Zinc in PDB 5gha: Sulfur Transferase Ttua in Complex with Sulfur Carrier Ttub

The structure of Sulfur Transferase Ttua in Complex with Sulfur Carrier Ttub, PDB code: 5gha 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)	47.84 / 2.50
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	54.139, 93.873, 97.532, 109.21, 104.57, 106.86
R / Rfree (%)	19.6 / 24.7

The binding sites of Zinc atom in the Sulfur Transferase Ttua in Complex with Sulfur Carrier Ttub (pdb code 5gha). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Sulfur Transferase Ttua in Complex with Sulfur Carrier Ttub, PDB code: 5gha:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Sulfur Transferase Ttua in Complex with Sulfur Carrier Ttub


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 Sulfur Carrier Ttub within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:59.0 occ:1.00 ND1 A:HIS25 2.2 56.2 1.0 SG A:CYS22 2.4 39.7 1.0 SG A:CYS3 2.4 42.0 1.0 SG A:CYS6 2.5 60.3 1.0 CE1 A:HIS25 3.0 46.1 1.0 CG A:HIS25 3.2 50.4 1.0 CB A:CYS3 3.5 53.9 1.0 CB A:CYS22 3.5 39.7 1.0 CB A:CYS6 3.5 47.7 1.0 CB A:HIS25 3.6 45.1 1.0 N A:CYS6 3.8 50.8 1.0 N A:CYS22 4.0 41.9 1.0 NE2 A:HIS25 4.1 55.0 1.0 CB A:VAL5 4.2 51.4 1.0 CD2 A:HIS25 4.2 49.1 1.0 CA A:CYS6 4.3 51.1 1.0 CA A:CYS22 4.3 47.6 1.0 C A:VAL5 4.6 51.5 1.0 N A:HIS25 4.6 46.2 1.0 CA A:HIS25 4.7 44.7 1.0 CA A:VAL5 4.8 53.9 1.0 CG1 A:VAL5 4.8 37.3 1.0 N A:VAL5 4.8 46.9 1.0 CA A:CYS3 4.9 45.5 1.0 C A:CYS22 5.0 40.8 1.0 C A:CYS6 5.0 55.0 1.0

Zinc binding site 2 out of 8 in the Sulfur Transferase Ttua in Complex with Sulfur Carrier Ttub


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 Sulfur Carrier Ttub within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:56.8 occ:1.00 SG A:CYS277 2.3 41.4 1.0 SG A:CYS286 2.4 40.2 1.0 SG A:CYS274 2.4 48.1 1.0 SG A:CYS289 2.5 42.9 1.0 CB A:CYS274 3.1 55.8 1.0 CB A:CYS277 3.4 43.1 1.0 CB A:CYS289 3.4 38.5 1.0 CB A:CYS286 3.7 47.4 1.0 N A:CYS277 3.7 45.5 1.0 CA A:CYS277 4.1 46.2 1.0 N A:CYS286 4.2 49.4 1.0 CB A:ARG276 4.2 48.2 1.0 N A:CYS289 4.4 40.0 1.0 OH A:TYR139 4.5 31.5 1.0 CA A:CYS289 4.5 41.7 1.0 CA A:CYS286 4.5 45.3 1.0 CE1 A:TYR139 4.5 29.3 1.0 CA A:CYS274 4.6 47.1 1.0 C A:ARG276 4.7 46.3 1.0 N A:GLY278 4.9 43.5 1.0 C A:CYS277 4.9 42.0 1.0 CA A:ARG276 4.9 52.8 1.0 CG1 A:VAL285 4.9 41.9 1.0 CZ A:TYR139 4.9 32.8 1.0 O A:CYS286 5.0 42.2 1.0 N A:ARG276 5.0 48.7 1.0

Zinc binding site 3 out of 8 in the Sulfur Transferase Ttua in Complex with Sulfur Carrier Ttub


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Sulfur Transferase Ttua in Complex with Sulfur Carrier Ttub within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn401 b:51.7 occ:1.00 ND1 D:HIS25 2.1 40.4 1.0 SG D:CYS22 2.3 36.7 1.0 SG D:CYS3 2.4 42.6 1.0 SG D:CYS6 2.5 45.1 1.0 CE1 D:HIS25 3.0 47.1 1.0 CG D:HIS25 3.2 38.9 1.0 CB D:CYS22 3.4 35.8 1.0 CB D:CYS3 3.5 50.2 1.0 CB D:HIS25 3.6 27.6 1.0 N D:CYS6 3.6 55.3 1.0 CB D:CYS6 3.6 49.4 1.0 N D:CYS22 4.0 38.9 1.0 CA D:CYS6 4.1 53.1 1.0 NE2 D:HIS25 4.2 42.8 1.0 CB D:VAL5 4.3 52.1 1.0 CD2 D:HIS25 4.3 37.0 1.0 CA D:CYS22 4.3 41.1 1.0 O D:CYS6 4.3 62.5 1.0 C D:CYS6 4.5 56.9 1.0 N D:HIS25 4.6 39.8 1.0 C D:VAL5 4.7 56.5 1.0 CA D:HIS25 4.7 36.9 1.0 CA D:VAL5 4.8 49.9 1.0 N D:VAL5 4.9 57.4 1.0 CB D:GLN8 4.9 53.9 1.0 CA D:CYS3 4.9 52.4 1.0 C D:CYS22 5.0 39.5 1.0 CG1 D:VAL5 5.0 43.5 1.0

Zinc binding site 4 out of 8 in the Sulfur Transferase Ttua in Complex with Sulfur Carrier Ttub


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Sulfur Transferase Ttua in Complex with Sulfur Carrier Ttub within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn402 b:53.7 occ:1.00 SG D:CYS286 2.4 35.5 1.0 SG D:CYS289 2.4 40.4 1.0 SG D:CYS277 2.4 39.6 1.0 SG D:CYS274 2.5 42.2 1.0 CB D:CYS277 3.2 39.3 1.0 CB D:CYS274 3.3 43.3 1.0 CB D:CYS289 3.4 31.6 1.0 CB D:CYS286 3.4 35.3 1.0 N D:CYS277 3.9 44.7 1.0 N D:CYS286 3.9 37.1 1.0 CA D:CYS277 4.1 44.6 1.0 OH D:TYR139 4.2 32.2 1.0 CA D:CYS286 4.2 37.3 1.0 N D:CYS289 4.3 39.0 1.0 CE1 D:TYR139 4.4 24.5 1.0 CA D:CYS289 4.4 43.1 1.0 CG1 D:VAL285 4.7 49.9 1.0 CZ D:TYR139 4.7 28.2 1.0 C D:CYS277 4.8 37.1 1.0 CA D:CYS274 4.8 43.6 1.0 N D:GLY278 4.8 43.2 1.0 C D:ARG276 4.8 41.8 1.0 C D:CYS286 4.8 38.7 1.0 O D:CYS286 4.9 41.5 1.0

Zinc binding site 5 out of 8 in the Sulfur Transferase Ttua in Complex with Sulfur Carrier Ttub


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Sulfur Transferase Ttua in Complex with Sulfur Carrier Ttub within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:65.6 occ:1.00 ND1 B:HIS25 2.2 48.2 1.0 SG B:CYS6 2.3 72.2 1.0 SG B:CYS3 2.5 57.2 1.0 SG B:CYS22 2.6 46.2 1.0 CG B:HIS25 3.0 54.9 1.0 CB B:HIS25 3.1 37.6 1.0 CE1 B:HIS25 3.3 55.0 1.0 CB B:CYS6 3.3 72.2 1.0 CB B:CYS3 3.5 55.9 1.0 N B:CYS6 3.8 66.6 1.0 CB B:CYS22 4.0 48.7 1.0 CA B:CYS6 4.1 74.0 1.0 CD2 B:HIS25 4.2 55.8 1.0 N B:CYS22 4.2 48.0 1.0 NE2 B:HIS25 4.3 56.5 1.0 CB B:VAL5 4.3 66.3 1.0 CA B:HIS25 4.3 49.2 1.0 N B:HIS25 4.4 45.3 1.0 CA B:CYS22 4.6 51.0 1.0 C B:VAL5 4.7 66.8 1.0 N B:VAL5 4.7 68.2 1.0 N B:GLY7 4.8 69.9 1.0 CA B:VAL5 4.8 62.3 1.0 C B:CYS6 4.9 73.5 1.0 CG2 B:VAL5 4.9 72.2 1.0 CA B:CYS3 5.0 57.6 1.0

Zinc binding site 6 out of 8 in the Sulfur Transferase Ttua in Complex with Sulfur Carrier Ttub


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Sulfur Transferase Ttua in Complex with Sulfur Carrier Ttub within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:65.2 occ:1.00 SG B:CYS286 2.3 52.6 1.0 SG B:CYS274 2.4 61.4 1.0 SG B:CYS277 2.4 47.5 1.0 SG B:CYS289 2.5 55.8 1.0 CB B:CYS274 3.2 51.6 1.0 CB B:CYS289 3.3 52.3 1.0 CB B:CYS286 3.4 60.8 1.0 CB B:CYS277 3.6 57.3 1.0 N B:CYS277 3.9 56.8 1.0 N B:CYS286 3.9 50.6 1.0 N B:CYS289 4.1 50.4 1.0 CA B:CYS286 4.2 51.5 1.0 CA B:CYS277 4.3 59.7 1.0 CA B:CYS289 4.4 57.2 1.0 CE1 B:TYR139 4.4 33.8 1.0 OH B:TYR139 4.4 45.0 1.0 CB B:ARG276 4.6 67.5 1.0 CG1 B:VAL285 4.7 65.1 1.0 CA B:CYS274 4.7 52.2 1.0 N B:GLY278 4.8 58.3 1.0 C B:CYS286 4.8 50.5 1.0 O B:CYS286 4.8 56.2 1.0 CZ B:TYR139 4.8 38.9 1.0 C B:CYS277 4.9 60.9 1.0 C B:ARG276 5.0 63.2 1.0 C B:VAL285 5.0 58.0 1.0

Zinc binding site 7 out of 8 in the Sulfur Transferase Ttua in Complex with Sulfur Carrier Ttub


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Sulfur Transferase Ttua in Complex with Sulfur Carrier Ttub within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn401 b:75.5 occ:1.00 ND1 C:HIS25 2.1 50.0 1.0 SG C:CYS3 2.3 52.7 1.0 SG C:CYS6 2.4 75.2 1.0 SG C:CYS22 2.4 45.1 1.0 CE1 C:HIS25 2.9 47.6 1.0 CG C:HIS25 3.2 52.4 1.0 CB C:CYS3 3.3 55.0 1.0 CB C:CYS6 3.5 55.0 1.0 CB C:HIS25 3.6 44.8 1.0 CB C:CYS22 3.7 45.6 1.0 N C:CYS6 3.8 54.9 1.0 NE2 C:HIS25 4.0 53.0 1.0 NE2 C:GLN8 4.0 65.7 1.0 N C:CYS22 4.1 45.0 1.0 CD2 C:HIS25 4.2 48.6 1.0 CA C:CYS6 4.2 57.6 1.0 CA C:CYS22 4.5 49.8 1.0 CB C:VAL5 4.5 47.7 1.0 N C:HIS25 4.6 54.3 1.0 CA C:CYS3 4.7 51.8 1.0 N C:GLY7 4.7 57.2 1.0 CA C:HIS25 4.8 48.4 1.0 C C:VAL5 4.8 53.8 1.0 N C:VAL5 4.8 59.9 1.0 CB C:GLN8 4.9 61.1 1.0 C C:CYS6 4.9 62.2 1.0 CA C:VAL5 5.0 62.3 1.0 N C:GLN8 5.0 64.2 1.0

Zinc binding site 8 out of 8 in the Sulfur Transferase Ttua in Complex with Sulfur Carrier Ttub


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Sulfur Transferase Ttua in Complex with Sulfur Carrier Ttub within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn402 b:54.4 occ:1.00 SG C:CYS277 2.3 40.2 1.0 SG C:CYS286 2.3 36.7 1.0 SG C:CYS289 2.4 41.2 1.0 SG C:CYS274 2.5 45.0 1.0 CB C:CYS277 3.2 40.2 1.0 CB C:CYS274 3.3 52.4 1.0 CB C:CYS289 3.3 39.3 1.0 CB C:CYS286 3.5 44.4 1.0 N C:CYS277 3.8 45.5 1.0 N C:CYS286 4.1 48.0 1.0 CA C:CYS277 4.1 43.5 1.0 N C:CYS289 4.3 39.8 1.0 CA C:CYS286 4.3 47.8 1.0 CA C:CYS289 4.4 38.5 1.0 CE1 C:TYR139 4.4 34.1 1.0 OH C:TYR139 4.4 40.6 1.0 CB C:ARG276 4.6 48.5 1.0 CA C:CYS274 4.8 49.1 1.0 N C:GLY278 4.8 44.4 1.0 C C:CYS277 4.8 40.6 1.0 O C:CYS286 4.8 41.0 1.0 CG1 C:VAL285 4.8 43.4 1.0 CZ C:TYR139 4.8 34.5 1.0 C C:ARG276 4.9 48.4 1.0 C C:CYS286 4.9 40.0 1.0

M.Chen, S.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