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Iron in PDB 9jn8: Crystal Structure of A Thioredoxin-Like Ferredoxin of Rhodobacter Capsulatus

Protein crystallography data

The structure of Crystal Structure of A Thioredoxin-Like Ferredoxin of Rhodobacter Capsulatus, PDB code: 9jn8 was solved by Y.Shen, L.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 58.68 / 2.12
Space group P 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 60.04, 60.04, 277.2, 90, 90, 90
R / Rfree (%) 20 / 24.1

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of A Thioredoxin-Like Ferredoxin of Rhodobacter Capsulatus (pdb code 9jn8). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Crystal Structure of A Thioredoxin-Like Ferredoxin of Rhodobacter Capsulatus, PDB code: 9jn8:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 9jn8

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Iron binding site 1 out of 6 in the Crystal Structure of A Thioredoxin-Like Ferredoxin of Rhodobacter Capsulatus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of A Thioredoxin-Like Ferredoxin of Rhodobacter Capsulatus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe201

b:52.6
occ:1.00
 FE1 A:FES201 0.0 52.6 1.0
S2 A:FES201 2.2 56.8 1.0
S1 A:FES201 2.2 51.2 1.0
SG A:CYS8 2.5 54.0 1.0
SG A:CYS11 2.6 52.2 1.0
FE2 A:FES201 2.7 54.5 1.0
CB A:CYS8 3.3 52.5 1.0
CB A:CYS11 3.4 58.2 1.0
CA A:CYS11 3.5 56.4 1.0
N A:CYS11 3.5 56.4 1.0
C A:THR10 4.3 57.4 1.0
N A:LEU52 4.4 56.5 1.0
CA A:CYS51 4.5 61.7 1.0
CA A:CYS55 4.5 60.3 1.0
O A:HOH341 4.7 67.5 1.0
CB A:THR10 4.7 59.6 1.0
CA A:CYS8 4.8 56.2 1.0
SG A:CYS51 4.8 55.7 1.0
N A:THR10 4.8 58.1 1.0
SG A:CYS55 4.9 62.1 1.0
CB A:ALA60 4.9 49.7 1.0
CA A:THR10 4.9 57.1 1.0
O A:GLU50 4.9 65.0 1.0
C A:CYS11 4.9 63.1 1.0
N A:CYS55 4.9 58.8 1.0
CB A:CYS55 5.0 61.8 1.0

Iron binding site 2 out of 6 in 9jn8

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Iron binding site 2 out of 6 in the Crystal Structure of A Thioredoxin-Like Ferredoxin of Rhodobacter Capsulatus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of A Thioredoxin-Like Ferredoxin of Rhodobacter Capsulatus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe201

b:54.5
occ:1.00
 FE2 A:FES201 0.0 54.5 1.0
S1 A:FES201 2.2 51.2 1.0
S2 A:FES201 2.2 56.8 1.0
SG A:CYS55 2.6 62.1 1.0
SG A:CYS51 2.7 55.7 1.0
FE1 A:FES201 2.7 52.6 1.0
CB A:CYS55 3.5 61.8 1.0
CA A:CYS55 3.7 60.3 1.0
CB A:CYS51 3.7 59.1 1.0
N A:CYS55 3.8 58.8 1.0
CA A:CYS51 3.9 61.7 1.0
N A:SER53 4.0 52.4 1.0
N A:LEU52 4.0 56.5 1.0
N A:ALA54 4.2 55.2 1.0
SG A:CYS8 4.3 54.0 1.0
CA A:SER53 4.4 53.7 1.0
C A:CYS51 4.4 61.6 1.0
C A:ALA54 4.5 61.8 1.0
C A:SER53 4.7 55.1 1.0
C A:LEU52 4.7 53.1 1.0
SG A:CYS11 4.9 52.2 1.0
CA A:LEU52 4.9 55.3 1.0
O A:GLU50 5.0 65.0 1.0

Iron binding site 3 out of 6 in 9jn8

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Iron binding site 3 out of 6 in the Crystal Structure of A Thioredoxin-Like Ferredoxin of Rhodobacter Capsulatus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of A Thioredoxin-Like Ferredoxin of Rhodobacter Capsulatus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe201

b:56.0
occ:1.00
 FE1 B:FES201 0.0 56.0 1.0
S1 B:FES201 2.2 58.9 1.0
S2 B:FES201 2.2 60.6 1.0
SG B:CYS8 2.5 59.6 1.0
SG B:CYS11 2.6 57.9 1.0
FE2 B:FES201 2.7 59.1 1.0
CB B:CYS8 3.3 54.2 1.0
CB B:CYS11 3.5 60.4 1.0
CA B:CYS11 3.6 60.8 1.0
N B:CYS11 3.6 60.0 1.0
C B:THR10 4.3 64.5 1.0
N B:LEU52 4.4 54.6 1.0
CA B:CYS51 4.5 58.5 1.0
CA B:CYS55 4.5 61.4 1.0
CB B:THR10 4.7 66.1 1.0
CA B:CYS8 4.7 56.6 1.0
O B:GLU50 4.8 66.3 1.0
CA B:THR10 4.9 66.6 1.0
N B:THR10 4.9 63.4 1.0
SG B:CYS51 4.9 61.9 1.0
CB B:ALA60 4.9 50.1 1.0
SG B:CYS55 4.9 62.1 1.0
CB B:CYS55 4.9 61.4 1.0
N B:CYS55 5.0 57.9 1.0

Iron binding site 4 out of 6 in 9jn8

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Iron binding site 4 out of 6 in the Crystal Structure of A Thioredoxin-Like Ferredoxin of Rhodobacter Capsulatus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of A Thioredoxin-Like Ferredoxin of Rhodobacter Capsulatus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe201

b:59.1
occ:1.00
 FE2 B:FES201 0.0 59.1 1.0
S2 B:FES201 2.2 60.6 1.0
S1 B:FES201 2.2 58.9 1.0
SG B:CYS55 2.6 62.1 1.0
FE1 B:FES201 2.7 56.0 1.0
SG B:CYS51 2.7 61.9 1.0
CB B:CYS55 3.5 61.4 1.0
CB B:CYS51 3.6 61.5 1.0
CA B:CYS55 3.7 61.4 1.0
CA B:CYS51 3.8 58.5 1.0
N B:CYS55 3.9 57.9 1.0
N B:SER53 3.9 55.6 1.0
N B:LEU52 3.9 54.6 1.0
N B:ALA54 4.2 58.1 1.0
SG B:CYS8 4.3 59.6 1.0
C B:CYS51 4.3 56.6 1.0
CA B:SER53 4.4 58.3 1.0
C B:ALA54 4.6 61.9 1.0
C B:LEU52 4.7 57.5 1.0
C B:SER53 4.7 56.4 1.0
CA B:LEU52 4.9 53.8 1.0
SG B:CYS11 4.9 57.9 1.0
O B:GLU50 4.9 66.3 1.0

Iron binding site 5 out of 6 in 9jn8

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Iron binding site 5 out of 6 in the Crystal Structure of A Thioredoxin-Like Ferredoxin of Rhodobacter Capsulatus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of A Thioredoxin-Like Ferredoxin of Rhodobacter Capsulatus within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe201

b:50.1
occ:1.00
 FE1 C:FES201 0.0 50.1 1.0
S1 C:FES201 2.2 51.3 1.0
S2 C:FES201 2.2 57.4 1.0
SG C:CYS8 2.5 53.8 1.0
SG C:CYS11 2.5 50.5 1.0
FE2 C:FES201 2.7 53.3 1.0
CB C:CYS8 3.4 55.9 1.0
N C:CYS11 3.5 58.3 1.0
CA C:CYS11 3.5 55.9 1.0
CB C:CYS11 3.6 55.1 1.0
C C:THR10 4.3 60.2 1.0
CA C:CYS51 4.4 57.8 1.0
N C:LEU52 4.4 57.0 1.0
CA C:CYS55 4.6 61.0 1.0
CB C:THR10 4.7 60.2 1.0
SG C:CYS51 4.8 57.3 1.0
O C:GLU50 4.8 61.8 1.0
CA C:CYS8 4.8 55.6 1.0
CB C:CYS51 4.9 58.4 1.0
N C:THR10 4.9 54.9 1.0
CA C:THR10 4.9 54.0 1.0
CB C:ALA60 4.9 53.9 1.0
N C:CYS55 5.0 59.3 1.0
CB C:CYS55 5.0 58.1 1.0

Iron binding site 6 out of 6 in 9jn8

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Iron binding site 6 out of 6 in the Crystal Structure of A Thioredoxin-Like Ferredoxin of Rhodobacter Capsulatus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of A Thioredoxin-Like Ferredoxin of Rhodobacter Capsulatus within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe201

b:53.3
occ:1.00
 FE2 C:FES201 0.0 53.3 1.0
S1 C:FES201 2.2 51.3 1.0
S2 C:FES201 2.2 57.4 1.0
SG C:CYS55 2.6 60.6 1.0
SG C:CYS51 2.6 57.3 1.0
FE1 C:FES201 2.7 50.1 1.0
CB C:CYS55 3.3 58.1 1.0
CA C:CYS55 3.5 61.0 1.0
CB C:CYS51 3.6 58.4 1.0
N C:CYS55 3.6 59.3 1.0
O B:HOH390 3.9 66.5 1.0
N C:LEU52 3.9 57.0 1.0
CA C:CYS51 3.9 57.8 1.0
N C:SER53 4.0 52.1 1.0
N C:ALA54 4.1 60.8 1.0
C C:ALA54 4.3 59.5 1.0
C C:CYS51 4.4 54.1 1.0
SG C:CYS8 4.4 53.8 1.0
CA C:SER53 4.6 55.3 1.0
C C:SER53 4.7 57.7 1.0
O B:HOH327 4.8 62.8 1.0
C C:LEU52 4.8 55.6 1.0
CA C:ALA54 4.9 58.6 1.0
CA C:LEU52 4.9 54.6 1.0
SG C:CYS11 4.9 50.5 1.0
C C:CYS55 5.0 66.2 1.0
O C:ALA54 5.0 60.3 1.0

Reference:

Y.H.Shen, W.L.Cheng, X.Wang, H.E.Dai, M.Wang, L.Liu. Crystal Structure of A Thioredoxin-Like Ferredoxin Encoded Within A Cobalamin Biosynthetic Operon of Rhodobacter Capsulatus. Protein J. 2025.
ISSN: ISSN 1572-3887
PubMed: 39924633
DOI: 10.1007/S10930-025-10254-Z
Page generated: Tue Feb 25 10:02:47 2025

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