Zinc 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:

Iron

(Fe)

4 atoms

The binding sites of Zinc 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 Zinc atom.
In total 4 binding sites of Zinc where determined in the [2FE-2S] Cluster Containing Ttua in Complex with Amp., PDB code: 5mko:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc 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 Zinc with other atoms in the Zn 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:Zn402 b:0.7 occ:1.00 SG A:CYS3 2.2 0.8 1.0 ND1 A:HIS25 2.2 98.7 1.0 SG A:CYS6 2.4 0.7 1.0 SG A:CYS22 2.5 0.8 1.0 CB A:CYS3 2.9 0.9 1.0 CE1 A:HIS25 3.1 99.8 1.0 CB A:CYS22 3.2 95.9 1.0 CG A:HIS25 3.2 95.6 1.0 CB A:HIS25 3.5 89.9 1.0 CB A:CYS6 3.6 0.4 1.0 N A:CYS22 3.7 93.5 1.0 N A:CYS6 3.7 0.2 1.0 CA A:CYS22 4.0 93.6 1.0 CA A:CYS6 4.1 0.8 1.0 NE2 A:HIS25 4.2 0.1 1.0 CD2 A:HIS25 4.3 98.6 1.0 N A:HIS25 4.3 88.6 1.0 CA A:CYS3 4.4 0.5 1.0 C A:PHE5 4.6 0.3 1.0 CA A:HIS25 4.6 87.8 1.0 CB A:PHE5 4.7 0.5 1.0 C A:CYS6 4.7 0.6 1.0 NH1 A:ARG8 4.7 0.8 1.0 O A:CYS6 4.8 0.1 1.0 C A:CYS22 4.8 95.3 1.0 CB A:ARG8 4.8 0.9 1.0 N A:PHE5 4.8 0.1 1.0 CA A:PHE5 4.9 0.7 1.0 C A:LEU21 4.9 96.2 1.0 C A:CYS3 5.0 0.1 1.0

Zinc 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 Zinc with other atoms in the Zn 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:Zn403 b:90.2 occ:1.00 SG A:CYS284 2.2 87.2 1.0 SG A:CYS272 2.3 0.9 1.0 SG A:CYS275 2.5 87.4 1.0 SG A:CYS287 2.7 90.9 1.0 CB A:CYS272 3.2 97.6 1.0 CB A:CYS287 3.4 87.0 1.0 CB A:CYS284 3.6 83.4 1.0 CB A:CYS275 3.7 85.1 1.0 N A:CYS284 4.0 86.7 1.0 N A:CYS275 4.0 88.2 1.0 N A:CYS287 4.2 82.7 1.0 CA A:CYS284 4.3 83.8 1.0 CA A:CYS287 4.4 85.1 1.0 CA A:CYS275 4.4 87.0 1.0 CB A:ILE274 4.5 93.9 1.0 OH A:TYR137 4.5 80.0 1.0 CA A:CYS272 4.6 99.2 1.0 O A:CYS284 4.7 85.3 1.0 CE2 A:TYR137 4.8 73.7 1.0 C A:CYS284 4.8 85.4 1.0 C A:ILE274 4.9 94.0 1.0 CG2 A:ILE283 4.9 96.8 1.0

Zinc 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 Zinc with other atoms in the Zn 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:Zn402 b:98.7 occ:1.00 SG B:CYS3 2.2 0.0 1.0 ND1 B:HIS25 2.3 95.8 1.0 SG B:CYS6 2.3 0.2 1.0 SG B:CYS22 2.5 99.2 1.0 CB B:CYS3 2.9 0.3 1.0 CE1 B:HIS25 3.1 96.8 1.0 CB B:CYS22 3.1 94.5 1.0 CG B:HIS25 3.3 92.7 1.0 CB B:CYS6 3.6 0.2 1.0 CB B:HIS25 3.6 87.2 1.0 N B:CYS6 3.7 98.0 1.0 N B:CYS22 3.8 92.7 1.0 CA B:CYS22 4.0 92.3 1.0 CA B:CYS6 4.1 99.8 1.0 NE2 B:HIS25 4.3 97.0 1.0 CD2 B:HIS25 4.3 95.4 1.0 CA B:CYS3 4.4 0.3 1.0 N B:HIS25 4.4 85.8 1.0 C B:PHE5 4.6 0.4 1.0 C B:CYS6 4.6 0.0 1.0 NH1 B:ARG8 4.6 0.4 1.0 CA B:HIS25 4.6 85.5 1.0 CB B:ARG8 4.7 98.0 1.0 CB B:PHE5 4.7 99.5 1.0 O B:CYS6 4.7 0.7 1.0 C B:CYS22 4.8 92.9 1.0 N B:PHE5 4.9 97.8 1.0 CA B:PHE5 4.9 98.4 1.0 C B:LEU21 5.0 96.0 1.0 CD B:ARG8 5.0 0.2 1.0 C B:CYS3 5.0 0.1 1.0

Zinc 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 Zinc with other atoms in the Zn 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:Zn403 b:0.7 occ:1.00 SG B:CYS284 2.2 0.9 1.0 SG B:CYS272 2.3 0.0 1.0 SG B:CYS275 2.5 99.8 1.0 SG B:CYS287 2.8 0.7 1.0 CB B:CYS272 3.2 1.0 1.0 CB B:CYS287 3.4 0.1 1.0 CB B:CYS284 3.5 0.2 1.0 CB B:CYS275 3.8 97.6 1.0 N B:CYS284 3.9 0.5 1.0 N B:CYS275 4.1 0.5 1.0 N B:CYS287 4.1 0.5 1.0 CA B:CYS284 4.2 0.6 1.0 CA B:CYS287 4.4 0.4 1.0 CA B:CYS275 4.5 99.9 1.0 OH B:TYR137 4.5 85.2 1.0 CB B:ILE274 4.6 0.1 1.0 CA B:CYS272 4.7 0.5 1.0 CE2 B:TYR137 4.7 79.7 1.0 O B:CYS284 4.7 0.6 1.0 C B:CYS284 4.8 0.6 1.0 CG2 B:ILE283 4.9 0.1 1.0 CZ B:TYR137 5.0 85.0 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