7 13.7 1.0
O B:CYS42 4.9 9.1 1.0
C B:ARG38 4.9 13.0 1.0

Reference:

Y.Ohnishi, N.Muraki, D.Kiyota, H.Okumura, S.Baba, Y.Kawano, T.Kumasaka, H.Tanaka, G.Kurisu. X-Ray Dose-Dependent Structural Changes of the [2FE-2S] Ferredoxin From Chlamydomonas Reinhardtii. J.Biochem. 2020.
ISSN: ISSN 0021-924X
PubMed: 32282907
DOI: 10.1093/JB/MVAA045
Page generated: Wed Aug 7 00:26:38 2024

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