Magnesium in PDB 7tu7: Structure of the L. Blandensis Dgtpase H125A Mutant Bound to Dgtp

All present enzymatic activity of Structure of the L. Blandensis Dgtpase H125A Mutant Bound to Dgtp:
3.1.5.1;

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Magnesium atom in the Structure of the L. Blandensis Dgtpase H125A Mutant Bound to Dgtp (pdb code 7tu7). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 18 binding sites of Magnesium where determined in the Structure of the L. Blandensis Dgtpase H125A Mutant Bound to Dgtp, PDB code: 7tu7:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 18 in the Structure of the L. Blandensis Dgtpase H125A Mutant Bound to Dgtp


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 H125A Mutant Bound to Dgtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:33.3 occ:1.00 NE2 A:HIS68 1.9 45.2 1.0 NE2 A:HIS116 2.0 45.2 1.0 OD1 A:ASP253 2.4 45.2 1.0 CE1 A:HIS116 2.6 45.2 1.0 OD2 A:ASP117 2.6 45.2 1.0 O1A A:DGT501 2.7 43.4 1.0 CE1 A:HIS68 2.7 45.2 1.0 OD2 A:ASP253 3.0 45.2 1.0 CG A:ASP253 3.0 45.2 1.0 CD2 A:HIS68 3.1 45.2 1.0 CD2 A:HIS116 3.2 45.2 1.0 CG A:ASP117 3.3 45.2 1.0 ND1 A:HIS116 3.8 45.2 1.0 OD1 A:ASP117 3.9 45.2 1.0 ND1 A:HIS68 3.9 45.2 1.0 PA A:DGT501 4.0 43.4 1.0 NH1 A:ARG65 4.1 45.2 1.0 CB A:ASP117 4.1 45.2 1.0 CG A:HIS68 4.1 45.2 1.0 CG A:HIS116 4.1 45.2 1.0 O2A A:DGT501 4.3 43.4 1.0 CB A:ASP253 4.5 45.2 1.0 MG A:MG503 4.6 47.0 1.0 CG2 A:VAL72 4.7 45.2 1.0 O3A A:DGT501 4.9 43.4 1.0

Magnesium binding site 2 out of 18 in the Structure of the L. Blandensis Dgtpase H125A Mutant Bound to Dgtp


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 H125A Mutant Bound to Dgtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:47.0 occ:1.00 OD1 A:ASP117 2.2 45.2 1.0 O2A A:DGT501 2.3 43.4 1.0 O2G A:DGT501 2.8 43.4 1.0 CG A:ASP117 3.3 45.2 1.0 PA A:DGT501 3.5 43.4 1.0 OD2 A:ASP117 3.9 45.2 1.0 O3A A:DGT501 3.9 43.4 1.0 O1A A:DGT501 4.0 43.4 1.0 PG A:DGT501 4.0 43.4 1.0 O A:HIS116 4.1 45.2 1.0 OD1 A:ASN120 4.2 45.2 1.0 CD2 A:HIS116 4.2 45.2 1.0 O1G A:DGT501 4.3 43.4 1.0 CB A:ASP117 4.4 45.2 1.0 NE2 A:HIS116 4.5 45.2 1.0 O3B A:DGT501 4.5 43.4 1.0 CA A:ASP117 4.5 45.2 1.0 ND2 A:ASN120 4.6 45.2 1.0 MG A:MG502 4.6 33.3 1.0 OD1 A:ASN161 4.6 45.2 1.0 OD2 A:ASP253 4.7 45.2 1.0 NH1 A:ARG65 4.7 45.2 1.0 O5' A:DGT501 4.7 43.4 1.0 CG A:ASN120 4.8 45.2 1.0 PB A:DGT501 5.0 43.4 1.0

Magnesium binding site 3 out of 18 in the Structure of the L. Blandensis Dgtpase H125A Mutant Bound to Dgtp


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 H125A Mutant Bound to Dgtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg504 b:45.3 occ:1.00 O2B A:DGT501 2.2 43.4 1.0 O1G A:DGT501 2.4 43.4 1.0 PB A:DGT501 3.2 43.4 1.0 O3B A:DGT501 3.3 43.4 1.0 PG A:DGT501 3.3 43.4 1.0 O3A A:DGT501 3.5 43.4 1.0 NZ A:LYS191 3.6 45.2 1.0 O3G A:DGT501 4.2 43.4 1.0 O1B A:DGT501 4.5 43.4 1.0 O2G A:DGT501 4.6 43.4 1.0 OD2 A:ASP254 4.6 45.2 1.0 OD2 A:ASP253 4.6 45.2 1.0 CE A:LYS191 4.7 45.2 1.0 OE2 A:GLU250 4.7 45.2 1.0 OD1 A:ASP254 4.7 45.2 1.0 CE2 A:TYR257 4.7 45.2 1.0 OH A:TYR257 4.8 45.2 1.0 CG A:ASP254 4.9 45.2 1.0 PA A:DGT501 5.0 43.4 1.0 CG A:GLU250 5.0 45.2 1.0

Magnesium binding site 4 out of 18 in the Structure of the L. Blandensis Dgtpase H125A Mutant Bound to Dgtp


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 L. Blandensis Dgtpase H125A Mutant Bound to Dgtp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:33.3 occ:1.00 NE2 B:HIS68 1.9 45.2 1.0 NE2 B:HIS116 2.0 45.2 1.0 OD1 B:ASP253 2.4 45.2 1.0 CE1 B:HIS116 2.6 45.2 1.0 OD2 B:ASP117 2.6 45.2 1.0 O1A B:DGT501 2.7 43.4 1.0 CE1 B:HIS68 2.7 45.2 1.0 OD2 B:ASP253 3.0 45.2 1.0 CG B:ASP253 3.0 45.2 1.0 CD2 B:HIS68 3.1 45.2 1.0 CD2 B:HIS116 3.2 45.2 1.0 CG B:ASP117 3.3 45.2 1.0 ND1 B:HIS116 3.8 45.2 1.0 OD1 B:ASP117 3.9 45.2 1.0 ND1 B:HIS68 3.9 45.2 1.0 PA B:DGT501 4.0 43.4 1.0 NH1 B:ARG65 4.1 45.2 1.0 CB B:ASP117 4.1 45.2 1.0 CG B:HIS68 4.1 45.2 1.0 CG B:HIS116 4.1 45.2 1.0 O2A B:DGT501 4.3 43.4 1.0 CB B:ASP253 4.5 45.2 1.0 MG B:MG503 4.6 47.0 1.0 CG2 B:VAL72 4.7 45.2 1.0 O3A B:DGT501 4.9 43.4 1.0

Magnesium binding site 5 out of 18 in the Structure of the L. Blandensis Dgtpase H125A Mutant Bound to Dgtp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of the L. Blandensis Dgtpase H125A Mutant Bound to Dgtp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg503 b:47.0 occ:1.00 OD1 B:ASP117 2.2 45.2 1.0 O2A B:DGT501 2.3 43.4 1.0 O2G B:DGT501 2.8 43.4 1.0 CG B:ASP117 3.3 45.2 1.0 PA B:DGT501 3.5 43.4 1.0 OD2 B:ASP117 3.9 45.2 1.0 O3A B:DGT501 3.9 43.4 1.0 O1A B:DGT501 4.0 43.4 1.0 PG B:DGT501 4.0 43.4 1.0 O B:HIS116 4.1 45.2 1.0 OD1 B:ASN120 4.2 45.2 1.0 CD2 B:HIS116 4.2 45.2 1.0 O1G B:DGT501 4.3 43.4 1.0 CB B:ASP117 4.4 45.2 1.0 NE2 B:HIS116 4.5 45.2 1.0 O3B B:DGT501 4.5 43.4 1.0 CA B:ASP117 4.5 45.2 1.0 ND2 B:ASN120 4.6 45.2 1.0 MG B:MG502 4.6 33.3 1.0 OD1 B:ASN161 4.6 45.2 1.0 OD2 B:ASP253 4.7 45.2 1.0 NH1 B:ARG65 4.7 45.2 1.0 O5' B:DGT501 4.7 43.4 1.0 CG B:ASN120 4.8 45.2 1.0 PB B:DGT501 5.0 43.4 1.0

Magnesium binding site 6 out of 18 in the Structure of the L. Blandensis Dgtpase H125A Mutant Bound to Dgtp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of the L. Blandensis Dgtpase H125A Mutant Bound to Dgtp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg504 b:45.3 occ:1.00 O2B B:DGT501 2.2 43.4 1.0 O1G B:DGT501 2.4 43.4 1.0 PB B:DGT501 3.2 43.4 1.0 O3B B:DGT501 3.3 43.4 1.0 PG B:DGT501 3.3 43.4 1.0 O3A B:DGT501 3.5 43.4 1.0 NZ B:LYS191 3.6 45.2 1.0 O3G B:DGT501 4.2 43.4 1.0 O1B B:DGT501 4.5 43.4 1.0 O2G B:DGT501 4.6 43.4 1.0 OD2 B:ASP254 4.6 45.2 1.0 OD2 B:ASP253 4.6 45.2 1.0 CE B:LYS191 4.7 45.2 1.0 OE2 B:GLU250 4.7 45.2 1.0 OD1 B:ASP254 4.7 45.2 1.0 CE2 B:TYR257 4.7 45.2 1.0 OH B:TYR257 4.8 45.2 1.0 CG B:ASP254 4.9 45.2 1.0 PA B:DGT501 5.0 43.4 1.0 CG B:GLU250 5.0 45.2 1.0

Magnesium binding site 7 out of 18 in the Structure of the L. Blandensis Dgtpase H125A Mutant Bound to Dgtp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure of the L. Blandensis Dgtpase H125A Mutant Bound to Dgtp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:33.3 occ:1.00 NE2 C:HIS68 1.9 45.2 1.0 NE2 C:HIS116 2.0 45.2 1.0 OD1 C:ASP253 2.4 45.2 1.0 CE1 C:HIS116 2.6 45.2 1.0 OD2 C:ASP117 2.6 45.2 1.0 O1A C:DGT501 2.7 43.4 1.0 CE1 C:HIS68 2.7 45.2 1.0 OD2 C:ASP253 3.0 45.2 1.0 CG C:ASP253 3.0 45.2 1.0 CD2 C:HIS68 3.1 45.2 1.0 CD2 C:HIS116 3.2 45.2 1.0 CG C:ASP117 3.3 45.2 1.0 ND1 C:HIS116 3.8 45.2 1.0 OD1 C:ASP117 3.9 45.2 1.0 ND1 C:HIS68 3.9 45.2 1.0 PA C:DGT501 4.0 43.4 1.0 NH1 C:ARG65 4.1 45.2 1.0 CB C:ASP117 4.1 45.2 1.0 CG C:HIS68 4.1 45.2 1.0 CG C:HIS116 4.1 45.2 1.0 O2A C:DGT501 4.3 43.4 1.0 CB C:ASP253 4.5 45.2 1.0 MG C:MG503 4.6 47.0 1.0 CG2 C:VAL72 4.7 45.2 1.0 O3A C:DGT501 4.9 43.4 1.0

Magnesium binding site 8 out of 18 in the Structure of the L. Blandensis Dgtpase H125A Mutant Bound to Dgtp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structure of the L. Blandensis Dgtpase H125A Mutant Bound to Dgtp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg503 b:47.0 occ:1.00 OD1 C:ASP117 2.2 45.2 1.0 O2A C:DGT501 2.3 43.4 1.0 O2G C:DGT501 2.8 43.4 1.0 CG C:ASP117 3.3 45.2 1.0 PA C:DGT501 3.5 43.4 1.0 OD2 C:ASP117 3.9 45.2 1.0 O3A C:DGT501 3.9 43.4 1.0 O1A C:DGT501 4.0 43.4 1.0 PG C:DGT501 4.0 43.4 1.0 O C:HIS116 4.1 45.2 1.0 OD1 C:ASN120 4.2 45.2 1.0 CD2 C:HIS116 4.2 45.2 1.0 O1G C:DGT501 4.3 43.4 1.0 CB C:ASP117 4.4 45.2 1.0 NE2 C:HIS116 4.5 45.2 1.0 O3B C:DGT501 4.5 43.4 1.0 CA C:ASP117 4.5 45.2 1.0 ND2 C:ASN120 4.6 45.2 1.0 MG C:MG502 4.6 33.3 1.0 OD1 C:ASN161 4.6 45.2 1.0 OD2 C:ASP253 4.7 45.2 1.0 NH1 C:ARG65 4.7 45.2 1.0 O5' C:DGT501 4.7 43.4 1.0 CG C:ASN120 4.8 45.2 1.0 PB C:DGT501 5.0 43.4 1.0

Magnesium binding site 9 out of 18 in the Structure of the L. Blandensis Dgtpase H125A Mutant Bound to Dgtp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Structure of the L. Blandensis Dgtpase H125A Mutant Bound to Dgtp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg504 b:45.3 occ:1.00 O2B C:DGT501 2.2 43.4 1.0 O1G C:DGT501 2.4 43.4 1.0 PB C:DGT501 3.2 43.4 1.0 O3B C:DGT501 3.3 43.4 1.0 PG C:DGT501 3.3 43.4 1.0 O3A C:DGT501 3.5 43.4 1.0 NZ C:LYS191 3.6 45.2 1.0 O3G C:DGT501 4.2 43.4 1.0 O1B C:DGT501 4.5 43.4 1.0 O2G C:DGT501 4.6 43.4 1.0 OD2 C:ASP254 4.6 45.2 1.0 OD2 C:ASP253 4.6 45.2 1.0 CE C:LYS191 4.7 45.2 1.0 OE2 C:GLU250 4.7 45.2 1.0 OD1 C:ASP254 4.7 45.2 1.0 CE2 C:TYR257 4.7 45.2 1.0 OH C:TYR257 4.8 45.2 1.0 CG C:ASP254 4.9 45.2 1.0 PA C:DGT501 5.0 43.4 1.0 CG C:GLU250 5.0 45.2 1.0

Magnesium binding site 10 out of 18 in the Structure of the L. Blandensis Dgtpase H125A Mutant Bound to Dgtp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Structure of the L. Blandensis Dgtpase H125A Mutant Bound to Dgtp within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:33.3 occ:1.00 NE2 D:HIS68 1.9 45.2 1.0 NE2 D:HIS116 2.0 45.2 1.0 OD1 D:ASP253 2.4 45.2 1.0 CE1 D:HIS116 2.6 45.2 1.0 OD2 D:ASP117 2.6 45.2 1.0 O1A D:DGT501 2.7 43.4 1.0 CE1 D:HIS68 2.7 45.2 1.0 OD2 D:ASP253 3.0 45.2 1.0 CG D:ASP253 3.0 45.2 1.0 CD2 D:HIS68 3.1 45.2 1.0 CD2 D:HIS116 3.2 45.2 1.0 CG D:ASP117 3.3 45.2 1.0 ND1 D:HIS116 3.8 45.2 1.0 OD1 D:ASP117 3.9 45.2 1.0 ND1 D:HIS68 3.9 45.2 1.0 PA D:DGT501 4.0 43.4 1.0 NH1 D:ARG65 4.1 45.2 1.0 CG D:HIS68 4.1 45.2 1.0 CB D:ASP117 4.1 45.2 1.0 CG D:HIS116 4.1 45.2 1.0 O2A D:DGT501 4.3 43.4 1.0 CB D:ASP253 4.5 45.2 1.0 MG D:MG503 4.6 47.0 1.0 CG2 D:VAL72 4.7 45.2 1.0 O3A D:DGT501 4.9 43.4 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