Magnesium in PDB 6bt2: Structure of the Human Nocturnin Catalytic Domain with Bound Sulfate Anion

All present enzymatic activity of Structure of the Human Nocturnin Catalytic Domain with Bound Sulfate Anion:
3.1.13.4;

The structure of Structure of the Human Nocturnin Catalytic Domain with Bound Sulfate Anion, PDB code: 6bt2 was solved by E.T.Abshire, J.Chasseur, P.Del Rizzo, R.Trievel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.23 / 2.41
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	62.004, 69.437, 153.496, 90.00, 90.00, 90.00
R / Rfree (%)	16.1 / 22.4

The binding sites of Magnesium atom in the Structure of the Human Nocturnin Catalytic Domain with Bound Sulfate Anion (pdb code 6bt2). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structure of the Human Nocturnin Catalytic Domain with Bound Sulfate Anion, PDB code: 6bt2:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Structure of the Human Nocturnin Catalytic Domain with Bound Sulfate Anion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of the Human Nocturnin Catalytic Domain with Bound Sulfate Anion within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:37.4 occ:1.00 O A:HOH641 1.7 26.5 1.0 O A:HOH611 2.0 27.9 1.0 O A:HOH644 2.0 19.8 1.0 O A:HOH629 2.0 37.2 1.0 OE2 A:GLU195 2.3 34.1 1.0 O A:HOH689 2.3 32.4 1.0 CD A:GLU195 3.2 40.4 1.0 O A:HOH701 3.4 20.6 1.0 OE1 A:GLU195 3.4 32.1 1.0 MG A:MG502 3.8 19.8 1.0 O A:HOH620 3.9 27.0 1.0 NE2 A:HIS414 4.0 30.4 1.0 ND2 A:ASN149 4.0 22.4 1.0 OD2 A:ASP413 4.0 47.9 1.0 O A:HOH682 4.1 42.8 1.0 OD1 A:ASP413 4.2 37.9 1.0 OD1 A:ASN149 4.3 38.8 1.0 O A:HOH661 4.4 44.8 1.0 CD2 A:HIS414 4.5 32.1 1.0 CD1 A:LEU151 4.5 27.6 1.0 CG A:GLU195 4.5 37.9 1.0 CG A:ASN149 4.6 32.2 1.0 CG A:ASP413 4.6 45.4 1.0 O A:HOH692 4.6 71.5 1.0 O A:HOH696 4.8 33.9 1.0 O A:HOH704 4.9 51.2 1.0

Magnesium binding site 2 out of 4 in the Structure of the Human Nocturnin Catalytic Domain with Bound Sulfate Anion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of the Human Nocturnin Catalytic Domain with Bound Sulfate Anion within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:19.8 occ:1.00 O A:HOH620 1.9 27.0 1.0 O A:HOH641 2.1 26.5 1.0 O A:HOH701 2.1 20.6 1.0 O A:HOH692 2.7 71.5 1.0 OD1 A:ASN326 3.1 30.8 1.0 OD2 A:ASP324 3.1 36.8 1.0 NE2 A:HIS414 3.4 30.4 1.0 ND2 A:ASN326 3.5 30.0 1.0 CE1 A:HIS414 3.6 27.6 1.0 O A:HOH704 3.7 51.2 1.0 CG A:ASN326 3.7 29.6 1.0 MG A:MG501 3.8 37.4 1.0 CG A:ASP324 4.0 27.5 1.0 O A:HOH689 4.1 32.4 1.0 OD1 A:ASP324 4.1 26.8 1.0 O A:HOH696 4.2 33.9 1.0 O A:HOH611 4.2 27.9 1.0 ND2 A:ASN149 4.2 22.4 1.0 NE2 A:HIS286 4.3 25.5 1.0 OE2 A:GLU195 4.5 34.1 1.0 CB A:ALA289 4.5 25.6 1.0 O A:HOH698 4.6 42.2 1.0 CD2 A:HIS414 4.7 32.1 1.0 CD1 A:LEU376 4.8 30.8 1.0 O A:HOH644 4.8 19.8 1.0 ND1 A:HIS414 4.9 28.8 1.0 O A:HOH625 4.9 29.0 1.0

Magnesium binding site 3 out of 4 in the Structure of the Human Nocturnin Catalytic Domain with Bound Sulfate Anion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of the Human Nocturnin Catalytic Domain with Bound Sulfate Anion within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg501 b:34.6 occ:1.00 OE2 B:GLU195 2.0 26.7 1.0 O B:HOH672 2.0 28.3 1.0 O B:HOH639 2.0 25.1 1.0 O B:HOH636 2.1 26.5 1.0 O B:HOH708 2.2 31.1 1.0 O B:HOH634 2.4 21.6 1.0 CD B:GLU195 2.9 35.9 1.0 OE1 B:GLU195 3.2 25.9 1.0 O B:HOH710 3.5 52.2 1.0 O B:HOH673 3.6 38.0 1.0 MG B:MG502 4.0 39.3 1.0 O B:HOH631 4.1 30.9 1.0 ND2 B:ASN149 4.1 24.7 1.0 CG B:GLU195 4.3 29.8 1.0 O B:HOH706 4.3 35.5 1.0 OD1 B:ASN149 4.3 28.8 1.0 OD2 B:ASP413 4.4 42.9 1.0 O B:HOH700 4.5 52.3 1.0 NE2 B:HIS414 4.5 41.4 1.0 OD1 B:ASP413 4.6 35.7 1.0 CG B:ASN149 4.6 34.0 1.0 CD1 B:LEU151 4.9 29.4 1.0 CD1 B:LEU155 4.9 34.1 1.0 CG B:ASP413 5.0 39.1 1.0

Magnesium binding site 4 out of 4 in the Structure of the Human Nocturnin Catalytic Domain with Bound Sulfate Anion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of the Human Nocturnin Catalytic Domain with Bound Sulfate Anion within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:39.3 occ:1.00 O B:HOH631 1.8 30.9 1.0 O B:HOH710 1.9 52.2 1.0 O B:HOH672 2.1 28.3 1.0 OD1 B:ASN326 2.7 27.7 1.0 OD2 B:ASP324 3.3 33.5 1.0 NE2 B:HIS414 3.6 41.4 1.0 CG B:ASN326 3.7 31.2 1.0 CE1 B:HIS414 3.8 37.7 1.0 O B:HOH708 3.8 31.1 1.0 ND2 B:ASN326 3.9 30.1 1.0 MG B:MG501 4.0 34.6 1.0 O B:HOH700 4.0 52.3 1.0 OD1 B:ASP324 4.1 38.8 1.0 CG B:ASP324 4.1 36.8 1.0 O B:HOH639 4.3 25.1 1.0 ND2 B:ASN149 4.3 24.7 1.0 NE2 B:HIS286 4.5 24.9 1.0 CD1 B:LEU376 4.5 39.4 1.0 OE2 B:GLU195 4.7 26.7 1.0 CD2 B:HIS414 5.0 33.8 1.0

E.T Abshire, J.Chasseur, J.A.Bohn, P.A.Del Rizzo, P.L.Freddolino, A.C.Goldstrohm, R.C.Trievel. The Structure of Human Nocturnin Reveals A Conserved Ribonuclease Domain That Represses Target Transcript Translation and Abundance in Cells. Nucleic Acids Res. V. 46 6257 2018.
ISSN: ESSN 1362-4962
PubMed: 29860338
DOI: 10.1093/NAR/GKY412