Magnesium in PDB 4kgm: Bacterial Trna(His) Guanylyltransferase (THG1)-Like Protein in Complex with Atp

The structure of Bacterial Trna(His) Guanylyltransferase (THG1)-Like Protein in Complex with Atp, PDB code: 4kgm was solved by S.J.Hyde, B.S.Rao, B.E.Eckenroth, J.E.Jackman, S.Doublie, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.70 / 2.36
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	99.156, 218.343, 126.056, 90.00, 90.00, 90.00
R / Rfree (%)	19.9 / 23.2

The binding sites of Magnesium atom in the Bacterial Trna(His) Guanylyltransferase (THG1)-Like Protein in Complex with Atp (pdb code 4kgm). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Bacterial Trna(His) Guanylyltransferase (THG1)-Like Protein in Complex with Atp, PDB code: 4kgm:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in the Bacterial Trna(His) Guanylyltransferase (THG1)-Like Protein in Complex with Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Bacterial Trna(His) Guanylyltransferase (THG1)-Like Protein in Complex with Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg303 b:40.6 occ:1.00 O1B A:ATP301 2.1 45.2 0.5 OD1 A:ASP30 2.1 46.0 1.0 OD2 A:ASP75 2.1 41.8 1.0 O A:GLY31 2.2 37.5 1.0 O3G A:ATP301 2.3 40.8 0.5 O2A A:ATP301 2.4 43.1 0.5 PB A:ATP301 3.2 41.8 0.5 CG A:ASP30 3.2 42.3 1.0 CG A:ASP75 3.2 41.0 1.0 MG A:MG304 3.3 38.2 1.0 C A:GLY31 3.3 30.2 1.0 O3A A:ATP301 3.5 46.1 0.5 PA A:ATP301 3.5 48.1 0.5 PG A:ATP301 3.6 60.4 0.5 OD1 A:ASP75 3.7 38.9 1.0 OD2 A:ASP30 3.7 42.3 1.0 O3B A:ATP301 3.8 48.6 0.5 N A:GLY31 3.9 32.3 1.0 CA A:GLY31 4.0 27.0 1.0 O5' A:ATP301 4.2 41.4 0.5 C A:ASP30 4.3 32.9 1.0 O1G A:ATP301 4.3 49.5 0.5 N A:ALA32 4.4 31.9 1.0 CB A:ASP30 4.4 34.8 1.0 C5' A:ATP301 4.4 41.5 0.5 CB A:ASP75 4.5 36.1 1.0 CB A:PHE34 4.5 43.5 1.0 O2B A:ATP301 4.6 43.6 0.5 N A:PHE34 4.6 41.5 1.0 O A:HOH468 4.6 39.1 1.0 CA A:ALA32 4.7 34.5 1.0 N A:HIS33 4.7 50.2 1.0 O2G A:ATP301 4.7 41.7 0.5 O A:ASP30 4.7 31.4 1.0 O1A A:ATP301 4.8 52.8 0.5 CA A:ASP30 4.9 32.7 1.0 C A:ALA32 4.9 41.9 1.0

Magnesium binding site 2 out of 8 in the Bacterial Trna(His) Guanylyltransferase (THG1)-Like Protein in Complex with Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Bacterial Trna(His) Guanylyltransferase (THG1)-Like Protein in Complex with Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg304 b:38.2 occ:1.00 O A:HOH468 2.0 39.1 1.0 O2A A:ATP301 2.1 43.1 0.5 OD2 A:ASP30 2.3 42.3 1.0 OD1 A:ASP75 2.3 38.9 1.0 CG A:ASP30 3.1 42.3 1.0 OD1 A:ASP30 3.1 46.0 1.0 CG A:ASP75 3.1 41.0 1.0 OD2 A:ASP75 3.2 41.8 1.0 MG A:MG303 3.3 40.6 1.0 PA A:ATP301 3.3 48.1 0.5 O1A A:ATP301 3.8 52.8 0.5 O A:HOH466 4.0 37.7 1.0 C5' A:ATP301 4.2 41.5 0.5 O5' A:ATP301 4.3 41.4 0.5 O3A A:ATP301 4.5 46.1 0.5 CB A:ASP30 4.5 34.8 1.0 O1B A:ATP301 4.6 45.2 0.5 CB A:ASP75 4.6 36.1 1.0 CB A:GLU76 4.7 31.0 1.0 C A:ASP75 4.8 39.6 1.0 O3G A:ATP301 4.9 40.8 0.5 N A:ASP75 4.9 33.2 1.0 N A:GLU76 4.9 32.9 1.0 O A:ASP75 4.9 40.5 1.0 OE1 A:GLU76 5.0 35.8 1.0

Magnesium binding site 3 out of 8 in the Bacterial Trna(His) Guanylyltransferase (THG1)-Like Protein in Complex with Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Bacterial Trna(His) Guanylyltransferase (THG1)-Like Protein in Complex with Atp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg302 b:37.7 occ:1.00 O3G B:ATP301 2.0 35.1 0.3 OD1 B:ASP30 2.1 34.3 1.0 O1B B:ATP301 2.1 34.7 0.6 OD2 B:ASP75 2.3 32.0 1.0 O2A B:ATP301 2.3 43.1 0.6 O B:GLY31 2.4 24.4 1.0 PB B:ATP301 3.1 42.5 0.6 O3A B:ATP301 3.2 41.8 0.6 CG B:ASP30 3.3 37.7 1.0 CG B:ASP75 3.3 31.3 1.0 PA B:ATP301 3.4 48.9 0.6 PG B:ATP301 3.4 43.0 0.3 MG B:MG303 3.5 42.1 1.0 C B:GLY31 3.6 22.7 1.0 O3B B:ATP301 3.6 40.0 0.3 OD1 B:ASP75 3.7 32.3 1.0 OD2 B:ASP30 4.0 36.7 1.0 O1G B:ATP301 4.1 47.5 0.3 N B:GLY31 4.1 24.0 1.0 O5' B:ATP301 4.2 40.4 0.6 CA B:GLY31 4.3 22.4 1.0 CB B:ASP30 4.4 22.4 1.0 O2G B:ATP301 4.5 31.9 0.3 O2B B:ATP301 4.5 37.4 0.6 O1A B:ATP301 4.6 52.4 0.6 C B:ASP30 4.6 23.2 1.0 C5' B:ATP301 4.6 38.7 0.6 CB B:ASP75 4.6 28.2 1.0 N B:ALA32 4.7 25.4 1.0 CB B:PHE34 4.8 30.9 1.0 CA B:ALA32 4.9 25.2 1.0 N B:PHE34 4.9 32.8 1.0 N B:HIS33 4.9 34.6 1.0

Magnesium binding site 4 out of 8 in the Bacterial Trna(His) Guanylyltransferase (THG1)-Like Protein in Complex with Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Bacterial Trna(His) Guanylyltransferase (THG1)-Like Protein in Complex with Atp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg303 b:42.1 occ:1.00 OD1 B:ASP75 2.1 32.3 1.0 O2A B:ATP301 2.4 43.1 0.6 OD2 B:ASP30 2.6 36.7 1.0 CG B:ASP75 3.0 31.3 1.0 OD1 B:ASP30 3.1 34.3 1.0 CG B:ASP30 3.2 37.7 1.0 OD2 B:ASP75 3.3 32.0 1.0 MG B:MG302 3.5 37.7 1.0 PA B:ATP301 3.7 48.9 0.6 O B:HOH474 3.8 36.0 1.0 O1A B:ATP301 4.1 52.4 0.6 CB B:GLU76 4.3 23.4 1.0 CB B:ASP75 4.4 28.2 1.0 C B:ASP75 4.4 24.7 1.0 C5' B:ATP301 4.5 38.7 0.6 N B:GLU76 4.6 21.7 1.0 OE1 B:GLU76 4.6 33.9 1.0 N B:ASP75 4.6 29.8 1.0 O5' B:ATP301 4.6 40.4 0.6 O B:ASP75 4.6 25.9 1.0 CA B:ASP75 4.7 29.1 1.0 CB B:ASP30 4.7 22.4 1.0 OG B:SER74 4.8 34.7 1.0 O3A B:ATP301 4.8 41.8 0.6 O1B B:ATP301 4.9 34.7 0.6 CA B:GLU76 4.9 24.2 1.0

Magnesium binding site 5 out of 8 in the Bacterial Trna(His) Guanylyltransferase (THG1)-Like Protein in Complex with Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Bacterial Trna(His) Guanylyltransferase (THG1)-Like Protein in Complex with Atp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg303 b:25.4 occ:1.00 O1B C:ATP301 2.0 26.0 0.7 OD2 C:ASP30 2.0 31.4 1.0 O C:GLY31 2.1 17.4 1.0 OD2 C:ASP75 2.1 29.4 1.0 O3G C:ATP301 2.4 23.4 0.5 O2A C:ATP301 2.4 29.6 0.8 CG C:ASP30 3.0 26.1 1.0 CG C:ASP75 3.1 26.1 1.0 PB C:ATP301 3.2 30.4 0.7 C C:GLY31 3.3 18.5 1.0 OD1 C:ASP30 3.3 31.4 1.0 O3A C:ATP301 3.4 38.2 0.8 PA C:ATP301 3.5 40.8 0.8 OD1 C:ASP75 3.5 25.9 1.0 MG C:MG304 3.6 34.5 1.0 PG C:ATP301 3.6 34.8 0.5 O3B C:ATP301 3.7 32.5 0.2 N C:GLY31 3.8 17.4 1.0 CA C:GLY31 3.9 15.0 1.0 O C:HOH457 4.1 19.9 1.0 O5' C:ATP301 4.2 49.0 0.8 C C:ASP30 4.2 18.0 1.0 CB C:ASP30 4.3 21.8 1.0 N C:ALA32 4.3 14.4 1.0 C5' C:ATP301 4.4 40.6 1.0 CB C:PHE34 4.4 20.6 1.0 O1G C:ATP301 4.4 39.3 0.5 CB C:ASP75 4.5 21.7 1.0 O2B C:ATP301 4.5 31.2 0.7 O C:HOH448 4.6 28.2 1.0 CA C:ALA32 4.6 19.5 1.0 N C:PHE34 4.6 24.4 1.0 O C:ASP30 4.7 11.2 1.0 CA C:ASP30 4.8 16.0 1.0 O2G C:ATP301 4.8 24.0 0.5 N C:HIS33 4.8 28.1 1.0 O C:ASP75 4.8 18.0 1.0 O1A C:ATP301 4.8 40.9 0.8 O D:HOH503 4.9 32.1 1.0 C C:ALA32 4.9 23.2 1.0

Magnesium binding site 6 out of 8 in the Bacterial Trna(His) Guanylyltransferase (THG1)-Like Protein in Complex with Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Bacterial Trna(His) Guanylyltransferase (THG1)-Like Protein in Complex with Atp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg304 b:34.5 occ:1.00 O2A C:ATP301 2.1 29.6 0.8 OD1 C:ASP75 2.1 25.9 1.0 O C:HOH542 2.2 35.9 1.0 O C:HOH448 2.3 28.2 1.0 OD1 C:ASP30 2.5 31.4 1.0 CG C:ASP75 3.2 26.1 1.0 PA C:ATP301 3.2 40.8 0.8 OD2 C:ASP75 3.5 29.4 1.0 CG C:ASP30 3.6 26.1 1.0 MG C:MG303 3.6 25.4 1.0 O1A C:ATP301 3.7 40.9 0.8 OD2 C:ASP30 3.8 31.4 1.0 C5' C:ATP301 3.9 40.6 1.0 O5' C:ATP301 4.0 49.0 0.8 O C:HOH516 4.2 38.2 1.0 O C:HOH521 4.3 27.2 1.0 OG C:SER74 4.4 29.6 1.0 OE1 C:GLU76 4.5 25.3 1.0 CB C:ASP75 4.5 21.7 1.0 O3A C:ATP301 4.5 38.2 0.8 N C:ASP75 4.6 21.2 1.0 C C:ASP75 4.6 21.5 1.0 CB C:GLU76 4.6 18.6 1.0 O1B C:ATP301 4.6 26.0 0.7 CA C:ASP75 4.8 24.2 1.0 N C:GLU76 4.8 19.1 1.0 O C:ASP75 4.8 18.0 1.0 CB C:ASP30 4.9 21.8 1.0 CB C:SER74 4.9 22.2 1.0

Magnesium binding site 7 out of 8 in the Bacterial Trna(His) Guanylyltransferase (THG1)-Like Protein in Complex with Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Bacterial Trna(His) Guanylyltransferase (THG1)-Like Protein in Complex with Atp within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg302 b:26.9 occ:1.00 OD2 D:ASP30 2.0 28.9 1.0 O1B D:ATP301 2.1 27.0 0.5 O3G D:ATP301 2.2 27.3 0.5 O2A D:ATP301 2.2 33.9 0.5 O D:GLY31 2.3 18.0 1.0 OD2 D:ASP75 2.4 27.8 1.0 MG D:MG303 2.8 40.6 1.0 PB D:ATP301 3.1 31.6 0.5 CG D:ASP30 3.1 25.9 1.0 O3A D:ATP301 3.2 36.6 0.5 PA D:ATP301 3.3 41.0 0.5 O D:HOH480 3.3 44.7 1.0 CG D:ASP75 3.5 25.1 1.0 C D:GLY31 3.5 16.6 1.0 PG D:ATP301 3.5 34.0 0.5 OD1 D:ASP30 3.7 27.1 1.0 O3B D:ATP301 3.7 39.6 0.5 OD1 D:ASP75 3.8 24.7 1.0 N D:GLY31 4.0 14.9 1.0 O5' D:ATP301 4.2 37.7 0.6 CA D:GLY31 4.2 13.9 1.0 O D:HOH481 4.2 20.9 1.0 O1G D:ATP301 4.2 41.6 0.5 CB D:ASP30 4.4 17.0 1.0 C5' D:ATP301 4.4 35.7 0.6 O2B D:ATP301 4.5 35.3 0.5 C D:ASP30 4.5 13.0 1.0 N D:ALA32 4.5 12.9 1.0 O1A D:ATP301 4.5 39.5 0.5 O D:HOH523 4.6 39.1 1.0 O2G D:ATP301 4.6 24.5 0.5 N D:HIS33 4.6 33.0 1.0 N D:PHE34 4.7 31.5 1.0 CA D:ALA32 4.7 24.1 1.0 CB D:ASP75 4.8 20.3 1.0 CB D:PHE34 4.9 28.1 1.0 C D:ALA32 5.0 32.6 1.0 CA D:ASP30 5.0 9.7 1.0

Magnesium binding site 8 out of 8 in the Bacterial Trna(His) Guanylyltransferase (THG1)-Like Protein in Complex with Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Bacterial Trna(His) Guanylyltransferase (THG1)-Like Protein in Complex with Atp within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg303 b:40.6 occ:1.00 O2A D:ATP301 1.9 33.9 0.5 O D:HOH523 2.1 39.1 1.0 OD1 D:ASP30 2.1 27.1 1.0 O D:HOH465 2.4 30.1 1.0 OD2 D:ASP30 2.6 28.9 1.0 OD1 D:ASP75 2.6 24.7 1.0 CG D:ASP30 2.7 25.9 1.0 MG D:MG302 2.8 26.9 1.0 OD2 D:ASP75 3.2 27.8 1.0 PA D:ATP301 3.2 41.0 0.5 CG D:ASP75 3.3 25.1 1.0 O D:HOH480 3.4 44.7 1.0 O D:HOH532 3.6 34.1 1.0 O1A D:ATP301 3.7 39.5 0.5 CB D:ASP30 4.2 17.0 1.0 O3A D:ATP301 4.2 36.6 0.5 O5' D:ATP301 4.3 37.7 0.6 C5' D:ATP301 4.3 35.7 0.6 O1B D:ATP301 4.3 27.0 0.5 O3G D:ATP301 4.6 27.3 0.5 O D:ASP75 4.7 17.4 1.0 CB D:ASP75 4.7 20.3 1.0 CB D:GLU76 4.7 17.5 1.0 C D:ASP75 4.8 20.1 1.0 O D:GLY31 4.9 18.0 1.0 PB D:ATP301 5.0 31.6 0.5 OE1 D:GLU76 5.0 26.8 1.0

S.J.Hyde, B.S.Rao, B.E.Eckenroth, J.E.Jackman, S.Doublie. Structural Studies of A Bacterial Trna(His) Guanylyltransferase (THG1)-Like Protein, with Nucleotide in the Activation and Nucleotidyl Transfer Sites. Plos One V. 8 67465 2013.
ISSN: ESSN 1932-6203
PubMed: 23844012
DOI: 10.1371/JOURNAL.PONE.0067465