Manganese in PDB 7m4l: Dna Polymerase Lambda, Ttpas:at MN2+ Product State Ternary Complex, 60 Min

All present enzymatic activity of Dna Polymerase Lambda, Ttpas:at MN2+ Product State Ternary Complex, 60 Min:
2.7.7.7;

The structure of Dna Polymerase Lambda, Ttpas:at MN2+ Product State Ternary Complex, 60 Min, PDB code: 7m4l 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)	40.03 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	55.97, 62.753, 140.13, 90, 90, 90
R / Rfree (%)	18.9 / 21.5

The structure of Dna Polymerase Lambda, Ttpas:at MN2+ Product State Ternary Complex, 60 Min also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

The binding sites of Manganese atom in the Dna Polymerase Lambda, Ttpas:at MN2+ Product State Ternary Complex, 60 Min (pdb code 7m4l). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the Dna Polymerase Lambda, Ttpas:at MN2+ Product State Ternary Complex, 60 Min, PDB code: 7m4l:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in the Dna Polymerase Lambda, Ttpas:at MN2+ Product State Ternary Complex, 60 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, Ttpas:at MN2+ Product State Ternary Complex, 60 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn601 b:31.3 occ:1.00 O A:HOH701 2.1 38.6 1.0 O1A P:YQS7 2.1 34.6 1.0 OD1 A:ASP427 2.1 37.4 1.0 OD2 A:ASP429 2.1 36.4 1.0 O22 A:PPV606 2.1 38.3 0.8 O21 A:PPV606 2.1 35.1 0.8 P1 A:PPV606 3.0 36.2 0.8 O31 A:PPV606 3.0 48.9 0.8 CG A:ASP429 3.1 37.4 1.0 P2 A:PPV606 3.2 46.6 0.8 CG A:ASP427 3.2 40.5 1.0 OD1 A:ASP429 3.4 33.1 1.0 PA P:YQS7 3.4 39.6 1.0 MN A:MN602 3.5 45.8 1.0 OPP A:PPV606 3.5 45.8 0.8 O32 A:PPV606 3.7 46.0 0.8 OD2 A:ASP427 3.7 36.1 1.0 C5' P:YQS7 4.1 34.8 1.0 O5' P:YQS7 4.1 32.9 1.0 O A:ASP427 4.3 30.2 1.0 CA A:GLY416 4.4 29.7 1.0 N A:ASP427 4.4 32.9 1.0 O A:HOH766 4.4 33.4 1.0 CB A:ASP429 4.4 29.0 1.0 O11 A:PPV606 4.5 30.2 0.8 CB A:ASP427 4.5 33.2 1.0 C A:ASP427 4.5 29.9 1.0 O12 A:PPV606 4.5 47.0 0.8 S2A P:YQS7 4.6 34.3 1.0 N A:SER417 4.6 32.4 1.0 O3' P:DC6 4.6 36.4 1.0 CA A:ASP427 4.7 29.4 1.0 OG A:SER417 4.9 49.0 1.0 N A:ASP429 5.0 27.0 1.0

Manganese binding site 2 out of 3 in the Dna Polymerase Lambda, Ttpas:at MN2+ Product State Ternary Complex, 60 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, Ttpas:at MN2+ Product State Ternary Complex, 60 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn602 b:45.8 occ:1.00 OD2 A:ASP427 2.0 36.1 1.0 OD1 A:ASP429 2.1 33.1 1.0 OD2 A:ASP490 2.2 33.0 1.0 O1A P:YQS7 2.4 34.6 1.0 O A:HOH766 2.5 33.4 1.0 O3' P:DC6 2.8 36.4 1.0 CG A:ASP427 2.9 40.5 1.0 PA P:YQS7 3.1 39.6 1.0 CG A:ASP490 3.1 31.6 1.0 OD1 A:ASP427 3.1 37.4 1.0 CG A:ASP429 3.2 37.4 1.0 MN A:MN601 3.5 31.3 1.0 OD2 A:ASP429 3.6 36.4 1.0 CB A:ASP490 3.8 28.1 1.0 C3' P:DC6 4.0 30.6 1.0 OD1 A:ASP490 4.0 29.3 1.0 C4' P:DC6 4.3 30.9 1.0 O5' P:YQS7 4.3 32.9 1.0 CB A:ASP427 4.3 33.2 1.0 C5' P:DC6 4.3 28.8 1.0 C5' P:YQS7 4.4 34.8 1.0 S2A P:YQS7 4.4 34.3 1.0 NH2 A:ARG488 4.4 30.8 1.0 CB A:ASP429 4.4 29.0 1.0 O22 A:PPV606 4.5 38.3 0.8 CE1 A:PHE506 4.9 33.7 1.0 O A:VAL428 4.9 30.2 1.0 CA A:ASP429 4.9 27.1 1.0 O31 A:PPV606 5.0 48.9 0.8 O5' P:DC6 5.0 35.4 1.0

Manganese binding site 3 out of 3 in the Dna Polymerase Lambda, Ttpas:at MN2+ Product State Ternary Complex, 60 Min


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Dna Polymerase Lambda, Ttpas:at MN2+ Product State Ternary Complex, 60 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn603 b:32.3 occ:0.57 OD2 A:ASP382 2.2 38.7 1.0 O A:HOH804 2.3 38.0 1.0 ND1 A:HIS486 2.4 30.4 1.0 O A:HOH828 2.4 44.3 1.0 O A:HOH751 2.6 38.7 1.0 CG A:ASP382 3.2 37.6 1.0 CE1 A:HIS486 3.2 33.1 1.0 CG A:HIS486 3.5 31.0 1.0 N A:HIS486 3.6 27.4 1.0 OD1 A:ASP382 3.7 36.9 1.0 CB A:HIS486 3.8 27.2 1.0 ND1 A:HIS379 4.3 25.8 1.0 CA A:HIS486 4.3 28.7 1.0 NE2 A:HIS486 4.4 35.7 1.0 CB A:ASP382 4.4 28.4 1.0 CA A:ARG485 4.5 30.7 1.0 O A:HOH814 4.5 29.3 1.0 C A:ARG485 4.5 30.6 1.0 CD2 A:HIS486 4.6 29.7 1.0 CE1 A:HIS379 4.7 32.2 1.0 O A:HOH838 4.7 38.1 0.5 NH1 A:ARG478 4.9 37.2 1.0 O A:HOH838 5.0 39.1 0.5

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