Magnesium in PDB 7m4e: Dna Polymerase Lambda, Dctp:at MG2+ Reaction State Ternary Complex, 120 Min

All present enzymatic activity of Dna Polymerase Lambda, Dctp:at MG2+ Reaction State Ternary Complex, 120 Min:
2.7.7.7;

The structure of Dna Polymerase Lambda, Dctp:at MG2+ Reaction State Ternary Complex, 120 Min, PDB code: 7m4e 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)	31.22 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	55.825, 62.088, 142.096, 90, 90, 90
R / Rfree (%)	20.9 / 23.3

The structure of Dna Polymerase Lambda, Dctp:at MG2+ Reaction State Ternary Complex, 120 Min also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

The binding sites of Magnesium atom in the Dna Polymerase Lambda, Dctp:at MG2+ Reaction State Ternary Complex, 120 Min (pdb code 7m4e). 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, Dctp:at MG2+ Reaction State Ternary Complex, 120 Min, PDB code: 7m4e:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Dna Polymerase Lambda, Dctp:at MG2+ Reaction State Ternary Complex, 120 Min


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, Dctp:at MG2+ Reaction State Ternary Complex, 120 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:48.8 occ:1.00 OD2 A:ASP427 1.8 49.4 0.6 OD1 A:ASP429 2.0 50.7 1.0 O A:HOH722 2.3 40.3 0.5 OD2 A:ASP490 2.3 51.8 1.0 OP1 P:DC7 2.4 52.9 0.3 O1A A:DCP606 2.4 52.4 0.7 O3' P:DC6 2.5 54.1 0.7 O3' P:DC6 2.6 54.1 0.3 CG A:ASP427 2.8 47.1 0.6 OD1 A:ASP427 2.9 50.1 0.5 P P:DC7 3.0 50.9 0.3 CG A:ASP429 3.1 52.2 1.0 CG A:ASP427 3.1 46.7 0.5 OD2 A:ASP427 3.1 49.0 0.5 OD1 A:ASP427 3.2 50.9 0.6 CG A:ASP490 3.4 49.2 1.0 MG A:MG603 3.5 57.6 1.0 PA A:DCP606 3.5 57.1 0.7 OD2 A:ASP429 3.6 53.0 1.0 O A:HOH755 3.6 59.4 1.0 C3' P:DC6 3.8 52.4 0.7 C3' P:DC6 3.8 52.5 0.3 O5' A:DCP606 4.0 54.7 0.7 OP2 P:DC7 4.0 53.2 0.3 C4' P:DC6 4.1 51.0 0.3 O2A A:DCP606 4.1 52.1 0.7 C5' P:DC6 4.2 50.0 0.3 OD1 A:ASP490 4.2 50.3 1.0 CB A:ASP490 4.2 44.7 1.0 C4' P:DC6 4.2 51.1 0.7 CB A:ASP427 4.2 45.0 0.6 C5' P:DC6 4.2 49.9 0.7 CB A:ASP427 4.2 45.1 0.5 O5' P:DC7 4.3 53.4 0.3 CB A:ASP429 4.4 48.4 1.0 C5' A:DCP606 4.4 54.0 0.7 C5' P:DC7 4.5 53.6 0.3 O1G A:DCP606 4.6 63.6 0.7 O22 A:PPV601 4.6 70.7 0.3 NH2 A:ARG488 4.7 45.3 1.0 O5' P:DC6 4.8 48.3 0.3 O5' P:DC6 4.8 48.3 0.7 OP1 P:DC6 4.9 44.8 0.7 CA A:ASP429 4.9 41.9 1.0 OP1 P:DC6 4.9 45.0 0.3 C2' P:DC6 4.9 52.0 0.3 O3A A:DCP606 4.9 62.5 0.7 O A:VAL428 5.0 39.1 1.0 C2' P:DC6 5.0 52.0 0.7

Magnesium binding site 2 out of 2 in the Dna Polymerase Lambda, Dctp:at MG2+ Reaction State Ternary Complex, 120 Min


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, Dctp:at MG2+ Reaction State Ternary Complex, 120 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg603 b:57.6 occ:1.00 OD1 A:ASP427 1.9 50.9 0.6 O1A A:DCP606 2.0 52.4 0.7 OD1 A:ASP427 2.1 50.1 0.5 OD2 A:ASP429 2.1 53.0 1.0 O22 A:PPV601 2.1 70.7 0.3 O A:HOH706 2.1 50.5 1.0 O1B A:DCP606 2.1 63.3 0.7 O21 A:PPV601 2.2 70.7 0.3 O1G A:DCP606 2.2 63.6 0.7 OP1 P:DC7 2.4 52.9 0.3 CG A:ASP427 2.8 46.7 0.5 CG A:ASP427 3.0 47.1 0.6 OD2 A:ASP427 3.0 49.0 0.5 CG A:ASP429 3.0 52.2 1.0 PA A:DCP606 3.1 57.1 0.7 PB A:DCP606 3.2 72.9 0.7 P1 A:PPV601 3.2 72.5 0.3 OD1 A:ASP429 3.3 50.7 1.0 P2 A:PPV601 3.4 73.5 0.3 PG A:DCP606 3.4 72.7 0.7 O3A A:DCP606 3.4 62.5 0.7 O31 A:PPV601 3.4 68.5 0.3 OD2 A:ASP427 3.5 49.4 0.6 MG A:MG602 3.5 48.8 1.0 OPP A:PPV601 3.7 69.3 0.3 O3B A:DCP606 3.8 69.7 0.7 O2G A:DCP606 3.8 65.6 0.7 P P:DC7 3.9 50.9 0.3 O A:ASP427 3.9 41.3 0.6 O12 A:PPV601 4.0 73.4 0.3 O A:ASP427 4.1 41.3 0.5 C A:ASP427 4.2 41.2 0.6 CB A:ASP427 4.2 45.1 0.5 O5' A:DCP606 4.2 54.7 0.7 C A:ASP427 4.2 41.2 0.5 CB A:ASP427 4.2 45.0 0.6 C5' A:DCP606 4.3 54.0 0.7 O2A A:DCP606 4.3 52.1 0.7 N A:ASP427 4.3 42.1 0.6 CA A:GLY416 4.3 45.8 1.0 N A:ASP427 4.4 42.2 0.5 CB A:ASP429 4.4 48.4 1.0 C5' P:DC7 4.5 53.6 0.3 O5' P:DC7 4.5 53.4 0.3 CA A:ASP427 4.5 41.9 0.6 O2B A:DCP606 4.5 64.9 0.7 O A:HOH722 4.5 40.3 0.5 CA A:ASP427 4.5 41.9 0.5 O11 A:PPV601 4.6 73.2 0.3 N A:SER417 4.6 43.3 1.0 O32 A:PPV601 4.6 73.0 0.3 O3G A:DCP606 4.7 65.8 0.7 OG A:SER417 4.7 48.6 1.0 N A:ASP429 4.7 39.1 1.0 N A:VAL428 4.8 39.8 1.0 O3' P:DC6 4.8 54.1 0.3 OP2 P:DC7 4.8 53.2 0.3 O3' P:DC6 4.9 54.1 0.7

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