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

The structure of Bacterial Trna(His) Guanylyltransferase (THG1)-Like Protein in Complex with Gtp, PDB code: 4kgk 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)	39.41 / 2.95
Space group	P 41
Cell size a, b, c (Å), α, β, γ (°)	111.254, 111.254, 129.124, 90.00, 90.00, 90.00
R / Rfree (%)	20.8 / 22.9

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Magnesium atom in the Bacterial Trna(His) Guanylyltransferase (THG1)-Like Protein in Complex with Gtp (pdb code 4kgk). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 11 binding sites of Magnesium where determined in the Bacterial Trna(His) Guanylyltransferase (THG1)-Like Protein in Complex with Gtp, PDB code: 4kgk:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 11 in the Bacterial Trna(His) Guanylyltransferase (THG1)-Like Protein in Complex with Gtp


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 Gtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:48.9 occ:1.00 O1B A:GTP301 2.0 55.4 1.0 OD1 A:ASP30 2.0 50.9 1.0 O A:GLY31 2.1 50.5 1.0 OD2 A:ASP75 2.1 51.7 1.0 O3G A:GTP301 2.5 48.9 1.0 O2A A:GTP301 2.6 58.9 1.0 CG A:ASP30 3.0 47.4 1.0 PB A:GTP301 3.1 54.2 1.0 CG A:ASP75 3.2 59.3 1.0 C A:GLY31 3.2 49.2 1.0 O3A A:GTP301 3.3 53.9 1.0 OD2 A:ASP30 3.4 47.6 1.0 PG A:GTP301 3.4 59.9 1.0 PA A:GTP301 3.5 56.2 1.0 O1G A:GTP301 3.6 58.2 1.0 O3B A:GTP301 3.7 52.4 1.0 OD1 A:ASP75 3.7 61.8 1.0 N A:GLY31 3.8 46.7 1.0 CA A:GLY31 3.9 44.1 1.0 MG A:MG303 4.2 55.4 1.0 C5' A:GTP301 4.3 64.8 1.0 CB A:ASP30 4.3 45.2 1.0 C A:ASP30 4.3 46.0 1.0 N A:ALA32 4.3 49.9 1.0 O5' A:GTP301 4.4 59.8 1.0 O2B A:GTP301 4.4 60.6 1.0 CB A:ASP75 4.5 59.8 1.0 N A:HIS33 4.6 62.4 1.0 CA A:ALA32 4.6 52.7 1.0 O B:HOH402 4.6 48.9 1.0 N A:PHE34 4.6 54.0 1.0 O2G A:GTP301 4.8 60.1 1.0 O1A A:GTP301 4.8 54.1 1.0 CB A:PHE34 4.8 56.9 1.0 CA A:ASP30 4.8 45.5 1.0 C A:ALA32 4.9 60.2 1.0 O A:ASP30 4.9 41.4 1.0

Magnesium binding site 2 out of 11 in the Bacterial Trna(His) Guanylyltransferase (THG1)-Like Protein in Complex with Gtp


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 Gtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg303 b:55.4 occ:1.00 OD2 A:ASP30 2.3 47.6 1.0 OD1 A:ASP75 2.4 61.8 1.0 O2A A:GTP301 2.6 58.9 1.0 CG A:ASP30 3.4 47.4 1.0 CG A:ASP75 3.4 59.3 1.0 OD2 A:ASP75 3.8 51.7 1.0 PA A:GTP301 3.8 56.2 1.0 OD1 A:ASP30 3.9 50.9 1.0 CB A:GLU76 4.0 50.6 1.0 O1A A:GTP301 4.1 54.1 1.0 N A:GLU76 4.2 56.6 1.0 MG A:MG302 4.2 48.9 1.0 OG A:SER74 4.3 58.3 1.0 C5' A:GTP301 4.5 64.8 1.0 CG A:GLU76 4.5 54.9 1.0 N A:ASP75 4.5 55.2 1.0 O5' A:GTP301 4.6 59.8 1.0 CB A:ASP30 4.6 45.2 1.0 CB A:SER74 4.6 57.1 1.0 CA A:GLU76 4.6 51.9 1.0 CB A:ASP75 4.7 59.8 1.0 C A:ASP75 4.7 53.5 1.0 OE1 A:GLU76 4.8 61.8 1.0 CA A:ASP75 4.9 54.1 1.0

Magnesium binding site 3 out of 11 in the Bacterial Trna(His) Guanylyltransferase (THG1)-Like Protein in Complex with Gtp


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 Gtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg304 b:51.2 occ:1.00 O B:HOH402 2.0 48.9 1.0 O1B B:GTP301 2.1 49.1 1.0 O2A B:GTP301 2.2 45.0 1.0 O3G B:GTP301 2.5 54.7 1.0 PB B:GTP301 3.3 54.8 1.0 PA B:GTP301 3.4 56.6 1.0 O3G A:GTP301 3.6 48.9 1.0 O3A B:GTP301 3.6 52.6 1.0 PG B:GTP301 3.7 51.1 1.0 O3B B:GTP301 3.9 50.6 1.0 NZ B:LYS99 4.1 50.6 1.0 O1G B:GTP301 4.2 46.3 1.0 NH2 A:ARG131 4.3 48.8 1.0 OD1 A:ASP30 4.3 50.9 1.0 O2G A:GTP301 4.4 60.1 1.0 O5' B:GTP301 4.4 54.6 1.0 O1A B:GTP301 4.4 51.0 1.0 O2B B:GTP301 4.6 57.3 1.0 PG A:GTP301 4.6 59.9 1.0 CG A:ASP30 4.6 47.4 1.0 O2G B:GTP301 4.9 52.0 1.0 OD2 A:ASP129 5.0 48.2 0.5

Magnesium binding site 4 out of 11 in the Bacterial Trna(His) Guanylyltransferase (THG1)-Like Protein in Complex with Gtp


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 Gtp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg304 b:57.3 occ:1.00 OD2 B:ASP75 1.8 61.2 1.0 O B:GLY31 2.1 52.9 1.0 O1B B:GTP302 2.2 59.9 1.0 OD2 B:ASP30 2.2 59.5 1.0 O2A B:GTP302 2.4 68.3 1.0 O3G B:GTP302 2.6 61.9 1.0 C B:GLY31 2.8 50.9 1.0 CG B:ASP75 3.1 60.0 1.0 N B:GLY31 3.2 54.0 1.0 CA B:GLY31 3.2 49.3 1.0 PB B:GTP302 3.3 61.4 1.0 CG B:ASP30 3.4 57.5 1.0 PA B:GTP302 3.4 75.9 1.0 O3A B:GTP302 3.4 58.3 1.0 PG B:GTP302 3.6 86.0 1.0 OD1 B:ASP75 3.7 66.7 1.0 O3B B:GTP302 3.8 77.9 1.0 O1G B:GTP302 3.8 63.2 1.0 N B:ALA32 4.0 48.2 1.0 C B:ASP30 4.1 51.4 1.0 CB B:PHE34 4.1 60.0 1.0 CB B:ASP75 4.2 59.4 1.0 OD1 B:ASP30 4.2 60.3 1.0 MG B:MG305 4.3 59.7 1.0 O1A B:GTP302 4.3 64.6 1.0 CB B:ASP30 4.4 57.1 1.0 N B:PHE34 4.5 58.5 1.0 CA B:ALA32 4.5 50.9 1.0 O2B B:GTP302 4.6 68.4 1.0 O5' B:GTP302 4.7 72.8 1.0 CG B:PHE34 4.7 58.5 1.0 CA B:ASP30 4.7 53.9 1.0 N B:HIS33 4.7 57.9 1.0 O B:ASP30 4.8 48.0 1.0 C5' B:GTP302 4.9 66.3 1.0 O B:ASP75 4.9 53.2 1.0 C B:ALA32 4.9 57.6 1.0 CD1 B:PHE34 4.9 56.3 1.0 O2G B:GTP302 4.9 87.0 1.0 CA B:PHE34 5.0 60.2 1.0

Magnesium binding site 5 out of 11 in the Bacterial Trna(His) Guanylyltransferase (THG1)-Like Protein in Complex with Gtp


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 Gtp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg305 b:59.7 occ:1.00 OD1 B:ASP30 2.3 60.3 1.0 O2A B:GTP302 2.5 68.3 1.0 OD1 B:ASP75 2.8 66.7 1.0 CG B:ASP30 3.1 57.5 1.0 OD2 B:ASP30 3.2 59.5 1.0 PA B:GTP302 3.4 75.9 1.0 O1A B:GTP302 3.6 64.6 1.0 O5' B:GTP302 3.7 72.8 1.0 CG B:ASP75 3.7 60.0 1.0 OD2 B:ASP75 3.9 61.2 1.0 C5' B:GTP302 4.2 66.3 1.0 MG B:MG304 4.3 57.3 1.0 O3G B:GTP302 4.5 61.9 1.0 CB B:ASP30 4.5 57.1 1.0 O3A B:GTP302 4.9 58.3 1.0 O5' B:GTP303 4.9 68.0 0.8 OG B:SER74 5.0 51.7 1.0

Magnesium binding site 6 out of 11 in the Bacterial Trna(His) Guanylyltransferase (THG1)-Like Protein in Complex with Gtp


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 Gtp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg306 b:63.2 occ:0.80 O3G B:GTP303 2.4 68.7 0.8 O3A B:GTP303 2.5 67.5 0.8 O2A B:GTP303 2.7 67.8 0.8 PA B:GTP303 3.2 76.6 0.8 O1B B:GTP303 3.3 70.5 0.8 PB B:GTP303 3.4 68.6 0.8 O3G B:GTP302 3.5 61.9 1.0 PG B:GTP303 3.6 66.0 0.8 O2G B:GTP302 3.6 87.0 1.0 O3B B:GTP303 3.6 67.8 0.8 NH2 B:ARG131 4.1 67.6 1.0 PG B:GTP302 4.2 86.0 1.0 O1A B:GTP303 4.3 69.7 0.8 O5' B:GTP303 4.3 68.0 0.8 CG B:ASP30 4.3 57.5 1.0 OD2 B:ASP30 4.4 59.5 1.0 O2G B:GTP303 4.5 71.5 0.8 CB B:ASP30 4.6 57.1 1.0 O1G B:GTP303 4.6 63.0 0.8 OD1 B:ASP30 4.7 60.3 1.0 O2B B:GTP303 4.8 70.4 0.8 OD1 B:ASP129 4.8 66.5 1.0 CZ B:ARG131 4.9 62.7 1.0 NH1 B:ARG131 4.9 63.9 1.0

Magnesium binding site 7 out of 11 in the Bacterial Trna(His) Guanylyltransferase (THG1)-Like Protein in Complex with Gtp


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 Gtp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg303 b:71.6 occ:1.00 OD2 C:ASP75 2.0 70.6 1.0 OD1 C:ASP30 2.0 73.2 1.0 O C:GLY31 2.1 69.7 1.0 O2A C:GTP301 2.2 81.1 1.0 O3G C:GTP301 2.2 77.4 1.0 O1B C:GTP301 2.6 75.9 1.0 C C:GLY31 3.1 65.6 1.0 CG C:ASP75 3.1 72.6 1.0 CG C:ASP30 3.2 68.4 1.0 PG C:GTP301 3.2 91.0 1.0 PA C:GTP301 3.4 86.1 1.0 N C:GLY31 3.5 64.0 1.0 PB C:GTP301 3.5 78.2 1.0 O1G C:GTP301 3.5 79.3 1.0 CA C:GLY31 3.6 62.1 1.0 OD1 C:ASP75 3.7 71.5 1.0 O3A C:GTP301 3.7 80.1 1.0 O3B C:GTP301 3.7 90.3 1.0 OD2 C:ASP30 3.9 65.2 1.0 MG C:MG304 4.1 62.1 1.0 C C:ASP30 4.2 62.9 1.0 N C:ALA32 4.2 62.8 1.0 CB C:PHE34 4.3 71.2 1.0 CB C:ASP75 4.3 72.4 1.0 CB C:ASP30 4.3 67.0 1.0 O1A C:GTP301 4.4 83.9 1.0 N C:PHE34 4.5 66.2 1.0 O5' C:GTP301 4.5 84.5 1.0 O2G C:GTP301 4.6 87.6 1.0 C5' C:GTP301 4.6 84.3 1.0 N C:HIS33 4.7 77.9 1.0 CA C:ALA32 4.7 67.0 1.0 CA C:ASP30 4.8 65.3 1.0 O C:ASP30 4.8 59.2 1.0 O2B C:GTP301 4.9 75.8 1.0 CG C:PHE34 4.9 69.3 1.0 C C:ALA32 5.0 74.3 1.0

Magnesium binding site 8 out of 11 in the Bacterial Trna(His) Guanylyltransferase (THG1)-Like Protein in Complex with Gtp


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 Gtp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg304 b:62.1 occ:1.00 OD2 C:ASP30 2.1 65.2 1.0 OD1 C:ASP75 2.4 71.5 1.0 O2A C:GTP301 2.8 81.1 1.0 CG C:ASP30 3.1 68.4 1.0 OD1 C:ASP30 3.4 73.2 1.0 CG C:ASP75 3.4 72.6 1.0 PA C:GTP301 3.6 86.1 1.0 O5' C:GTP301 3.7 84.5 1.0 OD2 C:ASP75 3.8 70.6 1.0 C5' C:GTP301 3.9 84.3 1.0 O1A C:GTP301 4.0 83.9 1.0 MG C:MG303 4.1 71.6 1.0 OG C:SER74 4.2 76.2 1.0 CB C:ASP30 4.5 67.0 1.0 CB C:GLU76 4.5 60.4 1.0 N C:ASP75 4.6 69.0 1.0 CB C:SER74 4.6 75.4 1.0 N C:GLU76 4.7 65.9 1.0 CB C:ASP75 4.7 72.4 1.0 O3G C:GTP301 4.8 77.4 1.0 C C:ASP75 4.8 64.3 1.0 OE1 C:GLU76 4.8 76.9 1.0 CG C:GLU76 4.9 67.3 1.0 CA C:ASP75 5.0 67.7 1.0

Magnesium binding site 9 out of 11 in the Bacterial Trna(His) Guanylyltransferase (THG1)-Like Protein in Complex with Gtp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Bacterial Trna(His) Guanylyltransferase (THG1)-Like Protein in Complex with Gtp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg305 b:73.8 occ:0.70 O3G C:GTP302 2.6 73.6 0.7 O2A C:GTP302 3.1 74.2 0.7 O1B C:GTP302 3.2 73.7 0.7 O3A C:GTP302 3.4 75.2 0.7 NH2 C:ARG131 3.5 71.8 1.0 O3G C:GTP301 3.8 77.4 1.0 O2G C:GTP301 3.8 87.6 1.0 PB C:GTP302 3.8 80.3 0.7 PA C:GTP302 3.9 77.3 0.7 PG C:GTP302 3.9 71.7 0.7 OD1 C:ASP129 4.1 64.5 1.0 CB C:ASP30 4.1 67.0 1.0 OD2 C:ASP129 4.1 74.0 1.0 CG C:ASP30 4.2 68.4 1.0 O3B C:GTP302 4.3 74.2 0.7 OD1 C:ASP30 4.3 73.2 1.0 CG C:ASP129 4.4 69.5 1.0 NZ D:LYS99 4.5 75.0 1.0 PG C:GTP301 4.5 91.0 1.0 CZ C:ARG131 4.5 72.7 1.0 O1G C:GTP302 4.6 70.2 0.7 O1A C:GTP302 4.7 74.5 0.7 OD2 C:ASP30 4.8 65.2 1.0 CE D:LYS99 5.0 68.8 1.0

Magnesium binding site 10 out of 11 in the Bacterial Trna(His) Guanylyltransferase (THG1)-Like Protein in Complex with Gtp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Bacterial Trna(His) Guanylyltransferase (THG1)-Like Protein in Complex with Gtp within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg303 b:70.9 occ:1.00 OD2 D:ASP75 2.1 73.2 1.0 OD1 D:ASP30 2.1 68.5 1.0 O2A D:GTP301 2.2 72.8 0.8 O3G D:GTP301 2.3 78.8 0.8 O1B D:GTP301 2.3 73.8 0.8 O D:GLY31 2.8 72.0 1.0 O1G D:GTP301 2.8 76.7 0.8 PG D:GTP301 2.9 83.5 0.8 CG D:ASP30 3.0 69.2 1.0 OD2 D:ASP30 3.1 66.7 1.0 PB D:GTP301 3.1 70.3 0.8 CG D:ASP75 3.2 73.8 1.0 PA D:GTP301 3.2 76.1 0.8 MG D:MG304 3.3 75.1 1.0 O3A D:GTP301 3.3 73.3 0.8 O3B D:GTP301 3.4 75.6 0.8 OD1 D:ASP75 3.6 71.7 1.0 O1A D:GTP301 3.9 74.2 0.8 C D:GLY31 3.9 71.0 1.0 N D:GLY31 4.2 63.9 1.0 O2G D:GTP301 4.3 80.7 0.8 CB D:ASP30 4.4 67.8 1.0 CB D:ASP75 4.5 70.6 1.0 CA D:GLY31 4.5 60.2 1.0 O2B D:GTP301 4.6 71.1 0.8 O5' D:GTP301 4.6 79.5 0.8 C D:ASP30 4.8 62.1 1.0 C5' D:GTP301 4.9 78.1 0.8

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