Magnesium in PDB 5axn: Crystal Structure of THG1 Like Protein (Tlp) with Trna(Phe) and Gdpnp

The structure of Crystal Structure of THG1 Like Protein (Tlp) with Trna(Phe) and Gdpnp, PDB code: 5axn was solved by S.Kimura, T.Suzuki, J.Yu, K.Kato, M.Yao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.76 / 2.70
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	82.255, 134.052, 147.384, 90.00, 90.00, 90.00
R / Rfree (%)	22.5 / 26.7

The binding sites of Magnesium atom in the Crystal Structure of THG1 Like Protein (Tlp) with Trna(Phe) and Gdpnp (pdb code 5axn). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Crystal Structure of THG1 Like Protein (Tlp) with Trna(Phe) and Gdpnp, PDB code: 5axn:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Crystal Structure of THG1 Like Protein (Tlp) with Trna(Phe) and Gdpnp


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 THG1 Like Protein (Tlp) with Trna(Phe) and Gdpnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:46.0 occ:1.00 OD1 A:ASP69 2.5 43.0 1.0 OD2 A:ASP21 2.5 48.4 1.0 O1A P:GTP2 2.8 53.5 1.0 O3' A:GNP304 2.9 60.2 1.0 CG A:ASP21 3.4 44.1 1.0 OD1 A:ASP21 3.4 45.9 1.0 MG A:MG302 3.6 40.4 1.0 CG A:ASP69 3.7 46.5 1.0 C3' A:GNP304 3.7 65.2 1.0 N A:ASP69 3.9 53.8 1.0 PA P:GTP2 4.0 59.9 1.0 C4' A:GNP304 4.1 62.6 1.0 O2A P:GTP2 4.3 55.3 1.0 OD2 A:ASP69 4.3 52.1 1.0 C A:ASP69 4.4 44.0 1.0 O5' P:GTP2 4.5 58.9 1.0 CA A:ASP69 4.5 46.5 1.0 CB A:GLU70 4.6 36.6 1.0 O A:ASP69 4.6 39.5 1.0 N A:GLU70 4.7 40.4 1.0 CB A:ASP69 4.7 40.0 1.0 CB A:ASP21 4.8 41.7 1.0 OE2 A:GLU70 4.8 43.7 1.0 C5' A:GNP304 4.8 54.9 1.0 C A:SER68 4.8 49.5 1.0 O A:SER68 4.9 44.6 1.0

Magnesium binding site 2 out of 5 in the Crystal Structure of THG1 Like Protein (Tlp) with Trna(Phe) and Gdpnp


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 THG1 Like Protein (Tlp) with Trna(Phe) and Gdpnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:40.4 occ:1.00 O1B P:GTP2 2.1 55.5 1.0 O A:GLY22 2.1 45.0 1.0 O1A P:GTP2 2.3 53.5 1.0 OD1 A:ASP21 2.4 45.9 1.0 O2G P:GTP2 2.4 47.2 1.0 OD1 A:ASP69 2.7 43.0 1.0 OD2 A:ASP69 2.7 52.1 1.0 CG A:ASP69 3.0 46.5 1.0 C A:GLY22 3.2 40.0 1.0 PB P:GTP2 3.2 50.9 1.0 PA P:GTP2 3.3 59.9 1.0 CG A:ASP21 3.4 44.1 1.0 PG P:GTP2 3.6 50.0 1.0 O3A P:GTP2 3.6 54.7 1.0 MG A:MG301 3.6 46.0 1.0 N A:GLY22 3.7 38.2 1.0 O3B P:GTP2 3.8 57.9 1.0 CA A:GLY22 3.8 37.1 1.0 O2A P:GTP2 3.9 55.3 1.0 OD2 A:ASP21 4.0 48.4 1.0 O A:HOH405 4.2 35.2 1.0 C A:ASP21 4.2 34.3 1.0 N A:ARG23 4.3 36.3 1.0 CB A:ASP69 4.4 40.0 1.0 O2B P:GTP2 4.5 47.9 1.0 O3G P:GTP2 4.6 54.2 1.0 CB A:ASP21 4.6 41.7 1.0 O1G P:GTP2 4.6 48.2 1.0 O A:ASP21 4.7 33.6 1.0 CA A:ARG23 4.7 37.0 1.0 O5' P:GTP2 4.7 58.9 1.0 O A:ASP69 4.7 39.5 1.0 N A:ASN24 4.7 45.4 1.0 CB A:PHE25 4.8 40.1 1.0 N A:PHE25 4.8 48.8 1.0 CA A:ASP21 4.9 39.1 1.0 O3' A:GNP304 5.0 60.2 1.0

Magnesium binding site 3 out of 5 in the Crystal Structure of THG1 Like Protein (Tlp) with Trna(Phe) and Gdpnp


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 THG1 Like Protein (Tlp) with Trna(Phe) and Gdpnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg303 b:43.4 occ:1.00 O A:HOH401 2.0 51.8 1.0 O3G A:GNP304 2.1 44.4 1.0 O1B A:GNP304 2.1 52.1 1.0 O P:HOH102 2.2 53.6 1.0 O A:HOH406 2.5 35.3 1.0 O1A A:GNP304 2.8 48.7 1.0 PB A:GNP304 3.3 46.8 1.0 PG A:GNP304 3.4 42.9 1.0 NZ B:LYS86 3.5 42.8 1.0 N3B A:GNP304 3.7 49.1 1.0 NH2 A:ARG114 3.8 36.1 1.0 PA A:GNP304 3.9 52.0 1.0 O3G P:GTP2 4.0 54.2 1.0 O A:HOH405 4.0 35.2 1.0 O3A A:GNP304 4.0 53.7 1.0 O2G P:GTP2 4.1 47.2 1.0 O2G A:GNP304 4.2 40.5 1.0 PG P:GTP2 4.5 50.0 1.0 O A:HOH404 4.5 36.9 1.0 O1G A:GNP304 4.5 38.6 1.0 O1G P:GTP2 4.6 48.2 1.0 OD1 A:ASP21 4.6 45.9 1.0 O2B A:GNP304 4.6 47.9 1.0 O5' A:GNP304 4.6 53.9 1.0 CE B:LYS86 4.7 32.8 1.0 C3' A:GNP304 4.7 65.2 1.0 CG A:ASP21 4.8 44.1 1.0 C2' A:GNP304 4.9 67.6 1.0 CZ A:ARG114 4.9 31.2 1.0 C5' A:GNP304 5.0 54.9 1.0

Magnesium binding site 4 out of 5 in the Crystal Structure of THG1 Like Protein (Tlp) with Trna(Phe) and Gdpnp


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 THG1 Like Protein (Tlp) with Trna(Phe) and Gdpnp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg302 b:49.5 occ:1.00 O B:GLY22 2.0 44.2 1.0 O2A B:GNP301 2.1 51.8 1.0 O2G B:GNP301 2.1 45.1 1.0 O2B B:GNP301 2.2 48.5 1.0 OD2 B:ASP21 2.2 44.0 1.0 OD2 B:ASP69 2.2 44.2 1.0 C B:GLY22 3.2 37.5 1.0 PB B:GNP301 3.2 51.1 1.0 CG B:ASP21 3.2 34.8 1.0 PA B:GNP301 3.3 50.8 1.0 CG B:ASP69 3.3 43.8 1.0 PG B:GNP301 3.3 48.6 1.0 O3A B:GNP301 3.5 51.9 1.0 O B:HOH403 3.6 40.3 1.0 N3B B:GNP301 3.6 49.8 1.0 OD1 B:ASP69 3.7 43.1 1.0 OD1 B:ASP21 3.7 49.5 1.0 N B:GLY22 3.9 33.0 1.0 CA B:GLY22 3.9 32.7 1.0 O3G B:GNP301 4.0 48.8 1.0 C B:ASP21 4.1 38.3 1.0 N B:ARG23 4.2 37.2 1.0 O1A B:GNP301 4.3 52.1 1.0 MG B:MG303 4.3 61.3 1.0 O5' B:GNP301 4.3 55.1 1.0 C5' B:GNP301 4.4 46.6 1.0 O B:ASP21 4.4 41.5 1.0 CA B:ARG23 4.4 36.5 1.0 CB B:ASP21 4.4 37.7 1.0 O1B B:GNP301 4.6 50.0 1.0 CB B:ASP69 4.6 32.9 1.0 O1G B:GNP301 4.6 55.0 1.0 N B:ASN24 4.6 40.7 1.0 CA B:ASP21 4.8 38.3 1.0 N B:PHE25 4.8 47.9 1.0 CB B:PHE25 4.9 42.6 1.0 C B:ARG23 4.9 37.6 1.0

Magnesium binding site 5 out of 5 in the Crystal Structure of THG1 Like Protein (Tlp) with Trna(Phe) and Gdpnp


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 THG1 Like Protein (Tlp) with Trna(Phe) and Gdpnp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg303 b:61.3 occ:1.00 OD1 B:ASP21 2.7 49.5 1.0 O2A B:GNP301 2.8 51.8 1.0 O1A B:GNP301 2.9 52.1 1.0 O B:HOH403 2.9 40.3 1.0 PA B:GNP301 3.2 50.8 1.0 CG B:ASP21 3.6 34.8 1.0 O5' B:GNP301 3.7 55.1 1.0 OD1 B:ASP69 3.7 43.1 1.0 OD2 B:ASP21 3.8 44.0 1.0 C5' B:GNP301 4.3 46.6 1.0 MG B:MG302 4.3 49.5 1.0 O3A B:GNP301 4.7 51.9 1.0 CG B:ASP69 4.7 43.8 1.0 OD2 B:ASP69 4.8 44.2 1.0 OE1 B:GLU70 4.8 36.8 1.0 O2G B:GNP301 4.8 45.1 1.0 CB B:ASP21 5.0 37.7 1.0

S.Kimura, T.Suzuki, M.Chen, K.Kato, J.Yu, A.Nakamura, I.Tanaka, M.Yao. Template-Dependent Nucleotide Addition in the Reverse (3'-5') Direction By THG1-Like Protein Sci Adv V. 2 01397 2016.
ISSN: ESSN 2375-2548
PubMed: 27051866
DOI: 10.1126/SCIADV.1501397