Zinc in PDB 5mkq: Ttua Enzyme Containing A [4FE-4S]

The structure of Ttua Enzyme Containing A [4FE-4S], PDB code: 5mkq 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)	47.88 / 2.79
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	69.450, 72.190, 127.950, 90.00, 90.00, 90.00
R / Rfree (%)	20.7 / 24.4

The structure of Ttua Enzyme Containing A [4FE-4S] also contains other interesting chemical elements:

Iron

(Fe)

8 atoms

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

Zinc binding site 1 out of 4 in the Ttua Enzyme Containing A [4FE-4S]


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Ttua Enzyme Containing A [4FE-4S] within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:0.2 occ:1.00 SG A:CYS3 2.2 0.1 1.0 SG A:CYS6 2.2 0.2 1.0 SG A:CYS22 2.5 0.3 1.0 ND1 A:HIS25 2.7 0.8 1.0 CB A:CYS3 2.9 0.9 1.0 CG A:HIS25 3.2 0.0 1.0 CB A:CYS22 3.5 0.7 1.0 CE1 A:HIS25 3.5 0.5 1.0 CB A:HIS25 3.5 97.9 1.0 CB A:CYS6 3.7 0.3 1.0 N A:CYS6 3.9 0.6 1.0 N A:CYS22 4.0 0.8 1.0 CD2 A:HIS25 4.2 0.7 1.0 CA A:CYS6 4.3 0.5 1.0 NE2 A:HIS25 4.3 0.9 1.0 CA A:CYS22 4.3 0.8 1.0 CA A:CYS3 4.4 0.6 1.0 C A:PHE5 4.6 0.4 1.0 N A:HIS25 4.7 96.7 1.0 CB A:ARG8 4.7 0.8 1.0 CA A:HIS25 4.7 96.1 1.0 N A:PHE5 4.7 0.3 1.0 C A:CYS6 4.8 0.6 1.0 CB A:PHE5 4.8 1.0 1.0 O A:CYS6 4.8 0.8 1.0 C A:CYS3 4.9 0.9 1.0 CD A:ARG8 4.9 0.8 1.0 CA A:PHE5 4.9 0.9 1.0

Zinc binding site 2 out of 4 in the Ttua Enzyme Containing A [4FE-4S]


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Ttua Enzyme Containing A [4FE-4S] within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:0.3 occ:1.00 SG A:CYS275 2.2 99.6 1.0 SG A:CYS284 2.3 99.4 1.0 SG A:CYS272 2.6 0.8 1.0 SG A:CYS287 2.7 0.7 1.0 CB A:CYS287 3.0 0.1 1.0 CB A:CYS272 3.4 0.5 1.0 CB A:CYS284 3.4 96.6 1.0 CB A:CYS275 3.6 95.9 1.0 N A:CYS275 3.9 98.8 1.0 N A:CYS287 4.0 97.8 1.0 N A:CYS284 4.0 99.0 1.0 CA A:CYS287 4.1 99.5 1.0 CA A:CYS284 4.2 97.3 1.0 CA A:CYS275 4.3 97.1 1.0 CE2 A:TYR137 4.6 79.5 1.0 CB A:ILE274 4.7 1.0 1.0 O A:CYS284 4.8 100.0 1.0 OH A:TYR137 4.8 88.5 1.0 C A:CYS284 4.8 0.2 1.0 CA A:CYS272 4.8 0.8 1.0 C A:ILE274 5.0 0.6 1.0

Zinc binding site 3 out of 4 in the Ttua Enzyme Containing A [4FE-4S]


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Ttua Enzyme Containing A [4FE-4S] within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:0.6 occ:1.00 SG B:CYS3 2.2 0.8 1.0 SG B:CYS6 2.2 0.3 1.0 SG B:CYS22 2.5 1.0 1.0 ND1 B:HIS25 2.7 94.2 1.0 CB B:CYS3 2.9 0.0 1.0 CG B:HIS25 3.2 91.4 1.0 CB B:CYS22 3.5 97.5 1.0 CE1 B:HIS25 3.5 95.1 1.0 CB B:HIS25 3.5 86.2 1.0 CB B:CYS6 3.7 0.7 1.0 N B:CYS6 3.9 0.6 1.0 N B:CYS22 4.0 97.4 1.0 CD2 B:HIS25 4.2 94.2 1.0 NE2 B:HIS25 4.3 95.5 1.0 CA B:CYS6 4.3 0.3 1.0 CA B:CYS22 4.3 95.8 1.0 CA B:CYS3 4.4 0.3 1.0 C B:PHE5 4.6 0.0 1.0 N B:HIS25 4.6 84.7 1.0 CB B:ARG8 4.7 0.1 1.0 CA B:HIS25 4.7 84.2 1.0 N B:PHE5 4.7 0.8 1.0 C B:CYS6 4.8 0.4 1.0 O B:CYS6 4.8 0.1 1.0 CB B:PHE5 4.8 0.8 1.0 C B:CYS3 4.9 0.2 1.0 CD B:ARG8 4.9 0.0 1.0 CA B:PHE5 4.9 0.1 1.0

Zinc binding site 4 out of 4 in the Ttua Enzyme Containing A [4FE-4S]


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Ttua Enzyme Containing A [4FE-4S] within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:0.7 occ:1.00 SG B:CYS275 2.2 0.4 1.0 SG B:CYS284 2.3 0.4 1.0 SG B:CYS272 2.6 0.4 1.0 SG B:CYS287 2.7 0.2 1.0 CB B:CYS287 3.0 0.4 1.0 CB B:CYS284 3.4 0.9 1.0 CB B:CYS272 3.4 0.1 1.0 CB B:CYS275 3.6 0.1 1.0 N B:CYS275 3.9 0.8 1.0 N B:CYS287 4.0 1.0 1.0 N B:CYS284 4.0 0.0 1.0 CA B:CYS287 4.1 0.3 1.0 CA B:CYS284 4.2 0.5 1.0 CA B:CYS275 4.3 0.9 1.0 CE2 B:TYR137 4.6 75.8 1.0 CB B:ILE274 4.7 0.9 1.0 OH B:TYR137 4.8 82.1 1.0 O B:CYS284 4.8 0.4 1.0 C B:CYS284 4.8 0.8 1.0 CA B:CYS272 4.9 0.1 1.0 CB B:MET277 5.0 0.7 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