Magnesium in PDB 3otb: Crystal Structure of Human Trnahis Guanylyltransferase (THG1) - Dgtp Complex

The structure of Crystal Structure of Human Trnahis Guanylyltransferase (THG1) - Dgtp Complex, PDB code: 3otb was solved by S.J.Hyde, B.E.Eckenroth, S.Doublie, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.95
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	140.912, 140.912, 81.227, 90.00, 90.00, 90.00
R / Rfree (%)	25.4 / 30.1

The binding sites of Magnesium atom in the Crystal Structure of Human Trnahis Guanylyltransferase (THG1) - Dgtp Complex (pdb code 3otb). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of Human Trnahis Guanylyltransferase (THG1) - Dgtp Complex, PDB code: 3otb:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Crystal Structure of Human Trnahis Guanylyltransferase (THG1) - Dgtp Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Human Trnahis Guanylyltransferase (THG1) - Dgtp Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:80.2 occ:1.00 O2A A:DGT301 2.0 88.2 1.0 O A:GLY30 2.1 70.8 1.0 OD1 A:ASP29 2.1 72.9 1.0 O2B A:DGT301 2.2 68.8 1.0 OD1 A:ASP76 2.3 59.1 1.0 O1G A:DGT301 2.5 84.0 1.0 O2G A:DGT301 2.5 88.3 1.0 PG A:DGT301 2.6 84.2 1.0 O3B A:DGT301 2.9 85.2 1.0 PB A:DGT301 3.0 90.4 1.0 CG A:ASP29 3.3 80.3 1.0 PA A:DGT301 3.3 91.9 1.0 C A:GLY30 3.3 58.7 1.0 CG A:ASP76 3.3 75.3 1.0 O3A A:DGT301 3.5 89.7 1.0 OD2 A:ASP76 3.7 87.8 1.0 OD2 A:ASP29 3.8 79.9 1.0 O3G A:DGT301 4.2 85.0 1.0 N A:GLY30 4.2 75.0 1.0 CA A:GLY30 4.2 65.0 1.0 C A:ASP29 4.2 77.7 1.0 N A:ARG31 4.2 60.4 1.0 O A:ASP29 4.2 75.8 1.0 O1A A:DGT301 4.2 86.6 1.0 MG A:MG403 4.3 72.4 1.0 CA A:ARG31 4.3 63.0 1.0 O5' A:DGT301 4.4 92.1 1.0 O1B A:DGT301 4.4 92.0 1.0 CB A:ASP29 4.5 76.1 1.0 C5' A:DGT301 4.5 92.3 1.0 N A:ASN32 4.5 81.3 1.0 C A:ARG31 4.6 72.3 1.0 N A:PHE33 4.6 82.3 1.0 CB A:PHE33 4.6 74.7 1.0 CB A:ASP76 4.7 67.1 1.0 CA A:ASP29 4.9 71.5 1.0

Magnesium binding site 2 out of 6 in the Crystal Structure of Human Trnahis Guanylyltransferase (THG1) - Dgtp Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Human Trnahis Guanylyltransferase (THG1) - Dgtp Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:61.5 occ:1.00 O2B B:3PO302 2.0 0.3 1.0 O1G B:3PO302 2.6 81.5 1.0 O2A B:3PO302 2.7 1.0 1.0 O1G A:DGT301 3.1 84.0 1.0 PB B:3PO302 3.3 83.6 1.0 PG B:3PO302 3.7 82.8 1.0 O3A B:3PO302 3.7 87.0 1.0 PA B:3PO302 3.8 0.4 1.0 O3B B:3PO302 3.8 82.2 1.0 OD1 A:ASP29 4.2 72.9 1.0 NZ B:LYS95 4.4 66.9 1.0 O2G B:3PO302 4.4 62.1 1.0 PG A:DGT301 4.5 84.2 1.0 O1B B:3PO302 4.6 86.7 1.0 O1A B:3PO302 4.6 0.5 1.0 CG A:ASP29 4.6 80.3 1.0 NH2 A:ARG130 4.7 90.2 1.0 O3G A:DGT301 4.7 85.0 1.0 O3G B:3PO302 5.0 72.1 1.0 O5' B:3PO302 5.0 91.5 1.0 CB A:ASP29 5.0 76.1 1.0

Magnesium binding site 3 out of 6 in the Crystal Structure of Human Trnahis Guanylyltransferase (THG1) - Dgtp Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Human Trnahis Guanylyltransferase (THG1) - Dgtp Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:72.4 occ:1.00 OD2 A:ASP76 2.3 87.8 1.0 OD2 A:ASP29 2.6 79.9 1.0 O2A A:DGT301 2.7 88.2 1.0 O5' A:DGT301 2.9 92.1 1.0 PA A:DGT301 3.0 91.9 1.0 C5' A:DGT301 3.3 92.3 1.0 CG A:ASP76 3.3 75.3 1.0 O1A A:DGT301 3.3 86.6 1.0 CG A:ASP29 3.6 80.3 1.0 OG A:SER75 3.7 70.8 1.0 OD1 A:ASP76 3.8 59.1 1.0 OD1 A:ASP29 3.9 72.9 1.0 CB A:SER75 4.3 66.1 1.0 N A:ASP76 4.3 68.4 1.0 MG A:MG401 4.3 80.2 1.0 OE1 A:GLU77 4.3 77.2 1.0 CB A:ASP76 4.5 67.1 1.0 O3A A:DGT301 4.6 89.7 1.0 CA A:ASP76 4.8 69.6 1.0 C A:ASP76 4.8 74.8 1.0 C4' A:DGT301 4.8 0.6 1.0 O A:ASP76 4.9 79.7 1.0

Magnesium binding site 4 out of 6 in the Crystal Structure of Human Trnahis Guanylyltransferase (THG1) - Dgtp Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Human Trnahis Guanylyltransferase (THG1) - Dgtp Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg401 b:84.2 occ:1.00 O2A B:DGT301 2.0 78.3 1.0 O B:GLY30 2.1 71.9 1.0 OD1 B:ASP29 2.1 75.3 1.0 OD1 B:ASP76 2.3 76.8 1.0 O2B B:DGT301 2.3 68.2 1.0 O1G B:DGT301 2.5 85.5 1.0 O2G B:DGT301 2.6 93.7 1.0 PG B:DGT301 2.7 79.8 1.0 O3B B:DGT301 3.0 89.5 1.0 PB B:DGT301 3.1 86.4 1.0 CG B:ASP29 3.2 79.3 1.0 PA B:DGT301 3.3 69.9 1.0 C B:GLY30 3.3 67.1 1.0 CG B:ASP76 3.3 83.6 1.0 O3A B:DGT301 3.5 69.3 1.0 OD2 B:ASP76 3.7 81.2 1.0 OD2 B:ASP29 3.8 75.3 1.0 N B:GLY30 4.2 70.8 1.0 O3G B:DGT301 4.2 87.4 1.0 CA B:GLY30 4.2 72.4 1.0 C B:ASP29 4.2 69.9 1.0 O1A B:DGT301 4.2 85.5 1.0 O B:ASP29 4.2 60.4 1.0 N B:ARG31 4.2 63.5 1.0 MG B:MG403 4.3 67.3 1.0 O5' B:DGT301 4.3 91.7 1.0 CA B:ARG31 4.3 66.8 1.0 C5' B:DGT301 4.4 98.4 1.0 O1B B:DGT301 4.5 82.9 1.0 CB B:ASP29 4.5 62.8 1.0 N B:ASN32 4.6 88.4 1.0 C B:ARG31 4.6 78.5 1.0 CB B:PHE33 4.6 77.5 1.0 N B:PHE33 4.6 86.3 1.0 CB B:ASP76 4.6 73.5 1.0 CA B:ASP29 4.9 59.2 1.0

Magnesium binding site 5 out of 6 in the Crystal Structure of Human Trnahis Guanylyltransferase (THG1) - Dgtp Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Human Trnahis Guanylyltransferase (THG1) - Dgtp Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:67.6 occ:1.00 O2B A:3PO302 2.1 96.7 1.0 O2A A:3PO302 2.6 0.2 1.0 O1G A:3PO302 2.6 95.1 1.0 O1G B:DGT301 3.2 85.5 1.0 PB A:3PO302 3.3 86.4 1.0 PA A:3PO302 3.7 0.8 1.0 O3A A:3PO302 3.7 88.2 1.0 PG A:3PO302 3.7 85.7 1.0 O3B A:3PO302 3.8 81.0 1.0 OD1 B:ASP29 4.2 75.3 1.0 NZ A:LYS95 4.3 69.2 1.0 O2G A:3PO302 4.4 63.7 1.0 O1A A:3PO302 4.5 0.8 1.0 NH2 B:ARG130 4.6 55.3 1.0 CG B:ASP29 4.6 79.3 1.0 PG B:DGT301 4.6 79.8 1.0 O1B A:3PO302 4.6 80.3 1.0 O3G B:DGT301 4.9 87.4 1.0 O5' A:3PO302 4.9 0.1 1.0 CB B:ASP29 4.9 62.8 1.0 O3G A:3PO302 4.9 81.5 1.0

Magnesium binding site 6 out of 6 in the Crystal Structure of Human Trnahis Guanylyltransferase (THG1) - Dgtp Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Human Trnahis Guanylyltransferase (THG1) - Dgtp Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg403 b:67.3 occ:1.00 OD2 B:ASP76 2.3 81.2 1.0 O2A B:DGT301 2.6 78.3 1.0 OD2 B:ASP29 2.7 75.3 1.0 O5' B:DGT301 2.8 91.7 1.0 PA B:DGT301 3.0 69.9 1.0 C5' B:DGT301 3.2 98.4 1.0 O1A B:DGT301 3.3 85.5 1.0 CG B:ASP76 3.3 83.6 1.0 OG B:SER75 3.6 69.8 1.0 CG B:ASP29 3.7 79.3 1.0 OD1 B:ASP76 3.8 76.8 1.0 OD1 B:ASP29 4.0 75.3 1.0 CB B:SER75 4.3 72.6 1.0 MG B:MG401 4.3 84.2 1.0 N B:ASP76 4.3 64.5 1.0 OE1 B:GLU77 4.4 75.0 1.0 CB B:ASP76 4.5 73.5 1.0 O3A B:DGT301 4.5 69.3 1.0 C4' B:DGT301 4.7 0.4 1.0 CA B:ASP76 4.8 68.5 1.0 C B:ASP76 4.8 69.5 1.0 O B:ASP76 5.0 63.4 1.0

S.J.Hyde, B.E.Eckenroth, B.A.Smith, W.A.Eberley, N.H.Heintz, J.E.Jackman, S.Doublie. Trnahis Guanylyltransferase (THG1), A Unique 3'-5' Nucleotidyl Transferase, Shares Unexpected Structural Homology with Canonical 5'-3' Dna Polymerases. Proc.Natl.Acad.Sci.Usa V. 107 20305 2010.
ISSN: ISSN 0027-8424
PubMed: 21059936
DOI: 10.1073/PNAS.1010436107