Magnesium in PDB 7tu8: Structure of the L. Blandensis Dgtpase H125A Mutant Bound to Dgtp and Datp

Enzymatic activity of Structure of the L. Blandensis Dgtpase H125A Mutant Bound to Dgtp and Datp

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

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Magnesium atom in the Structure of the L. Blandensis Dgtpase H125A Mutant Bound to Dgtp and Datp (pdb code 7tu8). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 12 binding sites of Magnesium where determined in the Structure of the L. Blandensis Dgtpase H125A Mutant Bound to Dgtp and Datp, PDB code: 7tu8:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 12 in 7tu8

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Magnesium binding site 1 out of 12 in the Structure of the L. Blandensis Dgtpase H125A Mutant Bound to Dgtp and Datp


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 and Datp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg503

b:34.6
occ:1.00
 NE2 A:HIS116 1.9 45.3 1.0
NE2 A:HIS68 2.0 45.3 1.0
OD1 A:ASP117 2.2 45.3 1.0
OD1 A:ASP253 2.4 45.3 1.0
CE1 A:HIS116 2.6 45.3 1.0
CE1 A:HIS68 3.0 45.3 1.0
CD2 A:HIS68 3.0 45.3 1.0
CD2 A:HIS116 3.1 45.3 1.0
CG A:ASP117 3.1 45.3 1.0
CG A:ASP253 3.4 45.3 1.0
OD2 A:ASP117 3.5 45.3 1.0
ND1 A:HIS116 3.8 45.3 1.0
OD2 A:ASP253 3.9 45.3 1.0
CG A:HIS116 4.0 45.3 1.0
ND1 A:HIS68 4.1 45.3 1.0
CG A:HIS68 4.1 45.3 1.0
O1A A:DGT501 4.2 46.2 1.0
NH1 A:ARG65 4.3 45.3 1.0
CB A:ASP117 4.4 45.3 1.0
CB A:ASP253 4.5 45.3 1.0
CG2 A:VAL72 4.9 45.3 1.0

Magnesium binding site 2 out of 12 in 7tu8

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Magnesium binding site 2 out of 12 in the Structure of the L. Blandensis Dgtpase H125A Mutant Bound to Dgtp and Datp


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 and Datp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg504

b:43.4
occ:1.00
 O1G A:DTP502 2.2 42.5 1.0
O2B A:DTP502 2.8 42.5 1.0
O2A A:DTP502 2.8 42.5 1.0
O3A A:DTP502 3.0 42.5 1.0
O3B A:DTP502 3.0 42.5 1.0
PG A:DTP502 3.2 42.5 1.0
PB A:DTP502 3.2 42.5 1.0
PA A:DTP502 3.6 42.5 1.0
O2G A:DTP502 4.2 42.5 1.0
O3G A:DTP502 4.2 42.5 1.0
N7 A:DTP502 4.5 42.5 1.0
O5' A:DTP502 4.5 42.5 1.0
NH1 A:ARG28 4.6 45.3 1.0
O1B A:DTP502 4.7 42.5 1.0
O B:ALA308 4.7 45.3 1.0
O1A A:DTP502 4.7 42.5 1.0
C8 A:DTP502 4.8 42.5 1.0

Magnesium binding site 3 out of 12 in 7tu8

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Magnesium binding site 3 out of 12 in the Structure of the L. Blandensis Dgtpase H125A Mutant Bound to Dgtp and Datp


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 and Datp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg505

b:43.4
occ:1.00
 O1G B:DTP502 2.2 42.5 1.0
O2B B:DTP502 2.8 42.5 1.0
O2A B:DTP502 2.8 42.5 1.0
O3A B:DTP502 3.0 42.5 1.0
O3B B:DTP502 3.0 42.5 1.0
PG B:DTP502 3.2 42.5 1.0
PB B:DTP502 3.2 42.5 1.0
PA B:DTP502 3.6 42.5 1.0
O2G B:DTP502 4.2 42.5 1.0
O3G B:DTP502 4.2 42.5 1.0
N7 B:DTP502 4.5 42.5 1.0
O5' B:DTP502 4.5 42.5 1.0
NH1 B:ARG28 4.6 45.3 1.0
O A:ALA308 4.6 45.3 1.0
O1B B:DTP502 4.7 42.5 1.0
O1A B:DTP502 4.7 42.5 1.0
C8 B:DTP502 4.8 42.5 1.0

Magnesium binding site 4 out of 12 in 7tu8

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Magnesium binding site 4 out of 12 in the Structure of the L. Blandensis Dgtpase H125A Mutant Bound to Dgtp and Datp


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 and Datp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg503

b:34.6
occ:1.00
 NE2 B:HIS116 1.9 45.3 1.0
NE2 B:HIS68 2.0 45.3 1.0
OD1 B:ASP117 2.2 45.3 1.0
OD1 B:ASP253 2.4 45.3 1.0
CE1 B:HIS116 2.6 45.3 1.0
CE1 B:HIS68 3.0 45.3 1.0
CD2 B:HIS68 3.0 45.3 1.0
CD2 B:HIS116 3.1 45.3 1.0
CG B:ASP117 3.1 45.3 1.0
CG B:ASP253 3.4 45.3 1.0
OD2 B:ASP117 3.5 45.3 1.0
ND1 B:HIS116 3.8 45.3 1.0
OD2 B:ASP253 3.9 45.3 1.0
CG B:HIS116 4.0 45.3 1.0
ND1 B:HIS68 4.1 45.3 1.0
CG B:HIS68 4.1 45.3 1.0
O1A B:DGT501 4.2 46.2 1.0
NH1 B:ARG65 4.3 45.3 1.0
CB B:ASP117 4.4 45.3 1.0
CB B:ASP253 4.5 45.3 1.0
CG2 B:VAL72 4.9 45.3 1.0

Magnesium binding site 5 out of 12 in 7tu8

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Magnesium binding site 5 out of 12 in the Structure of the L. Blandensis Dgtpase H125A Mutant Bound to Dgtp and Datp


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 and Datp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg503

b:34.6
occ:1.00
 NE2 C:HIS116 1.9 45.3 1.0
NE2 C:HIS68 2.0 45.3 1.0
OD1 C:ASP117 2.2 45.3 1.0
OD1 C:ASP253 2.4 45.3 1.0
CE1 C:HIS116 2.6 45.3 1.0
CE1 C:HIS68 3.0 45.3 1.0
CD2 C:HIS68 3.0 45.3 1.0
CD2 C:HIS116 3.1 45.3 1.0
CG C:ASP117 3.1 45.3 1.0
CG C:ASP253 3.4 45.3 1.0
OD2 C:ASP117 3.5 45.3 1.0
ND1 C:HIS116 3.8 45.3 1.0
OD2 C:ASP253 3.9 45.3 1.0
CG C:HIS116 4.0 45.3 1.0
ND1 C:HIS68 4.1 45.3 1.0
CG C:HIS68 4.1 45.3 1.0
O1A C:DGT501 4.2 46.2 1.0
NH1 C:ARG65 4.3 45.3 1.0
CB C:ASP117 4.4 45.3 1.0
CB C:ASP253 4.5 45.3 1.0
CG2 C:VAL72 4.9 45.3 1.0

Magnesium binding site 6 out of 12 in 7tu8

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Magnesium binding site 6 out of 12 in the Structure of the L. Blandensis Dgtpase H125A Mutant Bound to Dgtp and Datp


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 and Datp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg504

b:43.4
occ:1.00
 O1G C:DTP502 2.2 42.5 1.0
O2B C:DTP502 2.8 42.5 1.0
O2A C:DTP502 2.8 42.5 1.0
O3A C:DTP502 3.0 42.5 1.0
O3B C:DTP502 3.0 42.5 1.0
PG C:DTP502 3.2 42.5 1.0
PB C:DTP502 3.2 42.5 1.0
PA C:DTP502 3.6 42.5 1.0
O2G C:DTP502 4.2 42.5 1.0
O3G C:DTP502 4.2 42.5 1.0
N7 C:DTP502 4.5 42.5 1.0
O5' C:DTP502 4.5 42.5 1.0
NH1 C:ARG28 4.6 45.3 1.0
O D:ALA308 4.7 45.3 1.0
O1B C:DTP502 4.7 42.5 1.0
O1A C:DTP502 4.7 42.5 1.0
C8 C:DTP502 4.8 42.5 1.0

Magnesium binding site 7 out of 12 in 7tu8

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Magnesium binding site 7 out of 12 in the Structure of the L. Blandensis Dgtpase H125A Mutant Bound to Dgtp and Datp


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 and Datp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg505

b:43.4
occ:1.00
 O1G D:DTP502 2.2 42.5 1.0
O2B D:DTP502 2.8 42.5 1.0
O2A D:DTP502 2.8 42.5 1.0
O3A D:DTP502 3.0 42.5 1.0
O3B D:DTP502 3.0 42.5 1.0
PG D:DTP502 3.2 42.5 1.0
PB D:DTP502 3.2 42.5 1.0
PA D:DTP502 3.6 42.5 1.0
O2G D:DTP502 4.2 42.5 1.0
O3G D:DTP502 4.2 42.5 1.0
N7 D:DTP502 4.5 42.5 1.0
O5' D:DTP502 4.5 42.5 1.0
NH1 D:ARG28 4.6 45.3 1.0
O1B D:DTP502 4.7 42.5 1.0
O C:ALA308 4.7 45.3 1.0
O1A D:DTP502 4.7 42.5 1.0
C8 D:DTP502 4.8 42.5 1.0

Magnesium binding site 8 out of 12 in 7tu8

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Magnesium binding site 8 out of 12 in the Structure of the L. Blandensis Dgtpase H125A Mutant Bound to Dgtp and Datp


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 and Datp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg503

b:34.6
occ:1.00
 NE2 D:HIS116 1.9 45.3 1.0
NE2 D:HIS68 2.0 45.3 1.0
OD1 D:ASP117 2.2 45.3 1.0
OD1 D:ASP253 2.4 45.3 1.0
CE1 D:HIS116 2.6 45.3 1.0
CE1 D:HIS68 3.0 45.3 1.0
CD2 D:HIS68 3.0 45.3 1.0
CD2 D:HIS116 3.1 45.3 1.0
CG D:ASP117 3.1 45.3 1.0
CG D:ASP253 3.4 45.3 1.0
OD2 D:ASP117 3.5 45.3 1.0
ND1 D:HIS116 3.8 45.3 1.0
OD2 D:ASP253 3.9 45.3 1.0
CG D:HIS116 4.0 45.3 1.0
ND1 D:HIS68 4.1 45.3 1.0
CG D:HIS68 4.1 45.3 1.0
O1A D:DGT501 4.2 46.2 1.0
NH1 D:ARG65 4.3 45.3 1.0
CB D:ASP117 4.4 45.3 1.0
CB D:ASP253 4.5 45.3 1.0
CG2 D:VAL72 4.9 45.3 1.0

Magnesium binding site 9 out of 12 in 7tu8

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Magnesium binding site 9 out of 12 in the Structure of the L. Blandensis Dgtpase H125A Mutant Bound to Dgtp and Datp


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 and Datp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg503

b:34.6
occ:1.00
 NE2 E:HIS116 1.9 45.3 1.0
NE2 E:HIS68 2.0 45.3 1.0
OD1 E:ASP117 2.2 45.3 1.0
OD1 E:ASP253 2.4 45.3 1.0
CE1 E:HIS116 2.6 45.3 1.0
CE1 E:HIS68 3.0 45.3 1.0
CD2 E:HIS68 3.0 45.3 1.0
CD2 E:HIS116 3.1 45.3 1.0
CG E:ASP117 3.1 45.3 1.0
CG E:ASP253 3.4 45.3 1.0
OD2 E:ASP117 3.5 45.3 1.0
ND1 E:HIS116 3.8 45.3 1.0
OD2 E:ASP253 3.9 45.3 1.0
CG E:HIS116 4.0 45.3 1.0
ND1 E:HIS68 4.1 45.3 1.0
CG E:HIS68 4.1 45.3 1.0
O1A E:DGT501 4.2 46.2 1.0
NH1 E:ARG65 4.3 45.3 1.0
CB E:ASP117 4.4 45.3 1.0
CB E:ASP253 4.5 45.3 1.0
CG2 E:VAL72 4.9 45.3 1.0

Magnesium binding site 10 out of 12 in 7tu8

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Magnesium binding site 10 out of 12 in the Structure of the L. Blandensis Dgtpase H125A Mutant Bound to Dgtp and Datp


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 and Datp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg504

b:43.4
occ:1.00
 O1G E:DTP502 2.2 42.5 1.0
O2B E:DTP502 2.8 42.5 1.0
O2A E:DTP502 2.8 42.5 1.0
O3A E:DTP502 3.0 42.5 1.0
O3B E:DTP502 3.0 42.5 1.0
PG E:DTP502 3.2 42.5 1.0
PB E:DTP502 3.2 42.5 1.0
PA E:DTP502 3.6 42.5 1.0
O2G E:DTP502 4.2 42.5 1.0
O3G E:DTP502 4.2 42.5 1.0
N7 E:DTP502 4.5 42.5 1.0
O5' E:DTP502 4.5 42.5 1.0
NH1 E:ARG28 4.6 45.3 1.0
O F:ALA308 4.6 45.3 1.0
O1B E:DTP502 4.7 42.5 1.0
O1A E:DTP502 4.7 42.5 1.0
C8 E:DTP502 4.8 42.5 1.0

Reference:

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
Page generated: Thu Apr 6 23:11:25 2023

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