Manganese in PDB 7m4h: Dna Polymerase Lambda, Dctp:at MN2+ Reaction State Ternary Complex, 225 Min

All present enzymatic activity of Dna Polymerase Lambda, Dctp:at MN2+ Reaction State Ternary Complex, 225 Min:
2.7.7.7;

The structure of Dna Polymerase Lambda, Dctp:at MN2+ Reaction State Ternary Complex, 225 Min, PDB code: 7m4h 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)	41.57 / 1.92
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	55.814, 62.299, 142.057, 90, 90, 90
R / Rfree (%)	19.2 / 22.8

The structure of Dna Polymerase Lambda, Dctp:at MN2+ Reaction State Ternary Complex, 225 Min also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

The binding sites of Manganese atom in the Dna Polymerase Lambda, Dctp:at MN2+ Reaction State Ternary Complex, 225 Min (pdb code 7m4h). 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, Dctp:at MN2+ Reaction State Ternary Complex, 225 Min, PDB code: 7m4h:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in the Dna Polymerase Lambda, Dctp:at MN2+ Reaction State Ternary Complex, 225 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+ Reaction State Ternary Complex, 225 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn601 b:33.8 occ:1.00 OD1 A:ASP429 2.1 30.6 1.0 OD2 A:ASP427 2.1 35.2 1.0 OD2 A:ASP490 2.2 28.0 1.0 O P:HOH109 2.3 31.6 1.0 OP1 P:DC7 2.3 27.0 0.4 O3' P:DC6 2.3 47.4 0.4 O3' P:DC6 2.4 23.3 0.6 O1A A:DCP609 2.6 19.6 0.5 P P:DC7 2.8 36.0 0.4 CG A:ASP427 3.1 34.9 1.0 CG A:ASP429 3.2 30.4 1.0 CG A:ASP490 3.3 37.0 1.0 OD1 A:ASP427 3.3 31.7 1.0 O P:HOH102 3.5 32.8 1.0 MN A:MN602 3.5 31.0 1.0 C3' P:DC6 3.5 33.0 0.4 OD2 A:ASP429 3.5 26.7 1.0 C3' P:DC6 3.6 39.5 0.6 OP2 P:DC7 3.6 40.2 0.4 PA A:DCP609 3.6 24.3 0.5 C4' P:DC6 3.8 37.2 0.4 C5' P:DC6 3.9 32.3 0.4 O5' A:DCP609 4.0 28.2 0.5 CB A:ASP490 4.0 26.6 1.0 O2A A:DCP609 4.0 24.2 0.5 C4' P:DC6 4.1 30.4 0.6 C5' P:DC6 4.1 30.0 0.6 O5' P:DC7 4.1 27.6 0.4 O A:HOH747 4.2 39.0 1.0 OD1 A:ASP490 4.2 28.7 1.0 C5' A:DCP609 4.4 23.5 0.5 CB A:ASP427 4.4 23.9 1.0 C5' P:DC7 4.4 36.0 0.4 CB A:ASP429 4.5 26.2 1.0 O5' P:DC6 4.6 30.4 0.4 C2' P:DC6 4.6 30.2 0.4 O5' P:DC6 4.6 28.9 0.6 OP1 P:DC6 4.7 25.3 0.6 NH2 A:ARG488 4.7 30.5 1.0 O22 A:PPV608 4.8 32.7 0.4 O1G A:DCP609 4.8 31.8 0.5 OP1 P:DC6 4.8 25.7 0.4 C2' P:DC6 4.8 30.0 0.6 O31 A:PPV608 4.9 43.7 0.4

Manganese binding site 2 out of 3 in the Dna Polymerase Lambda, Dctp:at MN2+ Reaction State Ternary Complex, 225 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+ Reaction State Ternary Complex, 225 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn602 b:31.0 occ:1.00 O1A A:DCP609 2.0 19.6 0.5 OD2 A:ASP429 2.0 26.7 1.0 OD1 A:ASP427 2.0 31.7 1.0 O1B A:DCP609 2.1 39.9 0.5 OP1 P:DC7 2.2 27.0 0.4 O1G A:DCP609 2.3 31.8 0.5 O22 A:PPV608 2.3 32.7 0.4 O A:HOH729 2.4 32.3 1.0 O11 A:PPV608 2.4 32.5 0.4 CG A:ASP429 3.0 30.4 1.0 CG A:ASP427 3.1 34.9 1.0 O31 A:PPV608 3.2 43.7 0.4 P1 A:PPV608 3.2 29.2 0.4 PB A:DCP609 3.2 39.2 0.5 PA A:DCP609 3.3 24.3 0.5 OD1 A:ASP429 3.4 30.6 1.0 PG A:DCP609 3.4 41.7 0.5 OD2 A:ASP427 3.5 35.2 1.0 MN A:MN601 3.5 33.8 1.0 P2 A:PPV608 3.6 31.5 0.4 P P:DC7 3.6 36.0 0.4 O3A A:DCP609 3.6 34.8 0.5 OPP A:PPV608 3.8 42.8 0.4 O3B A:DCP609 3.8 29.6 0.5 O3G A:DCP609 3.9 32.5 0.5 O A:HOH747 3.9 39.0 1.0 C5' A:DCP609 4.1 23.5 0.5 O A:ASP427 4.1 25.7 1.0 O5' A:DCP609 4.2 28.2 0.5 O5' P:DC7 4.3 27.6 0.4 CB A:ASP429 4.3 26.2 1.0 O12 A:PPV608 4.3 34.3 0.4 C A:ASP427 4.3 27.8 1.0 CB A:ASP427 4.4 23.9 1.0 CA A:GLY416 4.4 29.8 1.0 C5' P:DC7 4.4 36.0 0.4 O P:HOH109 4.4 31.6 1.0 OP2 P:DC7 4.4 40.2 0.4 N A:ASP427 4.4 34.2 1.0 O2A A:DCP609 4.5 24.2 0.5 O2B A:DCP609 4.5 32.8 0.5 O A:HOH762 4.6 27.4 1.0 O3' P:DC6 4.6 47.4 0.4 N A:SER417 4.6 29.2 1.0 CA A:ASP427 4.6 24.6 1.0 O21 A:PPV608 4.6 33.1 0.4 OG A:SER417 4.7 40.0 1.0 O2G A:DCP609 4.7 31.0 0.5 O32 A:PPV608 4.7 40.2 0.4 N A:ASP429 4.7 26.2 1.0 N A:VAL428 4.9 25.8 1.0 O3' P:DC6 5.0 23.3 0.6

Manganese binding site 3 out of 3 in the Dna Polymerase Lambda, Dctp:at MN2+ Reaction State Ternary Complex, 225 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, Dctp:at MN2+ Reaction State Ternary Complex, 225 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn603 b:30.3 occ:0.60 OD2 A:ASP382 2.1 35.2 1.0 O A:HOH805 2.3 27.2 0.8 ND1 A:HIS486 2.4 28.5 1.0 O A:HOH759 2.4 36.2 0.8 O A:HOH834 2.5 24.7 0.6 O A:HOH751 2.6 32.1 0.8 CG A:ASP382 3.1 32.4 1.0 CE1 A:HIS486 3.2 33.1 1.0 CG A:HIS486 3.5 30.1 1.0 OD1 A:ASP382 3.6 32.4 1.0 N A:HIS486 3.7 29.1 1.0 CB A:HIS486 3.9 33.3 1.0 ND1 A:HIS379 4.3 27.9 1.0 CB A:ASP382 4.3 25.9 1.0 NE2 A:HIS486 4.4 33.2 1.0 CA A:HIS486 4.4 32.7 1.0 O A:HOH817 4.4 25.8 1.0 CA A:ARG485 4.5 28.5 1.0 CD2 A:HIS486 4.5 31.6 1.0 C A:ARG485 4.5 35.0 1.0 O A:HOH834 4.6 35.4 0.5 NH1 A:ARG478 4.7 34.0 1.0 CE1 A:HIS379 4.8 36.1 1.0 O A:HOH840 5.0 59.2 1.0 O A:ARG484 5.0 35.0 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