Iron in PDB 5hr6: X-Ray Crystal Structure of C118A Rlmn with Cross-Linked Trna Purified From Escherichia Coli

The structure of X-Ray Crystal Structure of C118A Rlmn with Cross-Linked Trna Purified From Escherichia Coli, PDB code: 5hr6 was solved by E.L.Schwalm, T.L.Grove, S.J.Booker, A.K.Boal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	88.66 / 2.88
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	88.664, 69.821, 149.298, 90.00, 90.30, 90.00
R / Rfree (%)	18.2 / 22.8

The structure of X-Ray Crystal Structure of C118A Rlmn with Cross-Linked Trna Purified From Escherichia Coli also contains other interesting chemical elements:

Magnesium

(Mg)

6 atoms

The binding sites of Iron atom in the X-Ray Crystal Structure of C118A Rlmn with Cross-Linked Trna Purified From Escherichia Coli (pdb code 5hr6). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the X-Ray Crystal Structure of C118A Rlmn with Cross-Linked Trna Purified From Escherichia Coli, PDB code: 5hr6:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in the X-Ray Crystal Structure of C118A Rlmn with Cross-Linked Trna Purified From Escherichia Coli


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of X-Ray Crystal Structure of C118A Rlmn with Cross-Linked Trna Purified From Escherichia Coli within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:49.9 occ:1.00 FE1 A:SF4502 0.0 49.9 1.0 S3 A:SF4502 2.1 44.9 1.0 S2 A:SF4502 2.1 40.8 1.0 S4 A:SF4502 2.1 40.5 1.0 SG A:CYS132 2.2 53.8 1.0 CB A:CYS132 2.9 52.1 1.0 FE2 A:SF4502 3.0 52.9 1.0 FE4 A:SF4502 3.0 55.8 1.0 FE3 A:SF4502 3.1 55.5 1.0 CE A:MET501 3.5 66.8 1.0 S1 A:SF4502 3.7 41.0 1.0 SD A:MET501 4.0 65.2 1.0 N A:ALA135 4.3 58.6 1.0 CB A:CYS129 4.3 50.4 1.0 CB A:THR134 4.3 49.4 1.0 CA A:CYS132 4.4 52.7 1.0 CB A:ALA135 4.6 55.4 1.0 C8 A:5AD503 4.7 60.3 1.0 SG A:CYS129 4.7 53.8 1.0 N A:MET501 4.7 66.3 1.0 O A:MET501 4.9 69.0 1.0 CA A:ALA135 4.9 54.9 1.0 OG1 A:THR134 4.9 49.7 1.0 N A:THR134 4.9 51.7 1.0 CB A:CYS125 5.0 63.2 1.0 C A:CYS132 5.0 53.3 1.0 CA A:THR134 5.0 51.6 1.0

Iron binding site 2 out of 8 in the X-Ray Crystal Structure of C118A Rlmn with Cross-Linked Trna Purified From Escherichia Coli


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of X-Ray Crystal Structure of C118A Rlmn with Cross-Linked Trna Purified From Escherichia Coli within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:52.9 occ:1.00 FE2 A:SF4502 0.0 52.9 1.0 S1 A:SF4502 2.1 41.0 1.0 S4 A:SF4502 2.1 40.5 1.0 S3 A:SF4502 2.1 44.9 1.0 SG A:CYS129 2.1 53.8 1.0 CB A:CYS129 2.9 50.4 1.0 FE4 A:SF4502 3.0 55.8 1.0 FE3 A:SF4502 3.0 55.5 1.0 FE1 A:SF4502 3.0 49.9 1.0 O A:HOH603 3.5 45.9 1.0 S2 A:SF4502 3.7 40.8 1.0 OG A:SER213 3.7 64.1 1.0 N A:CYS129 3.8 50.5 1.0 CA A:CYS129 3.9 50.8 1.0 O A:MET501 4.1 69.0 1.0 CB A:LEU127 4.2 58.7 1.0 N A:MET501 4.6 66.3 1.0 CB A:CYS132 4.7 52.1 1.0 CB A:SER213 4.8 60.1 1.0 CD1 A:LEU127 4.8 54.5 1.0 SG A:CYS125 4.8 65.8 1.0 SG A:CYS132 4.9 53.8 1.0

Iron binding site 3 out of 8 in the X-Ray Crystal Structure of C118A Rlmn with Cross-Linked Trna Purified From Escherichia Coli


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of X-Ray Crystal Structure of C118A Rlmn with Cross-Linked Trna Purified From Escherichia Coli within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:55.5 occ:1.00 FE3 A:SF4502 0.0 55.5 1.0 N A:MET501 1.9 66.3 1.0 O A:MET501 2.1 69.0 1.0 S1 A:SF4502 2.1 41.0 1.0 S4 A:SF4502 2.2 40.5 1.0 S2 A:SF4502 2.2 40.8 1.0 SD A:MET501 2.4 65.2 1.0 C A:MET501 2.9 72.7 1.0 CA A:MET501 3.0 66.9 1.0 FE2 A:SF4502 3.0 52.9 1.0 FE4 A:SF4502 3.0 55.8 1.0 FE1 A:SF4502 3.1 49.9 1.0 CE A:MET501 3.5 66.8 1.0 CG A:MET501 3.5 60.6 1.0 S3 A:SF4502 3.7 44.9 1.0 CB A:MET501 3.8 64.7 1.0 O A:HOH603 4.1 45.9 1.0 OXT A:MET501 4.1 67.2 1.0 OG A:SER213 4.2 64.1 1.0 O A:GLY179 4.5 58.5 1.0 OE2 A:GLU180 4.6 60.6 1.0 O2' A:5AD503 4.8 57.9 1.0 C2' A:5AD503 4.8 59.2 1.0 SG A:CYS125 4.8 65.8 1.0 SG A:CYS129 4.8 53.8 1.0 C A:GLY179 5.0 56.1 1.0

Iron binding site 4 out of 8 in the X-Ray Crystal Structure of C118A Rlmn with Cross-Linked Trna Purified From Escherichia Coli


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of X-Ray Crystal Structure of C118A Rlmn with Cross-Linked Trna Purified From Escherichia Coli within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:55.8 occ:1.00 FE4 A:SF4502 0.0 55.8 1.0 S3 A:SF4502 2.1 44.9 1.0 S1 A:SF4502 2.1 41.0 1.0 S2 A:SF4502 2.1 40.8 1.0 SG A:CYS125 2.1 65.8 1.0 CB A:CYS125 2.9 63.2 1.0 FE2 A:SF4502 3.0 52.9 1.0 FE1 A:SF4502 3.0 49.9 1.0 FE3 A:SF4502 3.0 55.5 1.0 S4 A:SF4502 3.7 40.5 1.0 N A:MET501 3.7 66.3 1.0 CB A:LEU127 3.9 58.7 1.0 CA A:CYS125 4.4 59.8 1.0 C A:GLY179 4.4 56.1 1.0 N A:GLU180 4.5 56.5 1.0 CG A:LEU127 4.5 54.2 1.0 O A:LEU127 4.6 73.1 1.0 CA A:LEU127 4.6 62.9 1.0 N A:LEU127 4.7 64.8 1.0 C A:LEU127 4.7 67.8 1.0 O A:GLY179 4.7 58.5 1.0 CB A:GLU180 4.7 52.3 1.0 CA A:GLY179 4.7 58.2 1.0 CD1 A:LEU127 4.8 54.5 1.0 SD A:MET501 4.9 65.2 1.0 CA A:GLU180 4.9 55.0 1.0 O A:MET501 4.9 69.0 1.0 N A:GLY179 5.0 57.8 1.0 C A:CYS125 5.0 66.7 1.0

Iron binding site 5 out of 8 in the X-Ray Crystal Structure of C118A Rlmn with Cross-Linked Trna Purified From Escherichia Coli


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of X-Ray Crystal Structure of C118A Rlmn with Cross-Linked Trna Purified From Escherichia Coli within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe502 b:59.9 occ:1.00 FE1 B:SF4502 0.0 59.9 1.0 N B:MET501 1.9 61.5 1.0 O B:MET501 2.1 69.4 1.0 S2 B:SF4502 2.1 43.1 1.0 S4 B:SF4502 2.1 42.9 1.0 S3 B:SF4502 2.2 43.2 1.0 SD B:MET501 2.4 62.6 1.0 C B:MET501 2.9 68.7 1.0 CA B:MET501 2.9 64.2 1.0 FE2 B:SF4502 3.0 57.3 1.0 FE4 B:SF4502 3.0 54.1 1.0 FE3 B:SF4502 3.1 56.0 1.0 CE B:MET501 3.4 68.1 1.0 CG B:MET501 3.6 56.9 1.0 S1 B:SF4502 3.7 42.3 1.0 CB B:MET501 3.8 60.8 1.0 OG B:SER213 4.0 69.1 1.0 OXT B:MET501 4.1 64.9 1.0 O B:HOH603 4.2 52.3 1.0 O B:GLY179 4.4 55.4 1.0 O2' B:5AD503 4.6 62.0 1.0 C2' B:5AD503 4.7 59.9 1.0 OE2 B:GLU180 4.8 59.7 1.0 SG B:CYS129 4.8 58.1 1.0 SG B:CYS125 4.8 58.8 1.0 C B:GLY179 4.9 56.4 1.0 SG B:CYS132 5.0 54.4 1.0

Iron binding site 6 out of 8 in the X-Ray Crystal Structure of C118A Rlmn with Cross-Linked Trna Purified From Escherichia Coli


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of X-Ray Crystal Structure of C118A Rlmn with Cross-Linked Trna Purified From Escherichia Coli within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe502 b:57.3 occ:1.00 FE2 B:SF4502 0.0 57.3 1.0 S3 B:SF4502 2.1 43.2 1.0 S4 B:SF4502 2.1 42.9 1.0 S1 B:SF4502 2.1 42.3 1.0 SG B:CYS132 2.2 54.4 1.0 FE3 B:SF4502 3.0 56.0 1.0 FE1 B:SF4502 3.0 59.9 1.0 CB B:CYS132 3.0 51.1 1.0 FE4 B:SF4502 3.0 54.1 1.0 S2 B:SF4502 3.7 43.1 1.0 CE B:MET501 3.7 68.1 1.0 SD B:MET501 4.1 62.6 1.0 CB B:THR134 4.2 50.1 1.0 N B:ALA135 4.3 58.5 1.0 CB B:CYS129 4.4 55.0 1.0 CA B:CYS132 4.5 53.6 1.0 CB B:ALA135 4.6 56.2 1.0 OG1 B:THR134 4.6 49.1 1.0 N B:MET501 4.7 61.5 1.0 C8 B:5AD503 4.7 58.8 1.0 SG B:CYS129 4.7 58.1 1.0 O B:MET501 4.7 69.4 1.0 CA B:ALA135 4.9 55.5 1.0 N B:THR134 4.9 54.5 1.0 SG B:CYS125 4.9 58.8 1.0 CA B:THR134 4.9 51.7 1.0 C B:THR134 5.0 52.8 1.0 C B:CYS132 5.0 53.3 1.0 CB B:CYS125 5.0 57.1 1.0

Iron binding site 7 out of 8 in the X-Ray Crystal Structure of C118A Rlmn with Cross-Linked Trna Purified From Escherichia Coli


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of X-Ray Crystal Structure of C118A Rlmn with Cross-Linked Trna Purified From Escherichia Coli within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe502 b:56.0 occ:1.00 FE3 B:SF4502 0.0 56.0 1.0 S2 B:SF4502 2.1 43.1 1.0 S4 B:SF4502 2.1 42.9 1.0 SG B:CYS129 2.1 58.1 1.0 S1 B:SF4502 2.1 42.3 1.0 CB B:CYS129 2.8 55.0 1.0 FE4 B:SF4502 2.9 54.1 1.0 FE2 B:SF4502 3.0 57.3 1.0 FE1 B:SF4502 3.1 59.9 1.0 O B:HOH603 3.6 52.3 1.0 S3 B:SF4502 3.6 43.2 1.0 OG B:SER213 3.8 69.1 1.0 N B:CYS129 3.8 53.4 1.0 CA B:CYS129 3.9 53.8 1.0 O B:MET501 4.1 69.4 1.0 CB B:LEU127 4.3 68.7 1.0 N B:MET501 4.5 61.5 1.0 CB B:CYS132 4.7 51.1 1.0 SG B:CYS125 4.8 58.8 1.0 C B:LEU127 4.8 71.8 1.0 CB B:SER213 4.8 67.9 1.0 O B:LEU127 4.9 76.3 1.0 SG B:CYS132 4.9 54.4 1.0 O B:HOH616 5.0 61.7 1.0 N B:GLU128 5.0 66.0 1.0

Iron binding site 8 out of 8 in the X-Ray Crystal Structure of C118A Rlmn with Cross-Linked Trna Purified From Escherichia Coli


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of X-Ray Crystal Structure of C118A Rlmn with Cross-Linked Trna Purified From Escherichia Coli within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe502 b:54.1 occ:1.00 FE4 B:SF4502 0.0 54.1 1.0 SG B:CYS125 2.1 58.8 1.0 S1 B:SF4502 2.1 42.3 1.0 S3 B:SF4502 2.1 43.2 1.0 S2 B:SF4502 2.1 43.1 1.0 FE3 B:SF4502 2.9 56.0 1.0 CB B:CYS125 3.0 57.1 1.0 FE2 B:SF4502 3.0 57.3 1.0 FE1 B:SF4502 3.0 59.9 1.0 S4 B:SF4502 3.6 42.9 1.0 N B:MET501 3.7 61.5 1.0 CB B:LEU127 4.0 68.7 1.0 O B:LEU127 4.2 76.3 1.0 CA B:CYS125 4.4 58.3 1.0 C B:GLY179 4.5 56.4 1.0 N B:GLU180 4.5 55.0 1.0 C B:LEU127 4.6 71.8 1.0 CA B:LEU127 4.7 68.2 1.0 N B:LEU127 4.7 62.5 1.0 O B:GLY179 4.7 55.4 1.0 CA B:GLY179 4.7 62.2 1.0 CG B:LEU127 4.8 61.1 1.0 CB B:GLU180 4.9 54.6 1.0 O B:MET501 5.0 69.4 1.0 N B:GLY179 5.0 64.2 1.0 SG B:CYS129 5.0 58.1 1.0 C B:CYS125 5.0 65.2 1.0

E.L.Schwalm, T.L.Grove, S.J.Booker, A.K.Boal. Crystallographic Capture of A Radical S-Adenosylmethionine Enzyme in the Act of Modifying Trna. Science V. 352 309 2016.
ISSN: ESSN 1095-9203
PubMed: 27081063
DOI: 10.1126/SCIENCE.AAD5367