Zinc in PDB 5b4f: Sulfur Transferase Ttua in Complex with Iron Sulfur Cluster

The structure of Sulfur Transferase Ttua in Complex with Iron Sulfur Cluster, PDB code: 5b4f was solved by M.Chen, S.Narai, Y.Tanaka, M.Yao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.96 / 2.75
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	93.920, 93.920, 264.500, 90.00, 90.00, 120.00
R / Rfree (%)	21.9 / 25.7

The structure of Sulfur Transferase Ttua in Complex with Iron Sulfur Cluster also contains other interesting chemical elements:

Iron

(Fe)

4 atoms

The binding sites of Zinc atom in the Sulfur Transferase Ttua in Complex with Iron Sulfur Cluster (pdb code 5b4f). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Sulfur Transferase Ttua in Complex with Iron Sulfur Cluster, PDB code: 5b4f:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Sulfur Transferase Ttua in Complex with Iron Sulfur Cluster


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Sulfur Transferase Ttua in Complex with Iron Sulfur Cluster within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn407 b:55.8 occ:1.00 ND1 A:HIS25 2.2 51.7 1.0 SG A:CYS3 2.2 49.8 1.0 SG A:CYS6 2.3 61.1 1.0 SG A:CYS22 2.3 53.0 1.0 CE1 A:HIS25 3.1 64.1 1.0 CG A:HIS25 3.2 68.1 1.0 CB A:CYS6 3.3 48.7 1.0 CB A:CYS3 3.4 53.8 1.0 CB A:CYS22 3.4 51.2 1.0 CB A:HIS25 3.5 61.7 1.0 N A:CYS6 3.7 50.0 1.0 N A:CYS22 3.9 60.6 1.0 CA A:CYS6 4.1 53.3 1.0 NE2 A:HIS25 4.2 66.0 1.0 CA A:CYS22 4.3 58.7 1.0 CD2 A:HIS25 4.3 65.2 1.0 CB A:VAL5 4.3 53.6 1.0 C A:VAL5 4.5 55.1 1.0 CG1 A:VAL5 4.7 53.4 1.0 N A:HIS25 4.7 61.7 1.0 N A:GLY7 4.8 50.2 1.0 CA A:CYS3 4.8 53.0 1.0 CA A:VAL5 4.8 56.5 1.0 N A:VAL5 4.8 55.5 1.0 CA A:HIS25 4.8 62.7 1.0 C A:CYS6 4.8 61.3 1.0 C A:CYS22 5.0 64.0 1.0

Zinc binding site 2 out of 2 in the Sulfur Transferase Ttua in Complex with Iron Sulfur Cluster


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Sulfur Transferase Ttua in Complex with Iron Sulfur Cluster within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn408 b:57.0 occ:1.00 SG A:CYS286 2.3 50.1 1.0 SG A:CYS289 2.3 45.5 1.0 SG A:CYS274 2.4 56.5 1.0 SG A:CYS277 2.4 53.4 1.0 CB A:CYS277 3.2 58.1 1.0 CB A:CYS274 3.2 62.0 1.0 CB A:CYS289 3.2 49.0 1.0 CB A:CYS286 3.3 51.6 1.0 N A:CYS277 3.9 59.7 1.0 N A:CYS286 4.0 56.6 1.0 CA A:CYS277 4.1 65.8 1.0 N A:CYS289 4.2 47.4 1.0 CA A:CYS286 4.2 56.2 1.0 CA A:CYS289 4.3 50.8 1.0 OH A:TYR139 4.4 53.9 1.0 CE2 A:TYR139 4.5 47.0 1.0 CB A:ARG276 4.6 60.2 1.0 CA A:CYS274 4.7 64.5 1.0 C A:CYS277 4.8 63.6 1.0 O A:CYS286 4.8 51.2 1.0 C A:ARG276 4.8 59.8 1.0 C A:CYS286 4.8 52.0 1.0 CZ A:TYR139 4.9 52.5 1.0 N A:GLY278 4.9 61.4 1.0

M.Chen, S.I.Asai, S.Narai, S.Nambu, N.Omura, Y.Sakaguchi, T.Suzuki, M.Ikeda-Saito, K.Watanabe, M.Yao, N.Shigi, Y.Tanaka. Biochemical and Structural Characterization of Oxygen-Sensitive 2-Thiouridine Synthesis Catalyzed By An Iron-Sulfur Protein Ttua Proc. Natl. Acad. Sci. V. 114 4954 2017U.S.A..
ISSN: ESSN 1091-6490
PubMed: 28439027
DOI: 10.1073/PNAS.1615585114