Magnesium in PDB 3al5: Crystal Structure of Human TYW5

The structure of Crystal Structure of Human TYW5, PDB code: 3al5 was solved by M.Kato, Y.Araiso, R.Ishitani, O.Nureki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.50
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	164.942, 164.942, 105.149, 90.00, 90.00, 90.00
R / Rfree (%)	22 / 28.1

The binding sites of Magnesium atom in the Crystal Structure of Human TYW5 (pdb code 3al5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Human TYW5, PDB code: 3al5:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Human TYW5


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 TYW5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg401 b:67.6 occ:1.00 OD1 B:ASP162 2.5 57.8 1.0 NE2 B:HIS160 2.6 70.6 1.0 NE2 B:HIS235 2.8 40.5 1.0 CE1 B:HIS235 3.3 47.6 1.0 CG B:ASP162 3.3 46.6 1.0 CD2 B:HIS160 3.4 66.9 1.0 OD2 B:ASP162 3.4 48.6 1.0 CE1 B:HIS160 3.7 70.5 1.0 NH2 B:ARG149 4.0 71.7 1.0 CZ B:PHE249 4.0 55.2 1.0 NH1 B:ARG149 4.1 70.2 1.0 CD2 B:HIS235 4.1 41.4 1.0 CE1 B:PHE249 4.5 50.9 1.0 CZ B:ARG149 4.5 66.6 1.0 ND1 B:HIS235 4.6 48.9 1.0 CG B:HIS160 4.6 58.6 1.0 ND2 B:ASN166 4.7 41.9 1.0 ND1 B:HIS160 4.7 68.2 1.0 CB B:ASP162 4.7 42.8 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Human TYW5


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 TYW5 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg401 b:59.5 occ:1.00 NE2 D:HIS235 2.7 51.1 1.0 NE2 D:HIS160 2.8 54.5 1.0 OD1 D:ASP162 2.9 56.2 1.0 CE1 D:HIS160 3.4 61.7 1.0 CD2 D:HIS235 3.5 42.2 1.0 NH2 D:ARG149 3.6 70.0 1.0 CE1 D:HIS235 3.9 58.9 1.0 CD2 D:HIS160 4.0 51.9 1.0 CG D:ASP162 4.0 46.2 1.0 CZ D:ARG149 4.1 55.4 1.0 NH1 D:ARG149 4.3 61.3 1.0 OD2 D:ASP162 4.4 54.6 1.0 CZ D:PHE249 4.4 19.6 1.0 ND2 D:ASN166 4.5 63.1 1.0 ND1 D:HIS160 4.7 59.4 1.0 CG D:HIS235 4.7 45.2 1.0 ND1 D:HIS235 4.9 53.1 1.0 CE1 D:PHE249 4.9 44.5 1.0 NE D:ARG149 4.9 46.0 1.0 CG D:HIS160 5.0 54.9 1.0

M.Kato, Y.Araiso, A.Noma, A.Nagao, T.Suzuki, R.Ishitani, O.Nureki. Crystal Structure of A Novel Jmjc-Domain-Containing Protein, TYW5, Involved in Trna Modification. Nucleic Acids Res. V. 39 1576 2011.
ISSN: ISSN 0305-1048
PubMed: 20972222
DOI: 10.1093/NAR/GKQ919