Iron 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:

Zinc

(Zn)

4 atoms

The binding sites of Iron 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 Iron atom.
In total 8 binding sites of Iron where determined in the U34-Trna Thiolase Ncsa From Methanococcus Maripaludis with Its [4FE- 4S] Cluster, PDB code: 6scy:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in the U34-Trna Thiolase Ncsa From Methanococcus Maripaludis with Its [4FE- 4S] Cluster


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe 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:Fe403 b:0.3 occ:0.80 FE1 A:SF4403 0.0 0.3 0.8 S3 A:SF4403 2.3 0.6 0.8 S2 A:SF4403 2.3 0.5 0.8 S4 A:SF4403 2.3 0.5 0.8 SG A:CYS142 2.3 0.8 1.0 FE4 A:SF4403 2.7 0.5 0.8 FE2 A:SF4403 2.8 0.1 0.8 FE3 A:SF4403 2.8 0.1 0.7 CB A:CYS142 3.2 0.8 1.0 CA A:CYS142 3.3 0.1 1.0 CB A:SER236 3.5 0.4 1.0 O A:CYS142 3.5 0.9 1.0 OG A:SER236 3.7 0.2 1.0 C A:CYS142 3.9 0.5 1.0 S1 A:SF4403 3.9 0.8 0.8 N A:CYS142 4.5 0.0 1.0 CB A:CYS145 4.5 0.6 1.0 SG A:CYS233 4.6 0.7 1.0 SG A:CYS145 4.7 0.2 1.0 O3 A:SO4405 4.8 1.0 0.7 CA A:SER236 5.0 1.0 1.0

Iron binding site 2 out of 8 in the U34-Trna Thiolase Ncsa From Methanococcus Maripaludis with Its [4FE- 4S] Cluster


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe 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:Fe403 b:0.1 occ:0.80 FE2 A:SF4403 0.0 0.1 0.8 SG A:CYS145 2.2 0.2 1.0 S4 A:SF4403 2.3 0.5 0.8 S1 A:SF4403 2.3 0.8 0.8 S3 A:SF4403 2.3 0.6 0.8 FE3 A:SF4403 2.7 0.1 0.7 FE1 A:SF4403 2.8 0.3 0.8 FE4 A:SF4403 2.8 0.5 0.8 CB A:CYS145 2.8 0.6 1.0 NH1 A:ARG149 3.7 82.1 0.5 S2 A:SF4403 3.9 0.5 0.8 CA A:CYS145 4.2 0.8 1.0 O3 A:SO4405 4.2 1.0 0.7 OE2 A:GLU88 4.2 0.0 1.0 O A:CYS142 4.4 0.9 1.0 C A:CYS145 4.4 0.6 1.0 NH2 A:ARG94 4.5 0.6 1.0 N A:GLY146 4.5 0.8 1.0 CD A:GLU88 4.6 0.3 1.0 CD1 A:ILE90 4.6 0.8 1.0 CG A:GLU88 4.8 0.3 1.0 CZ A:ARG149 4.9 94.3 0.5 CA A:CYS142 4.9 0.1 1.0 O A:CYS145 4.9 0.7 1.0 SG A:CYS233 5.0 0.7 1.0 SG A:CYS142 5.0 0.8 1.0

Iron binding site 3 out of 8 in the U34-Trna Thiolase Ncsa From Methanococcus Maripaludis with Its [4FE- 4S] Cluster


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe 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 A:Fe403 b:0.1 occ:0.70 FE3 A:SF4403 0.0 0.1 0.7 O3 A:SO4405 2.2 1.0 0.7 S1 A:SF4403 2.3 0.8 0.8 S4 A:SF4403 2.3 0.5 0.8 S2 A:SF4403 2.3 0.5 0.8 FE2 A:SF4403 2.7 0.1 0.8 FE4 A:SF4403 2.7 0.5 0.8 FE1 A:SF4403 2.8 0.3 0.8 S A:SO4405 3.3 0.9 0.7 O1 A:SO4405 3.5 0.9 0.7 O4 A:SO4405 3.7 0.9 0.7 S3 A:SF4403 3.9 0.6 0.8 NH1 A:ARG149 4.1 82.1 0.5 NH2 A:ARG149 4.3 78.0 0.5 SG A:CYS142 4.5 0.8 1.0 O2 A:SO4405 4.5 0.7 0.7 CZ A:ARG149 4.6 94.3 0.5 SG A:CYS145 4.6 0.2 1.0 SG A:CYS233 4.8 0.7 1.0 OE2 A:GLU88 4.8 0.0 1.0 O A:HOH556 4.9 66.1 1.0

Iron binding site 4 out of 8 in the U34-Trna Thiolase Ncsa From Methanococcus Maripaludis with Its [4FE- 4S] Cluster


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe 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 A:Fe403 b:0.5 occ:0.80 FE4 A:SF4403 0.0 0.5 0.8 S2 A:SF4403 2.3 0.5 0.8 S1 A:SF4403 2.3 0.8 0.8 S3 A:SF4403 2.3 0.6 0.8 SG A:CYS233 2.3 0.7 1.0 FE3 A:SF4403 2.7 0.1 0.7 FE1 A:SF4403 2.7 0.3 0.8 FE2 A:SF4403 2.8 0.1 0.8 NH2 A:ARG94 3.3 0.6 1.0 CB A:CYS233 3.4 0.9 1.0 CB A:SER236 3.8 0.4 1.0 S4 A:SF4403 3.9 0.5 0.8 OG A:SER236 4.3 0.2 1.0 CZ A:ARG94 4.3 0.8 1.0 NH1 A:ARG94 4.5 0.4 1.0 CA A:CYS233 4.7 0.4 1.0 SG A:CYS145 4.7 0.2 1.0 O3 A:SO4405 4.7 1.0 0.7 N A:SER236 4.8 0.4 1.0 CA A:SER236 4.8 1.0 1.0 SG A:CYS142 4.9 0.8 1.0 O1 A:SO4405 5.0 0.9 0.7

Iron binding site 5 out of 8 in the U34-Trna Thiolase Ncsa From Methanococcus Maripaludis with Its [4FE- 4S] Cluster


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 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:Fe403 b:0.2 occ:0.80 FE1 B:SF4403 0.0 0.2 0.8 S3 B:SF4403 2.3 0.8 0.8 S2 B:SF4403 2.3 0.9 0.8 S4 B:SF4403 2.3 0.7 0.8 SG B:CYS142 2.3 0.5 1.0 FE2 B:SF4403 2.8 0.3 0.8 FE4 B:SF4403 2.8 0.3 0.8 FE3 B:SF4403 2.8 0.9 0.7 CB B:CYS142 3.2 0.5 1.0 CA B:CYS142 3.3 0.1 1.0 CB B:SER236 3.5 0.0 1.0 O B:CYS142 3.6 0.8 1.0 OG B:SER236 3.7 0.5 1.0 C B:CYS142 3.9 0.4 1.0 S1 B:SF4403 3.9 0.3 0.8 N B:CYS142 4.5 0.0 1.0 CB B:CYS145 4.5 1.0 1.0 SG B:CYS233 4.7 0.6 1.0 SG B:CYS145 4.7 0.8 1.0 O2 B:SO4407 4.8 0.4 0.7 CA B:SER236 5.0 0.2 1.0

Iron binding site 6 out of 8 in the U34-Trna Thiolase Ncsa From Methanococcus Maripaludis with Its [4FE- 4S] Cluster


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 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:Fe403 b:0.3 occ:0.80 FE2 B:SF4403 0.0 0.3 0.8 SG B:CYS145 2.2 0.8 1.0 S4 B:SF4403 2.3 0.7 0.8 S1 B:SF4403 2.3 0.3 0.8 S3 B:SF4403 2.3 0.8 0.8 FE4 B:SF4403 2.7 0.3 0.8 FE3 B:SF4403 2.8 0.9 0.7 FE1 B:SF4403 2.8 0.2 0.8 CB B:CYS145 2.8 1.0 1.0 NH1 B:ARG149 3.6 0.5 1.0 S2 B:SF4403 3.9 0.9 0.8 CA B:CYS145 4.2 0.8 1.0 O B:CYS142 4.4 0.8 1.0 C B:CYS145 4.4 0.3 1.0 OE1 B:GLU88 4.5 0.7 1.0 N B:GLY146 4.5 0.4 1.0 CZ B:ARG149 4.7 0.7 1.0 CG B:GLU88 4.8 0.3 1.0 CD B:GLU88 4.8 0.9 1.0 O2 B:SO4407 4.9 0.4 0.7 NH2 B:ARG149 4.9 0.3 1.0 CA B:CYS142 4.9 0.1 1.0 SG B:CYS233 4.9 0.6 1.0 SG B:CYS142 4.9 0.5 1.0 O B:CYS145 5.0 0.7 1.0

Iron binding site 7 out of 8 in the U34-Trna Thiolase Ncsa From Methanococcus Maripaludis with Its [4FE- 4S] Cluster


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 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:Fe403 b:0.9 occ:0.70 FE3 B:SF4403 0.0 0.9 0.7 O2 B:SO4407 2.3 0.4 0.7 S1 B:SF4403 2.3 0.3 0.8 S2 B:SF4403 2.3 0.9 0.8 S4 B:SF4403 2.3 0.7 0.8 FE2 B:SF4403 2.8 0.3 0.8 FE4 B:SF4403 2.8 0.3 0.8 FE1 B:SF4403 2.8 0.2 0.8 S B:SO4407 3.7 0.3 0.7 S3 B:SF4403 3.9 0.8 0.8 NH1 B:ARG149 4.3 0.5 1.0 O1 B:SO4407 4.3 0.2 0.7 NH2 B:ARG149 4.4 0.3 1.0 O4 B:SO4407 4.4 0.5 0.7 SG B:CYS142 4.5 0.5 1.0 O3 B:SO4407 4.5 0.2 0.7 CZ B:ARG149 4.6 0.7 1.0 SG B:CYS145 4.7 0.8 1.0 SG B:CYS233 4.8 0.6 1.0 O B:HOH523 4.8 72.6 1.0 NH1 B:ARG94 4.9 0.8 1.0 NH2 B:ARG94 5.0 0.2 1.0

Iron binding site 8 out of 8 in the U34-Trna Thiolase Ncsa From Methanococcus Maripaludis with Its [4FE- 4S] Cluster


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 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:Fe403 b:0.3 occ:0.80 FE4 B:SF4403 0.0 0.3 0.8 S3 B:SF4403 2.3 0.8 0.8 S1 B:SF4403 2.3 0.3 0.8 SG B:CYS233 2.3 0.6 1.0 S2 B:SF4403 2.3 0.9 0.8 FE2 B:SF4403 2.7 0.3 0.8 FE3 B:SF4403 2.8 0.9 0.7 FE1 B:SF4403 2.8 0.2 0.8 CB B:CYS233 3.4 0.6 1.0 NH1 B:ARG94 3.5 0.8 1.0 CB B:SER236 3.8 0.0 1.0 S4 B:SF4403 3.9 0.7 0.8 O2 B:SO4407 4.2 0.4 0.7 OG B:SER236 4.3 0.5 1.0 CZ B:ARG94 4.4 0.7 1.0 NH2 B:ARG94 4.6 0.2 1.0 SG B:CYS145 4.7 0.8 1.0 CA B:CYS233 4.7 0.3 1.0 N B:SER236 4.8 0.1 1.0 CA B:SER236 4.8 0.2 1.0 SG B:CYS142 4.9 0.5 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.