Magnesium in PDB 7m44: Dna Polymerase Lambda, Ttp:at MG2+ Reaction State Ternary Complex, 90 Sec

All present enzymatic activity of Dna Polymerase Lambda, Ttp:at MG2+ Reaction State Ternary Complex, 90 Sec:
2.7.7.7;

The structure of Dna Polymerase Lambda, Ttp:at MG2+ Reaction State Ternary Complex, 90 Sec, PDB code: 7m44 was solved by J.A.Jamsen, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	21.89 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.042, 62.356, 140.228, 90, 90, 90
R / Rfree (%)	19.5 / 22.6

The structure of Dna Polymerase Lambda, Ttp:at MG2+ Reaction State Ternary Complex, 90 Sec also contains other interesting chemical elements:

Sodium

(Na)

3 atoms

The binding sites of Magnesium atom in the Dna Polymerase Lambda, Ttp:at MG2+ Reaction State Ternary Complex, 90 Sec (pdb code 7m44). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Dna Polymerase Lambda, Ttp:at MG2+ Reaction State Ternary Complex, 90 Sec, PDB code: 7m44:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Dna Polymerase Lambda, Ttp:at MG2+ Reaction State Ternary Complex, 90 Sec


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Dna Polymerase Lambda, Ttp:at MG2+ Reaction State Ternary Complex, 90 Sec within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:25.4 occ:1.00 O1A A:TTP601 1.9 22.6 0.7 OD1 A:ASP427 1.9 30.1 0.3 OD2 A:ASP429 2.0 29.9 1.0 O1B A:TTP601 2.1 24.3 0.7 O A:HOH721 2.1 32.5 1.0 OD1 A:ASP427 2.1 28.6 0.7 O2G A:TTP601 2.1 30.8 0.7 O21 A:PPV607 2.3 28.4 0.3 O22 A:PPV607 2.4 30.5 0.3 OP1 P:DT7 2.4 23.5 0.3 CG A:ASP427 3.0 29.1 0.3 CG A:ASP429 3.1 31.5 1.0 PA A:TTP601 3.1 23.7 0.7 O31 A:PPV607 3.1 30.4 0.3 PB A:TTP601 3.1 31.2 0.7 CG A:ASP427 3.1 29.7 0.7 P1 A:PPV607 3.2 30.4 0.3 PG A:TTP601 3.3 35.6 0.7 P2 A:PPV607 3.4 33.0 0.3 OD1 A:ASP429 3.4 26.7 1.0 O3A A:TTP601 3.4 32.9 0.7 OD2 A:ASP427 3.5 29.2 0.3 MG A:MG603 3.6 30.5 1.0 OD2 A:ASP427 3.6 29.7 0.7 O32 A:PPV607 3.6 32.3 0.3 O3B A:TTP601 3.6 32.1 0.7 OPP A:PPV607 3.8 30.9 0.3 P P:DT7 3.9 25.8 0.3 O3G A:TTP601 4.0 33.2 0.7 O A:ASP427 4.0 27.0 0.7 O A:HOH780 4.0 25.6 0.7 C5' A:TTP601 4.1 28.4 0.7 O5' A:TTP601 4.1 25.1 0.7 O A:ASP427 4.2 28.6 0.3 O2A A:TTP601 4.2 21.7 0.7 CB A:ASP427 4.2 28.5 0.3 C A:ASP427 4.3 28.7 0.7 N A:ASP427 4.3 27.7 0.7 C A:ASP427 4.4 28.6 0.3 C5' P:DT7 4.4 27.9 0.3 N A:ASP427 4.4 27.9 0.3 CB A:ASP427 4.4 28.7 0.7 CB A:ASP429 4.4 29.4 1.0 OG A:SER417 4.4 32.4 1.0 O A:HOH777 4.4 29.5 1.0 O2B A:TTP601 4.4 31.1 0.7 CA A:GLY416 4.5 29.0 1.0 O5' P:DT7 4.5 24.5 0.3 N A:SER417 4.5 31.2 1.0 O P:HOH110 4.5 25.8 0.3 O1G A:TTP601 4.5 32.6 0.7 O11 A:PPV607 4.6 30.6 0.3 CA A:ASP427 4.6 27.2 0.7 CA A:ASP427 4.6 27.5 0.3 OP2 P:DT7 4.7 26.2 0.3 O12 A:PPV607 4.8 32.1 0.3 O3' P:DC6 4.8 30.2 0.3 N A:VAL428 4.9 28.5 1.0 N A:ASP429 4.9 25.5 1.0

Magnesium binding site 2 out of 2 in the Dna Polymerase Lambda, Ttp:at MG2+ Reaction State Ternary Complex, 90 Sec


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Dna Polymerase Lambda, Ttp:at MG2+ Reaction State Ternary Complex, 90 Sec within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg603 b:30.5 occ:1.00 OD1 A:ASP429 2.2 26.7 1.0 OD2 A:ASP427 2.2 29.7 0.7 OD2 A:ASP490 2.3 27.4 1.0 O P:HOH110 2.3 25.8 0.3 OP1 P:DT7 2.3 23.5 0.3 O1A A:TTP601 2.6 22.6 0.7 O3' P:DC6 2.6 30.2 0.3 CG A:ASP427 3.0 29.7 0.7 OD1 A:ASP427 3.0 30.1 0.3 P P:DT7 3.1 25.8 0.3 OD1 A:ASP427 3.2 28.6 0.7 CG A:ASP490 3.2 26.8 1.0 CG A:ASP429 3.2 31.5 1.0 O3' P:DC6 3.2 31.5 0.7 CG A:ASP427 3.4 29.1 0.3 MG A:MG602 3.6 25.4 1.0 C3' P:DC6 3.6 28.0 0.7 OD2 A:ASP429 3.6 29.9 1.0 PA A:TTP601 3.6 23.7 0.7 CB A:ASP490 3.9 24.4 1.0 C3' P:DC6 3.9 26.6 0.3 OD2 A:ASP427 3.9 29.2 0.3 O5' A:TTP601 3.9 25.1 0.7 OD1 A:ASP490 4.0 26.7 1.0 O2A A:TTP601 4.1 21.7 0.7 OP2 P:DT7 4.1 26.2 0.3 C4' P:DC6 4.2 24.8 0.3 C5' A:TTP601 4.2 28.4 0.7 O5' P:DT7 4.2 24.5 0.3 CB A:ASP427 4.3 28.5 0.3 CB A:ASP427 4.3 28.7 0.7 C5' P:DT7 4.3 27.9 0.3 C5' P:DC6 4.4 24.9 0.3 C4' P:DC6 4.4 25.6 0.7 C5' P:DC6 4.4 25.4 0.7 CB A:ASP429 4.5 29.4 1.0 O A:HOH780 4.5 25.6 0.7 NH2 A:ARG488 4.6 27.0 1.0 O A:VAL428 4.7 24.2 1.0 O22 A:PPV607 4.7 30.5 0.3 O5' P:DC6 4.8 24.6 0.3 O5' P:DC6 4.8 25.6 0.7 C2' P:DC6 4.8 27.6 0.7 O2G A:TTP601 4.9 30.8 0.7 OP1 P:DC6 4.9 22.3 0.7 C2' P:DC6 4.9 27.5 0.3 O31 A:PPV607 5.0 30.4 0.3 CE1 A:PHE506 5.0 26.1 1.0

J.A.Jamsen, D.D.Shock, S.H.Wilson. Watching Right and Wrong Nucleotide Insertion Captures Hidden Polymerase Fidelity Checkpoints. Nat Commun V. 13 3193 2022.
ISSN: ESSN 2041-1723
PubMed: 35680862
DOI: 10.1038/S41467-022-30141-W