Magnesium in PDB 7tu3: Structure of the L. Blandensis Dgtpase DEL55-58 Mutant

The structure of Structure of the L. Blandensis Dgtpase DEL55-58 Mutant, PDB code: 7tu3 was solved by A.P.Sikkema, B.P.Klemm, J.C.Horng, T.M.T.Hall, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.89 / 2.17
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	181.41, 181.41, 110.858, 90, 90, 90
R / Rfree (%)	19.4 / 22.2

The binding sites of Magnesium atom in the Structure of the L. Blandensis Dgtpase DEL55-58 Mutant (pdb code 7tu3). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Structure of the L. Blandensis Dgtpase DEL55-58 Mutant, PDB code: 7tu3:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Structure of the L. Blandensis Dgtpase DEL55-58 Mutant


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 L. Blandensis Dgtpase DEL55-58 Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg506 b:58.5 occ:1.00 O A:HOH663 2.2 73.8 1.0 NE2 A:HIS112 2.3 58.8 1.0 OD1 A:ASP249 2.3 61.1 1.0 NE2 A:HIS64 2.4 62.4 1.0 O A:HOH665 2.4 68.8 1.0 CD2 A:HIS112 2.9 60.0 1.0 CD2 A:HIS64 3.1 54.1 1.0 CG A:ASP249 3.3 59.4 1.0 CE1 A:HIS112 3.4 58.1 1.0 OD2 A:ASP249 3.5 67.7 1.0 CE1 A:HIS64 3.5 58.5 1.0 CG A:HIS112 4.2 57.5 1.0 CG A:HIS64 4.3 55.5 1.0 ND1 A:HIS112 4.4 58.2 1.0 ND1 A:HIS64 4.5 57.0 1.0 CG2 A:VAL68 4.6 47.3 1.0 CB A:ASP249 4.7 55.2 1.0 CB A:ASP113 4.9 52.5 1.0

Magnesium binding site 2 out of 3 in the Structure of the L. Blandensis Dgtpase DEL55-58 Mutant


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 L. Blandensis Dgtpase DEL55-58 Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg505 b:54.5 occ:1.00 NE2 B:HIS112 2.2 62.6 1.0 O B:HOH654 2.2 65.8 1.0 OD1 B:ASP249 2.2 67.8 1.0 O B:HOH669 2.3 69.8 1.0 NE2 B:HIS64 2.4 63.5 1.0 O B:HOH634 2.4 68.0 1.0 CD2 B:HIS112 2.9 63.8 1.0 CG B:ASP249 3.1 66.3 1.0 CD2 B:HIS64 3.3 59.9 1.0 CE1 B:HIS112 3.3 62.6 1.0 CE1 B:HIS64 3.4 61.3 1.0 OD2 B:ASP249 3.5 70.2 1.0 CG B:HIS112 4.1 60.8 1.0 ND1 B:HIS112 4.3 60.9 1.0 CB B:ASP249 4.4 62.3 1.0 CG B:HIS64 4.4 59.8 1.0 ND1 B:HIS64 4.5 60.6 1.0 CB B:ASP113 4.9 54.5 1.0 CG2 B:VAL68 5.0 59.7 1.0

Magnesium binding site 3 out of 3 in the Structure of the L. Blandensis Dgtpase DEL55-58 Mutant


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 L. Blandensis Dgtpase DEL55-58 Mutant within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg503 b:54.5 occ:1.00 NE2 C:HIS112 1.9 64.1 1.0 O C:HOH627 2.1 69.0 1.0 OD1 C:ASP249 2.2 66.0 1.0 NE2 C:HIS64 2.4 66.7 1.0 O C:HOH641 2.5 79.7 1.0 CD2 C:HIS112 2.7 63.9 1.0 CG C:ASP249 2.9 66.3 1.0 OD2 C:ASP249 3.0 62.8 1.0 CE1 C:HIS112 3.0 62.0 1.0 CD2 C:HIS64 3.2 62.1 1.0 CE1 C:HIS64 3.4 64.4 1.0 CG C:HIS112 3.9 60.7 1.0 ND1 C:HIS112 4.0 62.3 1.0 CB C:ASP249 4.3 58.1 1.0 CG C:HIS64 4.4 63.3 1.0 ND1 C:HIS64 4.5 64.8 1.0 CG2 C:VAL68 4.8 53.8 1.0

B.P.Klemm, A.P.Sikkema, A.L.Hsu, J.C.Horng, T.M.T.Hall, M.J.Borgnia, R.M.Schaaper. High-Resolution Structures of the SAMHD1 Dgtpase Homolog From Leeuwenhoekiella Blandensis Reveal A Novel Mechanism of Allosteric Activation By Datp. J.Biol.Chem. V. 298 02073 2022.
ISSN: ESSN 1083-351X
PubMed: 35643313
DOI: 10.1016/J.JBC.2022.102073