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

Protein crystallography data

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

Magnesium Binding Sites:

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 7tu3

Go back to Magnesium Binding Sites List in 7tu3
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 7tu3

Go back to Magnesium Binding Sites List in 7tu3
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 7tu3

Go back to Magnesium Binding Sites List in 7tu3
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

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 Oct 3 09:29:36 2024

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