Manganese in PDB 7m4c: Dna Polymerase Lambda, Ttp:at MN2+ Product State Ternary Complex, 960 Min

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

The structure of Dna Polymerase Lambda, Ttp:at MN2+ Product State Ternary Complex, 960 Min, PDB code: 7m4c 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)	35.87 / 1.95
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.021, 62.641, 140.12, 90, 90, 90
R / Rfree (%)	18.1 / 21.4

The structure of Dna Polymerase Lambda, Ttp: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, Ttp:at MN2+ Product State Ternary Complex, 960 Min (pdb code 7m4c). 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, Ttp:at MN2+ Product State Ternary Complex, 960 Min, PDB code: 7m4c:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in the Dna Polymerase Lambda, Ttp: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, Ttp:at MN2+ Product State Ternary Complex, 960 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn602 b:23.5 occ:1.00 OD1 A:ASP427 1.9 28.8 0.5 O21 A:PPV601 2.0 29.3 1.0 OD2 A:ASP429 2.0 28.9 1.0 OP1 P:DT7 2.1 23.2 1.0 OD1 A:ASP427 2.1 28.8 0.5 O32 A:PPV601 2.2 31.5 0.9 O22 A:PPV601 2.4 36.3 1.0 P2 A:PPV601 2.8 41.0 0.3 CG A:ASP427 2.9 26.6 0.5 CG A:ASP429 3.0 27.4 1.0 P1 A:PPV601 3.1 37.5 0.5 CG A:ASP427 3.3 27.9 0.5 OD2 A:ASP427 3.3 27.6 0.5 OD1 A:ASP429 3.3 27.7 1.0 P P:DT7 3.4 23.6 1.0 MN A:MN603 3.5 37.7 1.0 OPP A:PPV601 3.5 45.3 0.5 OPP A:PPV601 3.5 45.3 0.5 O31 A:PPV601 3.5 32.8 0.1 OD2 A:ASP427 3.9 39.5 0.5 O A:HOH737 3.9 43.4 1.0 O5' P:DT7 3.9 24.7 1.0 C5' P:DT7 4.0 27.3 1.0 O12 A:PPV601 4.1 39.6 1.0 OP2 P:DT7 4.2 20.1 1.0 CB A:ASP427 4.2 25.8 0.5 CA A:GLY416 4.4 27.9 1.0 CB A:ASP429 4.4 26.6 1.0 O A:ASP427 4.4 23.9 0.5 O A:ASP427 4.4 24.0 0.5 O11 A:PPV601 4.4 28.7 1.0 O A:HOH785 4.4 30.0 1.0 O3' P:DC6 4.5 21.2 1.0 CB A:ASP427 4.5 25.2 0.5 C A:ASP427 4.6 24.3 0.5 C A:ASP427 4.6 24.4 0.5 N A:SER417 4.7 28.6 1.0 N A:ASP427 4.8 26.0 0.5 N A:ASP427 4.8 26.1 0.5 O A:HOH816 4.8 22.8 0.5 CA A:ASP427 4.8 25.1 0.5 CA A:ASP427 4.9 25.3 0.5

Manganese binding site 2 out of 3 in the Dna Polymerase Lambda, Ttp: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, Ttp:at MN2+ Product State Ternary Complex, 960 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn603 b:37.7 occ:1.00 OD2 A:ASP427 2.0 39.5 0.5 OD1 A:ASP429 2.1 27.7 1.0 OD2 A:ASP490 2.2 25.7 1.0 OP1 P:DT7 2.3 23.2 1.0 O A:HOH816 2.3 22.8 0.5 O A:HOH785 2.4 30.0 1.0 CG A:ASP427 2.8 27.9 0.5 OD1 A:ASP427 2.9 28.8 0.5 O3' P:DC6 3.0 21.2 1.0 OD1 A:ASP427 3.0 28.8 0.5 CG A:ASP490 3.0 25.3 1.0 CG A:ASP429 3.2 27.4 1.0 P P:DT7 3.3 23.6 1.0 CG A:ASP427 3.4 26.6 0.5 MN A:MN602 3.5 23.5 1.0 OD2 A:ASP429 3.6 28.9 1.0 CB A:ASP490 3.7 23.1 1.0 OD1 A:ASP490 3.8 26.7 1.0 OD2 A:ASP427 3.9 27.6 0.5 CB A:ASP427 4.0 25.8 0.5 C3' P:DC6 4.2 20.8 1.0 CB A:ASP427 4.2 25.2 0.5 OP2 P:DT7 4.3 20.1 1.0 NH2 A:ARG488 4.3 23.2 1.0 C5' P:DC6 4.5 20.5 1.0 C4' P:DC6 4.5 20.1 1.0 O5' P:DT7 4.5 24.7 1.0 O A:VAL428 4.5 23.3 1.0 CB A:ASP429 4.5 26.6 1.0 C5' P:DT7 4.6 27.3 1.0 N A:ASP490 4.8 22.6 1.0 C A:VAL428 4.9 23.9 1.0 CA A:ASP429 4.9 24.4 1.0 O22 A:PPV601 4.9 36.3 1.0 CA A:ASP490 4.9 22.5 1.0

Manganese binding site 3 out of 3 in the Dna Polymerase Lambda, Ttp: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 3 of Dna Polymerase Lambda, Ttp:at MN2+ Product State Ternary Complex, 960 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn604 b:29.2 occ:0.34 OD2 A:ASP382 2.1 37.2 1.0 ND1 A:HIS486 2.4 24.9 1.0 O A:HOH757 2.7 34.8 1.0 O A:HOH770 2.7 38.8 1.0 O A:HOH851 2.9 29.4 0.6 CG A:ASP382 3.2 30.6 1.0 CE1 A:HIS486 3.2 25.6 1.0 NH2 A:ARG485 3.4 38.7 0.6 N A:HIS486 3.5 24.0 1.0 CG A:HIS486 3.5 25.4 1.0 OD1 A:ASP382 3.7 31.9 1.0 CZ A:ARG485 3.8 34.6 0.6 CB A:HIS486 3.8 24.4 1.0 NE A:ARG485 4.1 32.8 0.6 CA A:HIS486 4.3 23.6 1.0 C A:ARG485 4.3 26.7 0.4 CA A:ARG485 4.3 27.8 0.4 CA A:ARG485 4.3 28.1 0.6 C A:ARG485 4.3 26.3 0.6 NE2 A:HIS486 4.4 27.2 1.0 CB A:ASP382 4.4 27.2 1.0 NH1 A:ARG485 4.5 31.2 0.6 O A:HOH851 4.5 31.1 0.4 ND1 A:HIS379 4.5 24.1 1.0 CD2 A:HIS486 4.6 25.4 1.0 NH1 A:ARG478 4.7 33.6 1.0 O A:ARG484 4.8 31.5 1.0 O A:HOH823 4.8 21.5 1.0 O A:HOH808 4.8 34.6 1.0 CE1 A:HIS379 4.9 26.8 1.0 CB A:ARG485 4.9 29.6 0.6 CB A:ARG485 4.9 29.7 0.4

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