Iron in PDB 2bh2: Crystal Structure of E. Coli 5-Methyluridine Methyltransferase Ruma in Complex with Ribosomal Rna Substrate and S-Adenosylhomocysteine.

The structure of Crystal Structure of E. Coli 5-Methyluridine Methyltransferase Ruma in Complex with Ribosomal Rna Substrate and S-Adenosylhomocysteine., PDB code: 2bh2 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 / 2.15
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	190.061, 63.542, 112.019, 90.00, 125.15, 90.00
R / Rfree (%)	17.4 / 22.9

The structure of Crystal Structure of E. Coli 5-Methyluridine Methyltransferase Ruma in Complex with Ribosomal Rna Substrate and S-Adenosylhomocysteine. also contains other interesting chemical elements:

Fluorine

(F)

2 atoms

The binding sites of Iron atom in the Crystal Structure of E. Coli 5-Methyluridine Methyltransferase Ruma in Complex with Ribosomal Rna Substrate and S-Adenosylhomocysteine. (pdb code 2bh2). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Crystal Structure of E. Coli 5-Methyluridine Methyltransferase Ruma in Complex with Ribosomal Rna Substrate and S-Adenosylhomocysteine., PDB code: 2bh2:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in the Crystal Structure of E. Coli 5-Methyluridine Methyltransferase Ruma in Complex with Ribosomal Rna Substrate and S-Adenosylhomocysteine.


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 E. Coli 5-Methyluridine Methyltransferase Ruma in Complex with Ribosomal Rna Substrate and S-Adenosylhomocysteine. within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:33.9 occ:1.00 FE1 A:SF4501 0.0 33.9 1.0 S2 A:SF4501 2.2 36.1 1.0 S4 A:SF4501 2.3 31.7 1.0 SG A:CYS87 2.3 39.0 1.0 S3 A:SF4501 2.3 36.7 1.0 FE3 A:SF4501 2.6 32.2 1.0 FE4 A:SF4501 2.7 35.5 1.0 FE2 A:SF4501 2.8 32.2 1.0 CB A:CYS87 3.1 40.1 1.0 S1 A:SF4501 3.9 35.0 1.0 CD2 A:PHE148 4.0 33.2 1.0 N A:GLY89 4.4 38.0 1.0 CA A:GLY89 4.4 35.7 1.0 CE2 A:PHE148 4.4 33.0 1.0 CA A:CYS87 4.6 41.2 1.0 N A:CYS90 4.6 35.1 1.0 SG A:CYS81 4.7 40.9 1.0 SG A:CYS162 4.7 32.8 1.0 SG A:CYS90 4.9 33.9 1.0 CB A:HIS83 4.9 42.3 1.0 C A:GLY89 4.9 35.2 1.0 C A:CYS87 4.9 40.4 1.0 CG A:PHE148 5.0 34.3 1.0

Iron binding site 2 out of 8 in the Crystal Structure of E. Coli 5-Methyluridine Methyltransferase Ruma in Complex with Ribosomal Rna Substrate and S-Adenosylhomocysteine.


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 E. Coli 5-Methyluridine Methyltransferase Ruma in Complex with Ribosomal Rna Substrate and S-Adenosylhomocysteine. within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:32.2 occ:1.00 FE2 A:SF4501 0.0 32.2 1.0 S3 A:SF4501 2.2 36.7 1.0 S1 A:SF4501 2.3 35.0 1.0 SG A:CYS90 2.3 33.9 1.0 S4 A:SF4501 2.4 31.7 1.0 FE3 A:SF4501 2.6 32.2 1.0 FE4 A:SF4501 2.7 35.5 1.0 FE1 A:SF4501 2.8 33.9 1.0 CB A:CYS90 3.3 34.6 1.0 NE2 A:GLN93 3.5 33.5 1.0 N A:CYS90 3.8 35.1 1.0 S2 A:SF4501 3.9 36.1 1.0 O A:HOH2019 4.1 34.9 1.0 CG1 A:ILE164 4.1 30.9 1.0 CA A:CYS90 4.2 34.6 1.0 C A:GLY89 4.4 35.2 1.0 CG2 A:ILE164 4.6 34.1 1.0 SG A:CYS162 4.7 32.8 1.0 SG A:CYS87 4.7 39.0 1.0 CD A:GLN93 4.8 37.2 1.0 SG A:CYS81 4.8 40.9 1.0 CA A:GLY89 4.8 35.7 1.0 CB A:CYS81 4.9 41.0 1.0

Iron binding site 3 out of 8 in the Crystal Structure of E. Coli 5-Methyluridine Methyltransferase Ruma in Complex with Ribosomal Rna Substrate and S-Adenosylhomocysteine.


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 E. Coli 5-Methyluridine Methyltransferase Ruma in Complex with Ribosomal Rna Substrate and S-Adenosylhomocysteine. within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:32.2 occ:1.00 FE3 A:SF4501 0.0 32.2 1.0 S4 A:SF4501 2.2 31.7 1.0 S2 A:SF4501 2.3 36.1 1.0 SG A:CYS162 2.3 32.8 1.0 S1 A:SF4501 2.4 35.0 1.0 FE1 A:SF4501 2.6 33.9 1.0 FE4 A:SF4501 2.6 35.5 1.0 FE2 A:SF4501 2.6 32.2 1.0 CB A:CYS162 3.4 33.1 1.0 S3 A:SF4501 3.7 36.7 1.0 CA A:CYS162 3.7 35.2 1.0 CG1 A:ILE164 3.9 30.9 1.0 CE2 A:PHE148 4.1 33.0 1.0 CD1 A:ILE164 4.4 29.9 1.0 C A:CYS162 4.4 34.1 1.0 CD2 A:PHE148 4.5 33.2 1.0 SG A:CYS81 4.5 40.9 1.0 SG A:CYS87 4.7 39.0 1.0 O A:GLN161 4.8 45.0 1.0 SG A:CYS90 4.8 33.9 1.0 N A:PRO163 4.9 34.5 1.0 CD A:PRO163 5.0 34.2 1.0 N A:ILE164 5.0 33.8 1.0

Iron binding site 4 out of 8 in the Crystal Structure of E. Coli 5-Methyluridine Methyltransferase Ruma in Complex with Ribosomal Rna Substrate and S-Adenosylhomocysteine.


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 E. Coli 5-Methyluridine Methyltransferase Ruma in Complex with Ribosomal Rna Substrate and S-Adenosylhomocysteine. within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:35.5 occ:1.00 FE4 A:SF4501 0.0 35.5 1.0 S3 A:SF4501 2.3 36.7 1.0 SG A:CYS81 2.3 40.9 1.0 S2 A:SF4501 2.3 36.1 1.0 S1 A:SF4501 2.3 35.0 1.0 FE3 A:SF4501 2.6 32.2 1.0 FE1 A:SF4501 2.7 33.9 1.0 FE2 A:SF4501 2.7 32.2 1.0 CB A:CYS81 3.1 41.0 1.0 S4 A:SF4501 3.9 31.7 1.0 NE2 A:GLN93 4.1 33.5 1.0 CB A:HIS83 4.3 42.3 1.0 CD A:PRO163 4.5 34.2 1.0 CA A:CYS162 4.5 35.2 1.0 CA A:CYS81 4.6 41.9 1.0 SG A:CYS162 4.6 32.8 1.0 O A:GLN161 4.6 45.0 1.0 N A:PHE84 4.6 42.9 1.0 SG A:CYS87 4.7 39.0 1.0 C A:HIS83 4.7 43.1 1.0 CD2 A:HIS83 4.8 39.9 1.0 CB A:CYS87 4.8 40.1 1.0 SG A:CYS90 4.8 33.9 1.0 CB A:CYS162 4.9 33.1 1.0 N A:HIS83 4.9 43.6 1.0 CA A:HIS83 4.9 43.3 1.0 CG A:HIS83 5.0 43.2 1.0

Iron binding site 5 out of 8 in the Crystal Structure of E. Coli 5-Methyluridine Methyltransferase Ruma in Complex with Ribosomal Rna Substrate and S-Adenosylhomocysteine.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of E. Coli 5-Methyluridine Methyltransferase Ruma in Complex with Ribosomal Rna Substrate and S-Adenosylhomocysteine. within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:27.4 occ:1.00 FE1 B:SF4501 0.0 27.4 1.0 S3 B:SF4501 2.3 28.5 1.0 S2 B:SF4501 2.3 28.6 1.0 SG B:CYS87 2.3 28.4 1.0 S4 B:SF4501 2.3 25.9 1.0 FE2 B:SF4501 2.6 26.3 1.0 FE4 B:SF4501 2.7 28.6 1.0 FE3 B:SF4501 2.7 28.7 1.0 CB B:CYS87 3.2 31.9 1.0 S1 B:SF4501 3.9 28.1 1.0 CD2 B:PHE148 4.1 29.4 1.0 CA B:GLY89 4.3 28.4 1.0 N B:GLY89 4.4 28.3 1.0 N B:CYS90 4.5 30.1 1.0 CA B:CYS87 4.6 32.0 1.0 CE2 B:PHE148 4.6 29.1 1.0 SG B:CYS81 4.7 30.2 1.0 SG B:CYS162 4.8 28.1 1.0 SG B:CYS90 4.8 29.7 1.0 C B:GLY89 4.8 29.0 1.0 C B:CYS87 4.8 31.1 1.0 CB B:HIS83 4.9 30.7 1.0 O B:CYS87 4.9 31.2 1.0 CG B:PHE148 4.9 27.2 1.0

Iron binding site 6 out of 8 in the Crystal Structure of E. Coli 5-Methyluridine Methyltransferase Ruma in Complex with Ribosomal Rna Substrate and S-Adenosylhomocysteine.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of E. Coli 5-Methyluridine Methyltransferase Ruma in Complex with Ribosomal Rna Substrate and S-Adenosylhomocysteine. within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:26.3 occ:1.00 FE2 B:SF4501 0.0 26.3 1.0 S4 B:SF4501 2.2 25.9 1.0 S3 B:SF4501 2.3 28.5 1.0 SG B:CYS162 2.3 28.1 1.0 S1 B:SF4501 2.3 28.1 1.0 FE4 B:SF4501 2.6 28.6 1.0 FE1 B:SF4501 2.6 27.4 1.0 FE3 B:SF4501 2.7 28.7 1.0 CB B:CYS162 3.2 27.6 1.0 CA B:CYS162 3.7 28.8 1.0 S2 B:SF4501 3.8 28.6 1.0 CG1 B:ILE164 3.9 29.1 1.0 CE2 B:PHE148 4.2 29.1 1.0 C B:CYS162 4.3 28.2 1.0 CD2 B:PHE148 4.5 29.4 1.0 SG B:CYS81 4.5 30.2 1.0 O B:GLN161 4.7 31.4 1.0 CD B:PRO163 4.7 28.6 1.0 CD1 B:ILE164 4.7 29.8 1.0 N B:PRO163 4.7 28.1 1.0 SG B:CYS90 4.8 29.7 1.0 SG B:CYS87 4.8 28.4 1.0 O B:CYS162 4.9 27.1 1.0 N B:ILE164 4.9 28.4 1.0 N B:CYS162 5.0 30.3 1.0

Iron binding site 7 out of 8 in the Crystal Structure of E. Coli 5-Methyluridine Methyltransferase Ruma in Complex with Ribosomal Rna Substrate and S-Adenosylhomocysteine.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure of E. Coli 5-Methyluridine Methyltransferase Ruma in Complex with Ribosomal Rna Substrate and S-Adenosylhomocysteine. within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:28.7 occ:1.00 FE3 B:SF4501 0.0 28.7 1.0 S1 B:SF4501 2.3 28.1 1.0 S4 B:SF4501 2.3 25.9 1.0 SG B:CYS90 2.3 29.7 1.0 S2 B:SF4501 2.3 28.6 1.0 FE2 B:SF4501 2.7 26.3 1.0 FE1 B:SF4501 2.7 27.4 1.0 FE4 B:SF4501 2.7 28.6 1.0 CB B:CYS90 3.3 29.4 1.0 NE2 B:GLN93 3.7 30.4 1.0 N B:CYS90 3.8 30.1 1.0 S3 B:SF4501 3.9 28.5 1.0 CA B:CYS90 4.1 29.9 1.0 O D:HOH2018 4.2 30.8 1.0 CG1 B:ILE164 4.2 29.1 1.0 C B:GLY89 4.3 29.0 1.0 CG2 B:ILE164 4.4 24.9 1.0 SG B:CYS162 4.7 28.1 1.0 SG B:CYS87 4.7 28.4 1.0 CA B:GLY89 4.7 28.4 1.0 SG B:CYS81 4.8 30.2 1.0 CD B:GLN93 4.9 32.7 1.0 CB B:ILE164 5.0 27.6 1.0

Iron binding site 8 out of 8 in the Crystal Structure of E. Coli 5-Methyluridine Methyltransferase Ruma in Complex with Ribosomal Rna Substrate and S-Adenosylhomocysteine.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure of E. Coli 5-Methyluridine Methyltransferase Ruma in Complex with Ribosomal Rna Substrate and S-Adenosylhomocysteine. within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:28.6 occ:1.00 FE4 B:SF4501 0.0 28.6 1.0 S1 B:SF4501 2.2 28.1 1.0 SG B:CYS81 2.3 30.2 1.0 S2 B:SF4501 2.3 28.6 1.0 S3 B:SF4501 2.3 28.5 1.0 FE2 B:SF4501 2.6 26.3 1.0 FE1 B:SF4501 2.7 27.4 1.0 FE3 B:SF4501 2.7 28.7 1.0 CB B:CYS81 3.1 30.8 1.0 S4 B:SF4501 3.8 25.9 1.0 NE2 B:GLN93 4.3 30.4 1.0 CB B:HIS83 4.3 30.7 1.0 CD B:PRO163 4.5 28.6 1.0 CA B:CYS81 4.6 32.8 1.0 CA B:CYS162 4.6 28.8 1.0 O B:GLN161 4.6 31.4 1.0 SG B:CYS162 4.6 28.1 1.0 N B:PHE84 4.6 31.4 1.0 SG B:CYS87 4.7 28.4 1.0 C B:HIS83 4.7 31.3 1.0 CB B:CYS87 4.8 31.9 1.0 SG B:CYS90 4.8 29.7 1.0 CB B:CYS162 4.9 27.6 1.0 CA B:HIS83 4.9 31.1 1.0 N B:HIS83 4.9 32.3 1.0 CD2 B:HIS83 4.9 29.0 1.0 CG B:HIS83 5.0 29.6 1.0

T.T.Lee, S.Agarwalla, R.M.Stroud. A Unique Rna Fold in the Ruma-Rna-Cofactor Ternary Complex Contributes to Substrate Selectivity and Enzymatic Function Cell(Cambridge,Mass.) V. 120 599 2005.
ISSN: ISSN 0092-8674
PubMed: 15766524
DOI: 10.1016/J.CELL.2004.12.037