Magnesium in PDB 3boy: Crystal Structure of the Hutp Antitermination Complex Bound to the Hut Mrna

The structure of Crystal Structure of the Hutp Antitermination Complex Bound to the Hut Mrna, PDB code: 3boy was solved by T.S.Kumarevel, D.Balasundaresan, J.Jeyakanthan, A.Shinkai, S.Yokoyama, P.K.R.Kumar, Riken Structural Genomics/Proteomics Initiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.24 / 1.70
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	99.635, 76.469, 62.790, 90.00, 109.06, 90.00
R / Rfree (%)	19.8 / 24.6

The binding sites of Magnesium atom in the Crystal Structure of the Hutp Antitermination Complex Bound to the Hut Mrna (pdb code 3boy). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of the Hutp Antitermination Complex Bound to the Hut Mrna, PDB code: 3boy:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of the Hutp Antitermination Complex Bound to the Hut Mrna


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 the Hutp Antitermination Complex Bound to the Hut Mrna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2002 b:15.7 occ:1.00 O A:HIS2001 2.1 13.3 1.0 O B:HOH3066 2.1 14.9 1.0 NE2 B:HIS138 2.2 15.6 1.0 NE2 A:HIS73 2.3 15.9 1.0 NE2 A:HIS77 2.3 15.1 1.0 N A:HIS2001 2.4 15.8 0.0 C A:HIS2001 2.9 14.2 1.0 CA A:HIS2001 3.0 14.3 1.0 CD2 A:HIS73 3.1 15.4 1.0 CD2 B:HIS138 3.2 15.0 1.0 CE1 A:HIS77 3.2 16.8 1.0 CE1 B:HIS138 3.2 14.2 1.0 CE1 A:HIS73 3.3 16.6 1.0 CD2 A:HIS77 3.3 13.7 1.0 OXT A:HIS2001 4.1 14.0 1.0 NH1 B:ARG88 4.2 14.6 1.0 CG A:HIS73 4.3 15.3 1.0 ND1 A:HIS73 4.3 16.8 1.0 ND1 B:HIS138 4.3 14.8 1.0 CG B:HIS138 4.3 16.8 1.0 ND1 A:HIS77 4.4 16.1 1.0 CB A:HIS2001 4.4 13.4 1.0 CG A:HIS77 4.4 13.5 1.0 OH A:TYR69 4.6 17.4 1.0 O B:HOH3014 5.0 24.8 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of the Hutp Antitermination Complex Bound to the Hut Mrna


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 the Hutp Antitermination Complex Bound to the Hut Mrna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg3002 b:14.9 occ:1.00 O A:HIS3001 2.0 12.8 1.0 O B:HOH3065 2.0 14.9 1.0 NE2 B:HIS73 2.2 14.8 1.0 NE2 C:HIS138 2.2 16.8 1.0 NE2 B:HIS77 2.3 16.3 1.0 N A:HIS3001 2.4 13.6 0.0 C A:HIS3001 2.9 12.7 1.0 CA A:HIS3001 3.0 13.1 1.0 CD2 B:HIS73 3.1 16.2 1.0 CE1 B:HIS77 3.2 17.5 1.0 CE1 B:HIS73 3.2 16.6 1.0 CD2 C:HIS138 3.2 16.9 1.0 CE1 C:HIS138 3.2 15.7 1.0 CD2 B:HIS77 3.3 16.0 1.0 OXT A:HIS3001 4.1 13.6 1.0 NH1 C:ARG88 4.2 15.6 1.0 CG B:HIS73 4.2 15.0 1.0 ND1 B:HIS73 4.2 16.6 1.0 ND1 C:HIS138 4.3 16.0 1.0 CB A:HIS3001 4.3 12.1 1.0 ND1 B:HIS77 4.3 16.9 1.0 CG C:HIS138 4.4 16.7 1.0 CG B:HIS77 4.4 14.6 1.0 OH B:TYR69 4.6 16.9 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of the Hutp Antitermination Complex Bound to the Hut Mrna


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 the Hutp Antitermination Complex Bound to the Hut Mrna within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1002 b:14.5 occ:1.00 O A:HIS1001 2.0 12.8 1.0 O C:HOH3103 2.1 14.5 1.0 NE2 A:HIS138 2.2 14.6 1.0 NE2 C:HIS73 2.3 15.3 1.0 NE2 C:HIS77 2.3 16.4 1.0 N A:HIS1001 2.4 15.6 0.0 C A:HIS1001 2.9 15.3 1.0 CA A:HIS1001 3.1 14.9 1.0 CD2 C:HIS73 3.1 15.2 1.0 CD2 A:HIS138 3.2 15.6 1.0 CE1 A:HIS138 3.2 13.1 1.0 CE1 C:HIS77 3.2 17.7 1.0 CE1 C:HIS73 3.3 15.0 1.0 CD2 C:HIS77 3.3 13.6 1.0 OXT A:HIS1001 4.1 15.3 1.0 NH1 A:ARG88 4.2 13.6 1.0 CG C:HIS73 4.3 15.2 1.0 ND1 C:HIS73 4.3 16.1 1.0 ND1 A:HIS138 4.3 15.5 1.0 CG A:HIS138 4.3 16.3 1.0 ND1 C:HIS77 4.4 16.6 1.0 CB A:HIS1001 4.4 14.8 1.0 CG C:HIS77 4.4 14.2 1.0 OH C:TYR69 4.6 17.0 1.0 O A:HOH3007 4.9 24.9 1.0

T.Kumarevel, D.Balasundaresan, J.Jeyakanthan, A.Shinkai, S.Yokoyama, P.K.R.Kumar. Crystal Structure of Hutp Complexed with the 55-Mer Rna To Be Published.