Iron in PDB 5mko: [2FE-2S] Cluster Containing Ttua in Complex with Amp.

The structure of [2FE-2S] Cluster Containing Ttua in Complex with Amp., PDB code: 5mko was solved by S.Arragain, O.Bimai, P.Legrand, B.Golinelli-Pimpaneau, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.00 / 2.65
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	68.860, 72.320, 128.280, 90.00, 90.00, 90.00
R / Rfree (%)	21.1 / 23.9

The structure of [2FE-2S] Cluster Containing Ttua in Complex with Amp. also contains other interesting chemical elements:

Zinc

(Zn)

4 atoms

The binding sites of Iron atom in the [2FE-2S] Cluster Containing Ttua in Complex with Amp. (pdb code 5mko). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the [2FE-2S] Cluster Containing Ttua in Complex with Amp., PDB code: 5mko:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the [2FE-2S] Cluster Containing Ttua in Complex with Amp.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of [2FE-2S] Cluster Containing Ttua in Complex with Amp. within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe404 b:0.6 occ:0.60 FE1 A:FES404 0.0 0.6 0.6 S1 A:FES404 2.2 0.4 0.6 S2 A:FES404 2.2 0.6 0.6 SG A:CYS128 2.5 0.4 1.0 SG A:CYS220 2.7 0.8 1.0 FE2 A:FES404 2.7 0.5 0.6 CB A:CYS220 2.8 0.6 1.0 CB A:CYS128 3.4 0.3 1.0 CA A:CYS128 3.8 0.0 1.0 CA A:CYS220 4.3 0.3 1.0 N A:CYS128 4.4 0.5 1.0 SG A:CYS131 4.5 99.9 1.0 CB A:TYR222 4.7 0.8 1.0 N A:ALA223 4.8 0.5 1.0 CB A:CYS131 4.8 96.1 1.0 C A:CYS220 4.8 0.3 1.0 C A:PRO127 4.9 0.5 1.0 O A:PRO127 4.9 0.6 1.0 C A:TYR222 4.9 0.5 1.0

Iron binding site 2 out of 4 in the [2FE-2S] Cluster Containing Ttua in Complex with Amp.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of [2FE-2S] Cluster Containing Ttua in Complex with Amp. within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe404 b:0.5 occ:0.60 FE2 A:FES404 0.0 0.5 0.6 SG A:CYS131 2.1 99.9 1.0 S2 A:FES404 2.2 0.6 0.6 S1 A:FES404 2.2 0.4 0.6 FE1 A:FES404 2.7 0.6 0.6 CB A:CYS131 3.2 96.1 1.0 SG A:CYS220 3.5 0.8 1.0 CB A:CYS220 4.4 0.6 1.0 NZ A:LYS135 4.5 99.6 1.0 CA A:CYS131 4.5 95.8 1.0 CA A:CYS128 4.6 0.0 1.0 O A:PRO127 4.7 0.6 1.0 SG A:CYS128 4.8 0.4 1.0 CE A:LYS135 4.9 87.9 1.0 CB A:CYS128 5.0 0.3 1.0 CD1 A:ILE83 5.0 80.1 1.0

Iron binding site 3 out of 4 in the [2FE-2S] Cluster Containing Ttua in Complex with Amp.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of [2FE-2S] Cluster Containing Ttua in Complex with Amp. within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe404 b:0.3 occ:0.70 FE1 B:FES404 0.0 0.3 0.7 S1 B:FES404 2.2 0.6 0.7 S2 B:FES404 2.2 0.8 0.7 SG B:CYS220 2.4 0.2 1.0 SG B:CYS128 2.6 0.3 1.0 FE2 B:FES404 2.7 0.0 0.7 CB B:CYS220 2.9 0.4 1.0 CB B:CYS128 3.6 0.3 1.0 CA B:CYS128 4.0 0.7 1.0 O B:TYR222 4.4 0.1 1.0 CA B:CYS220 4.4 0.3 1.0 N B:CYS128 4.4 0.5 1.0 SG B:CYS131 4.5 0.7 1.0 CB B:TYR222 4.8 0.1 1.0 CB B:CYS131 4.8 99.0 1.0

Iron binding site 4 out of 4 in the [2FE-2S] Cluster Containing Ttua in Complex with Amp.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of [2FE-2S] Cluster Containing Ttua in Complex with Amp. within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe404 b:0.0 occ:0.70 FE2 B:FES404 0.0 0.0 0.7 SG B:CYS131 2.1 0.7 1.0 S2 B:FES404 2.2 0.8 0.7 S1 B:FES404 2.2 0.6 0.7 FE1 B:FES404 2.7 0.3 0.7 CB B:CYS131 3.1 99.0 1.0 CD1 B:LEU81 3.7 76.8 1.0 O B:HOH522 4.0 98.0 1.0 NZ B:LYS135 4.0 97.0 1.0 SG B:CYS220 4.2 0.2 1.0 CA B:CYS131 4.5 98.9 1.0 CA B:CYS128 4.6 0.7 1.0 CE B:LYS135 4.8 93.4 1.0 SG B:CYS128 4.8 0.3 1.0 CD1 B:ILE83 4.9 86.0 1.0 CB B:CYS220 4.9 0.4 1.0

S.Arragain, O.Bimai, P.Legrand, S.Caillat, J.L.Ravanat, N.Touati, L.Binet, M.Atta, M.Fontecave, B.Golinelli-Pimpaneau. Nonredox Thiolation in Trna Occurring Via Sulfur Activation By A [4FE-4S] Cluster. Proc. Natl. Acad. Sci. V. 114 7355 2017U.S.A..
ISSN: ESSN 1091-6490
PubMed: 28655838
DOI: 10.1073/PNAS.1700902114