Magnesium in PDB 5vu8: Tna Polymerase, Closed Ternary Complex

All present enzymatic activity of Tna Polymerase, Closed Ternary Complex:
2.7.7.7;

The structure of Tna Polymerase, Closed Ternary Complex, PDB code: 5vu8 was solved by N.Chim, J.C.Chaput, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.42 / 3.20
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	72.288, 107.360, 147.732, 90.00, 90.00, 90.00
R / Rfree (%)	25.8 / 29.5

The binding sites of Magnesium atom in the Tna Polymerase, Closed Ternary Complex (pdb code 5vu8). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Tna Polymerase, Closed Ternary Complex, PDB code: 5vu8:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Tna Polymerase, Closed Ternary Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tna Polymerase, Closed Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg802 b:77.8 occ:1.00 O2A A:9O7801 1.3 88.6 0.6 PA A:9O7801 2.4 86.5 0.6 O1A A:9O7801 2.4 88.3 0.6 CB A:ASP542 3.4 0.1 1.0 O3A A:9O7801 3.5 86.0 0.6 OH A:TYR402 3.6 73.2 1.0 O3' A:9O7801 3.7 83.5 0.6 C4' A:9O7801 3.9 78.1 0.6 C3' P:9O412 4.0 82.6 1.0 C3' A:9O7801 4.0 79.9 0.6 CG A:ASP542 4.1 0.8 1.0 OD1 A:ASP404 4.3 0.9 1.0 C2' P:9O412 4.4 83.2 1.0 O2B A:9O7801 4.4 70.3 0.6 MG P:MG101 4.5 81.3 1.0 OD1 A:ASP542 4.5 0.3 1.0 O1P P:9O412 4.5 0.7 1.0 CB A:ASP404 4.6 95.5 1.0 PB A:9O7801 4.6 83.3 0.6 CA A:ASP542 4.6 0.5 1.0 C4' P:9O412 4.7 79.0 1.0 CZ A:TYR402 4.7 74.0 1.0 CG A:ASP404 4.7 0.7 1.0 OD2 A:ASP542 4.8 0.3 1.0 N A:ASP542 4.9 89.9 1.0 O3' P:9O412 4.9 94.5 1.0 CE2 A:TYR402 4.9 74.2 1.0 C1' P:9O412 5.0 85.6 1.0

Magnesium binding site 2 out of 3 in the Tna Polymerase, Closed Ternary Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tna Polymerase, Closed Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg803 b:61.9 occ:0.79 OE2 A:GLU580 1.3 0.7 1.0 O2G A:9O7801 2.0 96.9 0.6 CD A:GLU580 2.3 0.7 1.0 O1G A:9O7801 2.4 0.1 0.6 PG A:9O7801 2.6 99.0 0.6 O3G A:9O7801 2.8 97.8 0.6 OE1 A:GLU580 2.9 0.3 1.0 OE2 A:GLU578 3.0 0.7 1.0 CG A:GLU580 3.6 0.2 1.0 OD1 A:ASP404 4.1 0.9 1.0 OD2 A:ASP404 4.1 0.3 1.0 O3B A:9O7801 4.2 92.4 0.6 CD A:GLU578 4.2 0.8 1.0 CB A:GLU580 4.5 0.8 1.0 CG A:ASP404 4.5 0.7 1.0 NZ A:LYS464 4.9 87.5 1.0 OE1 A:GLU578 5.0 0.3 1.0 NH2 A:ARG460 5.0 80.1 1.0

Magnesium binding site 3 out of 3 in the Tna Polymerase, Closed Ternary Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tna Polymerase, Closed Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ P:Mg101 b:81.3 occ:1.00 O1A A:9O7801 2.5 88.3 0.6 O1P P:9O412 2.7 0.7 1.0 NZ A:LYS487 2.8 79.3 1.0 C2' P:9O412 3.2 83.2 1.0 PA A:9O7801 3.8 86.5 0.6 CE A:LYS487 3.9 77.5 1.0 P P:9O412 3.9 0.5 1.0 NH1 A:ARG606 4.0 0.9 1.0 C3' P:9O412 4.1 82.6 1.0 C8 P:9O412 4.1 89.7 1.0 C1' P:9O412 4.2 85.6 1.0 O3' A:9O7801 4.5 83.5 0.6 MG A:MG802 4.5 77.8 1.0 O3' P:9O412 4.5 94.5 1.0 O3A A:9O7801 4.5 86.0 0.6 O3' P:DG11 4.6 0.8 1.0 N9 P:9O412 4.6 89.8 1.0 O2A A:9O7801 4.7 88.6 0.6

N.Chim, C.Shi, S.P.Sau, A.Nikoomanzar, J.C.Chaput. Structural Basis For Tna Synthesis By An Engineered Tna Polymerase. Nat Commun V. 8 1810 2017.
ISSN: ESSN 2041-1723
PubMed: 29180809
DOI: 10.1038/S41467-017-02014-0