Manganese in PDB 7tu4: Structure of the L. Blandensis Dgtpase DEL55-58 Mutant Bound to Mn

The structure of Structure of the L. Blandensis Dgtpase DEL55-58 Mutant Bound to Mn, PDB code: 7tu4 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)	40.56 / 2.26
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	181.397, 181.397, 110.369, 90, 90, 90
R / Rfree (%)	19.8 / 22.8

The binding sites of Manganese atom in the Structure of the L. Blandensis Dgtpase DEL55-58 Mutant Bound to Mn (pdb code 7tu4). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the Structure of the L. Blandensis Dgtpase DEL55-58 Mutant Bound to Mn, PDB code: 7tu4:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in the Structure of the L. Blandensis Dgtpase DEL55-58 Mutant Bound to Mn


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Structure of the L. Blandensis Dgtpase DEL55-58 Mutant Bound to Mn within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn504 b:44.4 occ:1.00 O A:HOH648 2.1 53.4 1.0 OD1 A:ASP249 2.2 49.9 1.0 O A:HOH660 2.2 55.5 1.0 NE2 A:HIS112 2.2 50.8 1.0 NE2 A:HIS64 2.3 54.0 1.0 O A:HOH628 2.5 50.0 1.0 CG A:ASP249 3.0 47.7 1.0 CE1 A:HIS64 3.1 52.5 1.0 CE1 A:HIS112 3.2 46.1 1.0 CD2 A:HIS112 3.2 46.3 1.0 OD2 A:ASP249 3.3 50.0 1.0 CD2 A:HIS64 3.3 48.5 1.0 O A:HOH659 4.1 59.4 1.0 ND1 A:HIS64 4.3 50.6 1.0 ND1 A:HIS112 4.3 44.4 1.0 CB A:ASP249 4.3 46.6 1.0 CG A:HIS112 4.4 45.5 1.0 CG A:HIS64 4.4 51.3 1.0 CG2 A:VAL68 4.7 44.4 1.0 OE1 A:GLN52 4.8 81.7 1.0

Manganese binding site 2 out of 3 in the Structure of the L. Blandensis Dgtpase DEL55-58 Mutant Bound to Mn


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Structure of the L. Blandensis Dgtpase DEL55-58 Mutant Bound to Mn within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn504 b:52.5 occ:1.00 NE2 B:HIS64 2.0 56.5 1.0 OD1 B:ASP249 2.2 58.9 1.0 NE2 B:HIS112 2.2 56.1 1.0 O B:HOH649 2.3 66.6 1.0 O B:HOH614 2.4 53.3 1.0 O B:HOH657 2.5 61.0 1.0 CE1 B:HIS64 3.0 57.2 1.0 CD2 B:HIS64 3.0 56.8 1.0 CE1 B:HIS112 3.2 54.5 1.0 CG B:ASP249 3.2 56.2 1.0 CD2 B:HIS112 3.2 55.7 1.0 OD2 B:ASP249 3.6 59.6 1.0 O B:HOH658 3.6 60.4 1.0 ND1 B:HIS64 4.1 57.6 1.0 CG B:HIS64 4.2 57.9 1.0 ND1 B:HIS112 4.3 52.4 1.0 CG B:HIS112 4.4 52.0 1.0 CB B:ASP249 4.5 57.9 1.0 CG2 B:VAL68 4.9 55.0 1.0 CB B:ASP113 4.9 53.0 1.0

Manganese binding site 3 out of 3 in the Structure of the L. Blandensis Dgtpase DEL55-58 Mutant Bound to Mn


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Structure of the L. Blandensis Dgtpase DEL55-58 Mutant Bound to Mn within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn503 b:63.3 occ:1.00 OD1 C:ASP249 2.2 60.5 1.0 NE2 C:HIS64 2.2 57.1 1.0 NE2 C:HIS112 2.2 58.3 1.0 O C:HOH610 2.2 56.1 1.0 O C:HOH633 2.3 59.0 1.0 O C:HOH635 2.3 59.3 1.0 CE1 C:HIS112 3.0 55.5 1.0 CG C:ASP249 3.0 59.6 1.0 CD2 C:HIS64 3.1 52.8 1.0 CE1 C:HIS64 3.2 53.9 1.0 OD2 C:ASP249 3.3 60.3 1.0 CD2 C:HIS112 3.3 53.4 1.0 O C:HOH638 4.1 60.6 1.0 ND1 C:HIS112 4.2 52.4 1.0 ND1 C:HIS64 4.3 59.9 1.0 CG C:HIS64 4.3 58.5 1.0 CG C:HIS112 4.3 54.6 1.0 CB C:ASP249 4.4 54.6 1.0 CG2 C:VAL68 4.7 50.3 1.0 CB C:ASP113 4.8 59.6 1.0 CA C:ASP249 5.0 55.1 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