Manganese in PDB 7m4j: Dna Polymerase Lambda, Dctp:at MN2+ Product State Ternary Complex, 960 Min

All present enzymatic activity of Dna Polymerase Lambda, Dctp:at MN2+ Product State Ternary Complex, 960 Min:
2.7.7.7;

The structure of Dna Polymerase Lambda, Dctp:at MN2+ Product State Ternary Complex, 960 Min, PDB code: 7m4j 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)	42.04 / 2.38
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	55.975, 63.66, 139.97, 90, 90, 90
R / Rfree (%)	22.6 / 26.1

The structure of Dna Polymerase Lambda, Dctp:at MN2+ Product State Ternary Complex, 960 Min also contains other interesting chemical elements:

Sodium

(Na)

3 atoms

The binding sites of Manganese atom in the Dna Polymerase Lambda, Dctp:at MN2+ Product State Ternary Complex, 960 Min (pdb code 7m4j). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Dna Polymerase Lambda, Dctp:at MN2+ Product State Ternary Complex, 960 Min, PDB code: 7m4j:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Dna Polymerase Lambda, Dctp:at MN2+ Product State Ternary Complex, 960 Min


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Dna Polymerase Lambda, Dctp:at MN2+ Product State Ternary Complex, 960 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn601 b:30.6 occ:0.80 OD2 A:ASP429 2.0 40.3 1.0 OD1 A:ASP427 2.1 45.4 1.0 OP1 P:DC7 2.1 53.5 1.0 O3 A:PO4606 2.4 69.0 1.0 P A:PO4606 2.8 69.2 1.0 O2 A:PO4606 2.9 68.5 1.0 O1 A:PO4606 2.9 69.7 1.0 CG A:ASP429 2.9 36.9 1.0 CG A:ASP427 3.0 41.9 1.0 OD1 A:ASP429 3.3 37.4 1.0 OD2 A:ASP427 3.3 43.3 1.0 P P:DC7 3.4 48.6 1.0 NA A:NA605 3.6 33.4 1.0 O5' P:DC7 3.7 49.5 1.0 C5' P:DC7 4.0 51.3 1.0 CA A:GLY416 4.1 44.1 1.0 CB A:ASP429 4.3 34.8 1.0 O4 A:PO4606 4.3 69.4 1.0 OP2 P:DC7 4.3 47.1 1.0 CB A:ASP427 4.4 37.7 1.0 O3' P:DC6 4.5 58.9 1.0 O A:ASP427 4.7 32.6 1.0 C A:ASP427 4.7 33.7 1.0 N A:SER417 4.7 43.9 1.0 N A:ASP427 4.9 34.9 1.0 CA A:ASP427 4.9 35.0 1.0 N A:ASP429 4.9 32.5 1.0 C A:GLY416 5.0 45.0 1.0

Manganese binding site 2 out of 2 in the Dna Polymerase Lambda, Dctp:at MN2+ Product State Ternary Complex, 960 Min


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Dna Polymerase Lambda, Dctp:at MN2+ Product State Ternary Complex, 960 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn602 b:34.0 occ:0.49 OD2 A:ASP382 2.2 47.0 1.0 O A:HOH713 2.5 39.1 0.9 ND1 A:HIS486 2.5 36.4 1.0 O A:HOH728 2.6 46.6 1.0 O A:HOH747 2.9 35.3 0.9 CG A:ASP382 3.2 42.7 1.0 CE1 A:HIS486 3.3 37.0 1.0 CG A:HIS486 3.6 36.3 1.0 N A:HIS486 3.6 37.4 1.0 OD1 A:ASP382 3.7 44.6 1.0 CB A:HIS486 3.9 36.5 1.0 CA A:ARG485 4.3 36.8 1.0 CA A:HIS486 4.4 37.0 1.0 C A:ARG485 4.4 35.7 1.0 CB A:ASP382 4.5 37.8 1.0 NE2 A:HIS486 4.5 37.3 1.0 NH1 A:ARG478 4.6 45.2 1.0 CD2 A:HIS486 4.6 36.5 1.0 ND1 A:HIS379 4.7 34.9 1.0 O A:ARG484 4.8 41.0 1.0 O A:HOH740 4.8 35.9 1.0 CB A:ARG485 4.8 36.6 1.0 CG A:ARG485 5.0 37.5 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