Zinc in PDB 6scy: U34-Trna Thiolase Ncsa From Methanococcus Maripaludis with Its [4FE- 4S] Cluster

The structure of U34-Trna Thiolase Ncsa From Methanococcus Maripaludis with Its [4FE- 4S] Cluster, PDB code: 6scy was solved by O.Bimai, P.Legrand, B.Golinelli-Pimaneau, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.85 / 2.81
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	54.980, 84.480, 145.440, 90.00, 90.00, 90.00
R / Rfree (%)	20.9 / 28.7

The structure of U34-Trna Thiolase Ncsa From Methanococcus Maripaludis with Its [4FE- 4S] Cluster also contains other interesting chemical elements:

Iron

(Fe)

8 atoms

The binding sites of Zinc atom in the U34-Trna Thiolase Ncsa From Methanococcus Maripaludis with Its [4FE- 4S] Cluster (pdb code 6scy). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the U34-Trna Thiolase Ncsa From Methanococcus Maripaludis with Its [4FE- 4S] Cluster, PDB code: 6scy:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the U34-Trna Thiolase Ncsa From Methanococcus Maripaludis with Its [4FE- 4S] Cluster


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of U34-Trna Thiolase Ncsa From Methanococcus Maripaludis with Its [4FE- 4S] Cluster within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:63.6 occ:1.00 SG A:CYS28 2.2 66.4 1.0 SG A:CYS9 2.2 67.3 1.0 SG A:CYS6 2.2 70.9 1.0 SG A:CYS25 2.8 66.4 1.0 CB A:CYS28 3.1 62.2 1.0 CB A:CYS6 3.1 67.4 1.0 CB A:CYS9 3.4 63.2 1.0 N A:CYS9 3.7 62.9 1.0 CA A:CYS9 4.1 62.3 1.0 CB A:CYS25 4.1 62.6 1.0 N A:CYS25 4.3 63.3 1.0 CA A:CYS28 4.4 61.7 1.0 C A:LYS8 4.5 66.8 1.0 CB A:LYS8 4.5 67.4 1.0 N A:CYS28 4.5 62.2 1.0 CA A:CYS6 4.5 67.5 1.0 N A:LYS8 4.7 65.8 1.0 C A:CYS9 4.7 63.1 1.0 CA A:LYS8 4.8 64.8 1.0 CA A:CYS25 4.8 62.6 1.0 N A:GLY10 4.9 58.9 1.0 CB A:LYS11 4.9 60.0 1.0 C A:CYS6 5.0 71.6 1.0 N A:LYS11 5.0 58.7 1.0

Zinc binding site 2 out of 4 in the U34-Trna Thiolase Ncsa From Methanococcus Maripaludis with Its [4FE- 4S] Cluster


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of U34-Trna Thiolase Ncsa From Methanococcus Maripaludis with Its [4FE- 4S] Cluster within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:0.9 occ:1.00 SG A:CYS285 2.6 0.3 1.0 SG A:CYS297 2.8 0.2 1.0 CD1 A:LEU300 3.2 0.3 1.0 SG A:CYS282 3.3 0.0 1.0 CB A:CYS297 3.7 0.5 1.0 SG A:CYS294 4.1 0.1 1.0 O A:CYS294 4.3 0.7 1.0 CB A:CYS285 4.3 0.5 1.0 O A:LYS283 4.5 0.4 1.0 CG A:LEU300 4.7 0.0 1.0 CE A:LYS151 4.8 0.1 1.0 C A:CYS294 5.0 0.4 1.0 CA A:CYS294 5.0 0.2 1.0 CB A:CYS282 5.0 0.1 1.0 CB A:CYS294 5.0 0.3 1.0

Zinc binding site 3 out of 4 in the U34-Trna Thiolase Ncsa From Methanococcus Maripaludis with Its [4FE- 4S] Cluster


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of U34-Trna Thiolase Ncsa From Methanococcus Maripaludis with Its [4FE- 4S] Cluster within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:63.7 occ:1.00 SG B:CYS28 2.2 54.5 1.0 SG B:CYS9 2.2 58.8 1.0 SG B:CYS6 2.4 71.0 1.0 SG B:CYS25 2.5 61.0 1.0 CB B:CYS28 3.1 50.4 1.0 CB B:CYS6 3.3 67.0 1.0 CB B:CYS9 3.5 55.1 1.0 N B:CYS9 3.9 56.1 1.0 CB B:CYS25 3.9 56.8 1.0 CA B:CYS9 4.2 55.1 1.0 N B:CYS25 4.3 57.1 1.0 CA B:CYS28 4.3 49.1 1.0 NZ B:LYS11 4.3 0.0 1.0 N B:CYS28 4.3 48.6 1.0 CA B:CYS25 4.7 56.2 1.0 C B:LYS8 4.7 61.1 1.0 CA B:CYS6 4.7 66.4 1.0 CB B:LYS8 4.7 60.8 1.0 C B:CYS9 4.9 58.8 1.0 CB B:LYS11 4.9 58.5 1.0 N B:LYS8 5.0 60.1 1.0

Zinc binding site 4 out of 4 in the U34-Trna Thiolase Ncsa From Methanococcus Maripaludis with Its [4FE- 4S] Cluster


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of U34-Trna Thiolase Ncsa From Methanococcus Maripaludis with Its [4FE- 4S] Cluster within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:0.4 occ:1.00 SG B:CYS294 2.2 0.8 1.0 SG B:CYS285 2.2 0.8 1.0 SG B:CYS282 2.7 0.8 1.0 CB B:CYS294 2.9 0.1 1.0 SG B:CYS297 3.2 0.1 1.0 CB B:CYS285 4.0 0.0 1.0 O B:GLY286 4.2 0.6 1.0 O B:LYS283 4.2 0.6 1.0 CE B:LYS151 4.3 0.1 1.0 CA B:CYS294 4.4 0.1 1.0 CB B:CYS297 4.4 0.3 1.0 CB B:CYS282 4.4 0.9 1.0 NZ B:LYS151 4.6 0.0 1.0 N B:GLY286 4.6 0.7 1.0 N B:CYS297 4.8 0.9 1.0 CA B:CYS285 4.9 1.0 1.0 N B:CYS285 5.0 0.9 1.0 CB B:VAL296 5.0 0.2 1.0

O.Bimai, P.Legrand, N.He, N.Touati, L.Binet, M.Fontecave, B.Golinelli-Pimpaneau. The Thiolation of Uridine 34 in Trna, Which Controls Protein Translation, Depends on A [4FE-4S] Cluster in the Archeum Methanococcus Maripaludis. To Be Published.