Manganese in PDB 7tu2: Structure of the L. Blandensis Dgtpase R37A Mutant Bound to Mn

The structure of Structure of the L. Blandensis Dgtpase R37A Mutant Bound to Mn, PDB code: 7tu2 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)	36.22 / 2.13
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	179.934, 179.934, 110.941, 90, 90, 90
R / Rfree (%)	20.4 / 22.6

The binding sites of Manganese atom in the Structure of the L. Blandensis Dgtpase R37A Mutant Bound to Mn (pdb code 7tu2). 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 R37A Mutant Bound to Mn, PDB code: 7tu2:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in the Structure of the L. Blandensis Dgtpase R37A 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 R37A Mutant Bound to Mn within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn502 b:45.2 occ:1.00 NE2 A:HIS68 2.2 45.5 1.0 NE2 A:HIS116 2.2 46.0 1.0 OD2 A:ASP117 2.2 48.9 1.0 O A:HOH639 2.3 51.6 1.0 OD1 A:ASP253 2.3 43.8 1.0 O A:HOH605 2.5 43.5 1.0 CE1 A:HIS68 3.1 46.1 1.0 CE1 A:HIS116 3.2 43.8 1.0 CG A:ASP117 3.2 48.0 1.0 CD2 A:HIS68 3.2 45.8 1.0 CG A:ASP253 3.2 46.0 1.0 CD2 A:HIS116 3.2 44.8 1.0 OD2 A:ASP253 3.5 45.1 1.0 OD1 A:ASP117 3.5 47.0 1.0 O A:HOH669 3.7 51.3 1.0 NE2 A:GLN52 3.9 57.9 1.0 O A:HOH613 4.0 50.6 1.0 ND1 A:HIS68 4.3 46.9 1.0 ND1 A:HIS116 4.3 41.6 1.0 CG A:HIS68 4.3 47.5 1.0 CG A:HIS116 4.4 42.2 1.0 CB A:ASP117 4.5 45.1 1.0 CB A:ASP253 4.5 44.9 1.0 CG2 A:VAL72 4.8 42.4 1.0 CD2 A:TYR257 4.9 49.5 1.0 CD A:GLN52 4.9 59.3 1.0

Manganese binding site 2 out of 3 in the Structure of the L. Blandensis Dgtpase R37A 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 R37A Mutant Bound to Mn within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn502 b:47.5 occ:1.00 NE2 B:HIS116 2.2 50.4 1.0 OD2 B:ASP117 2.2 51.7 1.0 O B:HOH658 2.3 50.6 1.0 NE2 B:HIS68 2.3 52.5 1.0 OD1 B:ASP253 2.3 48.5 1.0 O B:HOH603 2.5 46.3 1.0 CE1 B:HIS116 3.1 49.5 1.0 CG B:ASP117 3.1 51.2 1.0 CG B:ASP253 3.2 49.3 1.0 CD2 B:HIS68 3.2 53.0 1.0 CE1 B:HIS68 3.2 53.2 1.0 CD2 B:HIS116 3.3 47.5 1.0 OD1 B:ASP117 3.4 50.9 1.0 OD2 B:ASP253 3.4 51.8 1.0 O B:HOH660 4.0 55.3 1.0 O B:HOH667 4.1 57.1 1.0 ND1 B:HIS116 4.2 47.6 1.0 NE2 B:GLN52 4.3 62.4 1.0 ND1 B:HIS68 4.3 54.6 1.0 CG B:HIS116 4.4 48.8 1.0 CG B:HIS68 4.4 54.0 1.0 CB B:ASP117 4.5 51.5 1.0 CB B:ASP253 4.5 48.0 1.0 CD2 B:TYR257 4.8 52.3 1.0 CG2 B:VAL72 4.9 48.5 1.0

Manganese binding site 3 out of 3 in the Structure of the L. Blandensis Dgtpase R37A 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 R37A Mutant Bound to Mn within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn502 b:75.1 occ:1.00 OD2 C:ASP117 2.0 61.6 1.0 O C:HOH605 2.2 54.9 1.0 NE2 C:HIS116 2.2 56.3 1.0 OD1 C:ASP253 2.2 55.6 1.0 NE2 C:HIS68 2.3 59.0 1.0 O C:HOH625 2.8 58.0 1.0 CG C:ASP253 3.1 55.3 1.0 CE1 C:HIS116 3.1 55.0 1.0 CG C:ASP117 3.1 60.6 1.0 CD2 C:HIS68 3.2 54.3 1.0 CD2 C:HIS116 3.2 50.4 1.0 OD2 C:ASP253 3.2 56.9 1.0 CE1 C:HIS68 3.3 56.9 1.0 OD1 C:ASP117 3.6 57.5 1.0 O C:HOH626 4.1 63.0 1.0 NE2 C:GLN52 4.1 72.8 1.0 ND1 C:HIS116 4.2 53.5 1.0 CG C:HIS116 4.3 53.2 1.0 CG C:HIS68 4.3 56.2 1.0 ND1 C:HIS68 4.4 53.0 1.0 CB C:ASP117 4.4 57.4 1.0 CB C:ASP253 4.4 53.5 1.0 CG2 C:VAL72 4.8 52.5 1.0 CD2 C:TYR257 4.9 58.0 1.0 CD C:GLN52 4.9 69.4 1.0 OE1 C:GLN52 4.9 71.0 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