Iron in PDB 8amp: Crystal Structure of M.Tuberculosis Ferredoxin Fdx

The structure of Crystal Structure of M.Tuberculosis Ferredoxin Fdx, PDB code: 8amp was solved by S.Bukhdruker, A.Kavaleuski, E.Marin, I.Kapranov, A.Mishin, A.Gilep, N.Strushkevich, V.Borshchevskiy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.76 / 2.00
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	46.959, 46.959, 162.674, 90, 90, 120
R / Rfree (%)	25 / 29.1

The binding sites of Iron atom in the Crystal Structure of M.Tuberculosis Ferredoxin Fdx (pdb code 8amp). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Crystal Structure of M.Tuberculosis Ferredoxin Fdx, PDB code: 8amp:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Crystal Structure of M.Tuberculosis Ferredoxin Fdx


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 M.Tuberculosis Ferredoxin Fdx within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe101 b:55.2 occ:1.00 FE1 A:F3S101 0.0 55.2 1.0 S1 A:F3S101 2.3 47.9 1.0 S3 A:F3S101 2.3 54.9 1.0 S2 A:F3S101 2.3 59.7 1.0 SG A:CYS56 2.3 56.2 1.0 FE4 A:F3S101 2.6 56.7 1.0 FE3 A:F3S101 2.6 50.9 1.0 CB A:CYS56 3.4 53.9 1.0 S4 A:F3S101 3.9 58.7 1.0 CA A:CYS56 3.9 42.2 1.0 OG1 A:THR58 4.1 70.6 1.0 CD A:PRO57 4.4 58.7 1.0 C A:CYS56 4.6 55.7 1.0 N A:PRO57 4.7 64.8 1.0 CB A:ALA60 4.8 55.5 1.0 SG A:CYS18 4.8 49.3 1.0 SG A:CYS12 4.8 73.8 1.0 CB A:HIS15 4.9 80.9 1.0

Iron binding site 2 out of 4 in the Crystal Structure of M.Tuberculosis Ferredoxin Fdx


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 M.Tuberculosis Ferredoxin Fdx within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe101 b:50.9 occ:1.00 FE3 A:F3S101 0.0 50.9 1.0 S1 A:F3S101 2.3 47.9 1.0 S3 A:F3S101 2.3 54.9 1.0 S4 A:F3S101 2.3 58.7 1.0 SG A:CYS18 2.3 49.3 1.0 FE4 A:F3S101 2.6 56.7 1.0 FE1 A:F3S101 2.6 55.2 1.0 CB A:CYS18 3.4 36.6 1.0 S2 A:F3S101 3.8 59.7 1.0 N A:CYS18 3.9 48.4 1.0 N A:ALA16 4.1 55.9 1.0 CB A:VAL34 4.2 53.8 1.0 CA A:CYS18 4.3 34.4 1.0 CA A:ALA16 4.3 51.9 1.0 N A:MET17 4.4 49.4 1.0 CG2 A:VAL34 4.5 45.2 1.0 SG A:CYS12 4.6 73.8 1.0 CD1 A:LEU61 4.6 44.2 1.0 SG A:CYS56 4.6 56.2 1.0 CG1 A:VAL34 4.6 53.4 1.0 C A:ALA16 4.7 55.9 1.0 CG2 A:VAL28 4.8 75.2 1.0

Iron binding site 3 out of 4 in the Crystal Structure of M.Tuberculosis Ferredoxin Fdx


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 M.Tuberculosis Ferredoxin Fdx within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe101 b:56.7 occ:1.00 FE4 A:F3S101 0.0 56.7 1.0 S3 A:F3S101 2.3 54.9 1.0 S2 A:F3S101 2.3 59.7 1.0 S4 A:F3S101 2.3 58.7 1.0 SG A:CYS12 2.3 73.8 1.0 FE3 A:F3S101 2.6 50.9 1.0 FE1 A:F3S101 2.6 55.2 1.0 CB A:CYS12 3.4 74.2 1.0 CA A:CYS12 3.7 83.9 1.0 S1 A:F3S101 3.8 47.9 1.0 N A:GLY14 3.9 66.0 1.0 N A:GLN13 4.2 86.2 1.0 C A:CYS12 4.2 78.9 1.0 CG1 A:VAL34 4.2 53.4 1.0 CA A:GLY14 4.3 74.4 1.0 CB A:VAL34 4.3 53.8 1.0 N A:HIS15 4.3 70.1 1.0 SG A:CYS56 4.6 56.2 1.0 SG A:CYS18 4.7 49.3 1.0 C A:GLY14 4.8 73.1 1.0 N A:ALA16 4.9 55.9 1.0 N A:VAL34 4.9 65.7 1.0 C A:GLN13 5.0 86.9 1.0

Iron binding site 4 out of 4 in the Crystal Structure of M.Tuberculosis Ferredoxin Fdx


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 M.Tuberculosis Ferredoxin Fdx within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe102 b:22.0 occ:0.33 NE2 A:HIS51 2.1 12.0 1.0 O A:HOH205 2.3 12.4 0.3 CE1 A:HIS51 3.0 16.0 1.0 CD2 A:HIS51 3.1 19.2 1.0 O A:GLY47 4.0 37.5 1.0 ND1 A:HIS51 4.1 22.3 1.0 CG A:HIS51 4.2 22.1 1.0 C A:GLY47 4.4 22.3 1.0 CA A:GLY47 4.7 24.9 1.0 CZ3 A:TRP54 4.8 27.6 1.0

A.Gilep, T.Varaksa, S.Bukhdruker, A.Kavaleuski, Y.Ryzhykau, S.Smolskaya, T.Sushko, K.Tsumoto, I.Grabovec, I.Kapranov, I.Okhrimenko, E.Marin, M.Shevtsov, A.Mishin, K.Kovalev, A.Kuklin, V.Gordeliy, L.Kaluzhskiy, O.Gnedenko, E.Yablokov, A.Ivanov, V.Borshchevskiy, N.Strushkevich. Structural Insights Into 3FE-4S Ferredoxins Diversity in M. Tuberculosis Highlighted By A First Redox Complex with P450. Front Mol Biosci V. 9 00032 2022.
ISSN: ESSN 2296-889X
PubMed: 36699703
DOI: 10.3389/FMOLB.2022.1100032