Iron in PDB 1uwv: Crystal Structure of Ruma, the Iron-Sulfur Cluster Containing E. Coli 23S Ribosomal Rna 5-Methyluridine Methyltransferase

The structure of Crystal Structure of Ruma, the Iron-Sulfur Cluster Containing E. Coli 23S Ribosomal Rna 5-Methyluridine Methyltransferase, PDB code: 1uwv was solved by T.T.Lee, S.Agarwalla, R.M.Stroud, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.95
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	35.938, 99.448, 58.519, 90.00, 100.57, 90.00
R / Rfree (%)	18.6 / 22.7

The structure of Crystal Structure of Ruma, the Iron-Sulfur Cluster Containing E. Coli 23S Ribosomal Rna 5-Methyluridine Methyltransferase also contains other interesting chemical elements:

Nickel	(Ni)	2 atoms
Chlorine	(Cl)	1 atom

The binding sites of Iron atom in the Crystal Structure of Ruma, the Iron-Sulfur Cluster Containing E. Coli 23S Ribosomal Rna 5-Methyluridine Methyltransferase (pdb code 1uwv). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Crystal Structure of Ruma, the Iron-Sulfur Cluster Containing E. Coli 23S Ribosomal Rna 5-Methyluridine Methyltransferase, PDB code: 1uwv:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Crystal Structure of Ruma, the Iron-Sulfur Cluster Containing E. Coli 23S Ribosomal Rna 5-Methyluridine Methyltransferase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of Ruma, the Iron-Sulfur Cluster Containing E. Coli 23S Ribosomal Rna 5-Methyluridine Methyltransferase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1432 b:18.2 occ:1.00 FE1 A:SF41432 0.0 18.2 1.0 S3 A:SF41432 2.3 17.1 1.0 S4 A:SF41432 2.3 19.0 1.0 S2 A:SF41432 2.3 19.1 1.0 SG A:CYS87 2.3 19.5 1.0 FE4 A:SF41432 2.7 19.5 1.0 FE2 A:SF41432 2.8 16.8 1.0 FE3 A:SF41432 2.8 18.7 1.0 CB A:CYS87 3.1 18.9 1.0 S1 A:SF41432 3.9 16.5 1.0 CD2 A:PHE148 4.0 14.7 1.0 CA A:GLY89 4.3 17.6 1.0 N A:GLY89 4.3 17.9 1.0 N A:CYS90 4.5 16.6 1.0 CE2 A:PHE148 4.5 15.7 1.0 CA A:CYS87 4.5 18.3 1.0 C A:GLY89 4.7 18.3 1.0 SG A:CYS81 4.8 20.7 1.0 SG A:CYS90 4.8 17.9 1.0 C A:CYS87 4.8 17.0 1.0 SG A:CYS162 4.9 15.4 1.0 CB A:HIS83 4.9 17.8 1.0 O A:CYS87 5.0 16.7 1.0

Iron binding site 2 out of 4 in the Crystal Structure of Ruma, the Iron-Sulfur Cluster Containing E. Coli 23S Ribosomal Rna 5-Methyluridine Methyltransferase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of Ruma, the Iron-Sulfur Cluster Containing E. Coli 23S Ribosomal Rna 5-Methyluridine Methyltransferase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1432 b:16.8 occ:1.00 FE2 A:SF41432 0.0 16.8 1.0 S3 A:SF41432 2.3 17.1 1.0 S1 A:SF41432 2.3 16.5 1.0 S4 A:SF41432 2.3 19.0 1.0 SG A:CYS162 2.3 15.4 1.0 FE4 A:SF41432 2.6 19.5 1.0 FE1 A:SF41432 2.8 18.2 1.0 FE3 A:SF41432 2.8 18.7 1.0 CB A:CYS162 3.3 15.0 1.0 CA A:CYS162 3.7 14.0 1.0 S2 A:SF41432 3.9 19.1 1.0 CG1 A:ILE164 3.9 13.0 1.0 CE2 A:PHE148 4.0 15.7 1.0 CD1 A:ILE164 4.2 17.2 1.0 C A:CYS162 4.4 14.3 1.0 CD2 A:PHE148 4.4 14.7 1.0 SG A:CYS81 4.5 20.7 1.0 O A:GLN161 4.7 16.3 1.0 CD A:PRO163 4.8 12.5 1.0 N A:PRO163 4.8 13.8 1.0 SG A:CYS90 4.9 17.9 1.0 SG A:CYS87 4.9 19.5 1.0 N A:CYS162 4.9 15.2 1.0 N A:ILE164 4.9 13.1 1.0

Iron binding site 3 out of 4 in the Crystal Structure of Ruma, the Iron-Sulfur Cluster Containing E. Coli 23S Ribosomal Rna 5-Methyluridine Methyltransferase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of Ruma, the Iron-Sulfur Cluster Containing E. Coli 23S Ribosomal Rna 5-Methyluridine Methyltransferase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1432 b:18.7 occ:1.00 FE3 A:SF41432 0.0 18.7 1.0 SG A:CYS90 2.3 17.9 1.0 S4 A:SF41432 2.3 19.0 1.0 S1 A:SF41432 2.3 16.5 1.0 S2 A:SF41432 2.3 19.1 1.0 FE4 A:SF41432 2.7 19.5 1.0 FE2 A:SF41432 2.8 16.8 1.0 FE1 A:SF41432 2.8 18.2 1.0 CB A:CYS90 3.2 16.6 1.0 NE2 A:GLN93 3.5 19.7 1.0 N A:CYS90 3.8 16.6 1.0 CD1 A:ILE164 4.0 17.2 1.0 S3 A:SF41432 4.0 17.1 1.0 CA A:CYS90 4.1 17.1 1.0 C A:GLY89 4.2 18.3 1.0 CG1 A:ILE164 4.2 13.0 1.0 CG2 A:ILE164 4.4 14.2 1.0 CA A:GLY89 4.6 17.6 1.0 SG A:CYS162 4.8 15.4 1.0 CD A:GLN93 4.8 17.6 1.0 SG A:CYS87 4.8 19.5 1.0 O A:GLY89 4.8 18.1 1.0 SG A:CYS81 4.9 20.7 1.0 CB A:CYS81 5.0 19.7 1.0 CB A:ILE164 5.0 13.8 1.0

Iron binding site 4 out of 4 in the Crystal Structure of Ruma, the Iron-Sulfur Cluster Containing E. Coli 23S Ribosomal Rna 5-Methyluridine Methyltransferase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of Ruma, the Iron-Sulfur Cluster Containing E. Coli 23S Ribosomal Rna 5-Methyluridine Methyltransferase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1432 b:19.5 occ:1.00 FE4 A:SF41432 0.0 19.5 1.0 S2 A:SF41432 2.3 19.1 1.0 S1 A:SF41432 2.3 16.5 1.0 S3 A:SF41432 2.3 17.1 1.0 SG A:CYS81 2.3 20.7 1.0 FE2 A:SF41432 2.6 16.8 1.0 FE3 A:SF41432 2.7 18.7 1.0 FE1 A:SF41432 2.7 18.2 1.0 CB A:CYS81 3.1 19.7 1.0 S4 A:SF41432 3.8 19.0 1.0 NE2 A:GLN93 4.0 19.7 1.0 CB A:HIS83 4.3 17.8 1.0 CD A:PRO163 4.4 12.5 1.0 CA A:CYS162 4.5 14.0 1.0 CA A:CYS81 4.6 18.8 1.0 O A:GLN161 4.6 16.3 1.0 SG A:CYS162 4.6 15.4 1.0 N A:PHE84 4.6 18.4 1.0 SG A:CYS90 4.7 17.9 1.0 SG A:CYS87 4.8 19.5 1.0 CB A:CYS87 4.9 18.9 1.0 C A:HIS83 4.9 17.9 1.0 CB A:CYS162 4.9 15.0 1.0 ND1 A:HIS83 5.0 19.6 1.0

T.T.Lee, S.Agarwalla, R.M.Stroud. Crystal Structure of Ruma, An Iron-Sulfur Cluster Containing E. Coli Ribosomal Rna 5-Methyluridine Methyltransferase. Structure V. 12 397 2004.
ISSN: ISSN 0969-2126
PubMed: 15016356
DOI: 10.1016/J.STR.2004.02.009