Magnesium 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:

Iron

(Fe)

8 atoms

The binding sites of Magnesium 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 Magnesium atom.
In total 6 binding sites of Magnesium where determined in the X-Ray Crystal Structure of C118A Rlmn with Cross-Linked Trna Purified From Escherichia Coli, PDB code: 5hr6:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 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 Magnesium with other atoms in the Mg 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:Mg504 b:56.4 occ:1.00 O A:LEU196 2.6 68.6 1.0 O2' C:A26 2.8 74.9 1.0 O A:LEU203 3.0 62.6 1.0 O3' C:A26 3.0 62.7 1.0 C A:LEU196 3.7 63.2 1.0 OP1 C:C27 3.7 63.9 1.0 C2' C:A26 3.8 63.5 1.0 C3' C:A26 3.8 62.5 1.0 P C:C27 4.0 59.0 1.0 C4' C:A26 4.0 59.7 1.0 C A:LEU203 4.1 56.0 1.0 C5' C:C27 4.1 52.1 1.0 OD1 A:ASP198 4.2 92.0 1.0 CA A:LEU196 4.3 58.8 1.0 C A:GLY202 4.4 54.4 1.0 CB A:LEU196 4.5 57.3 1.0 O A:GLY202 4.5 55.2 1.0 O5' C:C27 4.5 53.7 1.0 CA A:GLY202 4.7 55.1 1.0 N A:LEU203 4.7 52.8 1.0 CG A:ASP198 4.8 69.7 1.0 C1' C:A26 4.8 63.1 1.0 N A:ASP197 4.8 64.7 1.0 CA A:SER204 4.8 54.3 1.0 O4' C:A26 4.9 62.9 1.0 N A:SER204 4.9 56.5 1.0 OD2 A:ASP198 5.0 66.3 1.0

Magnesium binding site 2 out of 6 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 Magnesium with other atoms in the Mg 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 C:Mg101 b:29.4 occ:1.00 O2 C:C38 2.2 57.9 1.0 O2' C:C38 2.3 51.1 1.0 N7 C:G39 2.3 64.5 1.0 O A:HOH610 2.4 45.1 1.0 O C:HOH202 2.7 55.5 1.0 O6 C:G39 3.0 68.7 1.0 C5 C:G39 3.1 62.1 1.0 C2 C:C38 3.2 60.2 1.0 C6 C:G39 3.4 67.2 1.0 C8 C:G39 3.4 68.7 1.0 C2' C:C38 3.5 57.2 1.0 C1' C:C38 3.8 58.8 1.0 N1 C:C38 3.9 60.4 1.0 N3 C:C38 4.0 61.7 1.0 NZ A:LYS305 4.4 68.4 1.0 C4 C:G39 4.4 59.4 1.0 OP2 C:G39 4.5 59.3 1.0 O A:ARG206 4.5 50.7 1.0 N9 C:G39 4.5 60.2 1.0 N1 C:G39 4.8 66.6 1.0 CB A:ARG206 4.8 52.3 1.0 C3' C:C38 4.8 54.8 1.0 O3' C:C38 4.9 55.0 1.0

Magnesium binding site 3 out of 6 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 Magnesium with other atoms in the Mg 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 C:Mg102 b:70.1 occ:1.00 OP1 C:U7 2.3 62.9 1.0 OP2 C:C8 2.8 67.3 1.0 OP1 C:C8 3.1 75.6 1.0 P C:C8 3.4 64.7 1.0 P C:U7 3.8 68.9 1.0 OP2 C:U10 4.4 68.0 1.0 O5' C:C8 4.6 68.3 1.0 O3' C:U7 4.6 67.0 1.0 OP2 C:U7 4.6 82.5 1.0 O5' C:U7 4.7 67.5 1.0 O3' C:U6 4.7 74.2 1.0 C5' C:U7 4.8 66.1 1.0 C5' C:C8 4.9 67.3 1.0

Magnesium binding site 4 out of 6 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 Magnesium with other atoms in the Mg 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 C:Mg103 b:88.5 occ:1.00 OP2 C:A13 2.9 68.0 1.0 O4 C:U7 3.0 63.0 1.0 N7 C:G14 3.3 69.7 1.0 C4 C:U7 3.6 58.5 1.0 C5 C:U7 3.8 58.7 1.0 C8 C:G14 4.0 74.9 1.0 P C:A13 4.4 74.5 1.0 C5 C:G14 4.5 68.0 1.0 N3 C:U7 4.6 54.7 1.0 O5' C:A13 4.7 73.2 1.0 O6 C:G14 4.7 70.2 1.0 C6 C:U7 4.9 54.7 1.0 C6 C:G14 5.0 65.8 1.0

Magnesium binding site 5 out of 6 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 Magnesium with other atoms in the Mg 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:Mg504 b:68.0 occ:1.00 O D:HOH201 2.3 54.0 1.0 O B:HOH607 2.3 56.0 1.0 O B:LEU196 2.6 70.8 1.0 O B:LEU203 2.7 64.0 1.0 O3' D:A26 2.7 71.3 1.0 O2' D:A26 2.9 77.5 1.0 C3' D:A26 3.5 69.7 1.0 C2' D:A26 3.6 70.1 1.0 C4' D:A26 3.7 67.7 1.0 OD1 B:ASP198 3.7 0.5 1.0 C B:LEU196 3.7 70.5 1.0 C B:LEU203 3.8 65.8 1.0 C B:GLY202 3.8 63.0 1.0 O B:GLY202 3.9 68.3 1.0 OP1 D:C27 3.9 71.5 1.0 P D:C27 4.0 67.6 1.0 CA B:GLY202 4.1 60.5 1.0 N B:LEU203 4.2 62.8 1.0 CA B:LEU196 4.3 67.3 1.0 O4' D:A26 4.5 73.6 1.0 C5' D:C27 4.5 62.0 1.0 CA B:LEU203 4.6 63.1 1.0 C1' D:A26 4.6 71.5 1.0 CG B:ASP198 4.6 87.6 1.0 N B:SER204 4.6 63.7 1.0 CB B:LEU196 4.7 63.7 1.0 CA B:SER204 4.7 59.7 1.0 O5' D:C27 4.8 58.6 1.0 C5' D:A26 4.8 65.1 1.0 N B:ASP197 4.9 67.0 1.0 N B:ASP198 5.0 79.5 1.0 C B:ASP197 5.0 74.5 1.0

Magnesium binding site 6 out of 6 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 Magnesium with other atoms in the Mg 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 D:Mg101 b:41.9 occ:1.00 O2 D:C38 2.3 86.7 1.0 N7 D:G39 2.5 78.9 1.0 O B:HOH614 2.5 53.9 1.0 O2' D:C38 2.8 69.6 1.0 O D:HOH203 2.8 75.1 1.0 C2 D:C38 3.1 82.2 1.0 O6 D:G39 3.4 0.5 1.0 C5 D:G39 3.4 82.3 1.0 C8 D:G39 3.5 87.1 1.0 N1 D:C38 3.7 74.0 1.0 C6 D:G39 3.7 90.1 1.0 C1' D:C38 3.7 71.4 1.0 C2' D:C38 3.8 70.2 1.0 N3 D:C38 3.9 81.6 1.0 NZ B:LYS305 4.3 71.5 1.0 C4 D:G39 4.6 78.5 1.0 OP2 D:G39 4.7 67.3 1.0 N9 D:G39 4.7 80.6 1.0 O B:ARG206 4.7 61.4 1.0 CB B:ARG206 4.9 57.7 1.0 O3' D:C38 4.9 66.7 1.0 CG B:GLN272 4.9 74.4 1.0 C6 D:C38 4.9 70.3 1.0 C3' D:C38 4.9 67.7 1.0 O B:ALA270 5.0 60.3 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