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Magnesium in PDB 7m4f: Dna Polymerase Lambda, Dctp:at MG2+ Product State Ternary Complex, 300 Min

Enzymatic activity of Dna Polymerase Lambda, Dctp:at MG2+ Product State Ternary Complex, 300 Min

All present enzymatic activity of Dna Polymerase Lambda, Dctp:at MG2+ Product State Ternary Complex, 300 Min:
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase Lambda, Dctp:at MG2+ Product State Ternary Complex, 300 Min, PDB code: 7m4f 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) 36.13 / 1.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 55.869, 62.065, 142.087, 90, 90, 90
R / Rfree (%) 20.8 / 24.1

Other elements in 7m4f:

The structure of Dna Polymerase Lambda, Dctp:at MG2+ Product State Ternary Complex, 300 Min also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Sodium (Na) 3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Dna Polymerase Lambda, Dctp:at MG2+ Product State Ternary Complex, 300 Min (pdb code 7m4f). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Dna Polymerase Lambda, Dctp:at MG2+ Product State Ternary Complex, 300 Min, PDB code: 7m4f:

Magnesium binding site 1 out of 1 in 7m4f

Go back to Magnesium Binding Sites List in 7m4f
Magnesium binding site 1 out of 1 in the Dna Polymerase Lambda, Dctp:at MG2+ Product State Ternary Complex, 300 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+ Product State Ternary Complex, 300 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg604

b:44.5
occ:1.00
 OD1 A:ASP427 1.9 41.2 0.5
OD1 A:ASP427 2.0 47.3 0.5
O A:HOH702 2.0 42.0 1.0
OD2 A:ASP429 2.1 46.7 1.0
O21 A:PPV605 2.1 64.1 0.9
OP1 P:DC7 2.2 49.9 1.0
O22 A:PPV605 2.3 47.7 0.9
CG A:ASP427 3.0 39.1 0.5
CG A:ASP429 3.0 84.0 1.0
CG A:ASP427 3.1 59.8 0.5
P1 A:PPV605 3.2 53.5 0.5
OD1 A:ASP429 3.2 51.0 1.0
O31 A:PPV605 3.2 72.4 0.8
OD2 A:ASP427 3.3 63.0 0.5
NA A:NA601 3.4 44.1 1.0
P2 A:PPV605 3.5 59.1 0.5
P P:DC7 3.6 50.8 1.0
OD2 A:ASP427 3.6 36.3 0.5
OPP A:PPV605 3.9 55.0 0.9
O A:ASP427 3.9 39.9 0.5
O32 A:PPV605 4.0 42.1 0.9
C5' P:DC7 4.0 46.0 1.0
O5' P:DC7 4.2 46.0 1.0
CB A:ASP427 4.3 41.1 0.5
C A:ASP427 4.3 47.9 0.5
CA A:GLY416 4.3 50.0 1.0
CB A:ASP427 4.3 34.5 0.5
CB A:ASP429 4.4 45.8 1.0
O P:HOH113 4.4 41.8 0.5
C A:ASP427 4.5 48.4 0.5
O A:ASP427 4.5 42.4 0.5
O11 A:PPV605 4.5 40.6 0.7
OP2 P:DC7 4.6 67.3 1.0
O3' P:DC6 4.6 47.2 1.0
N A:ASP427 4.6 44.6 0.5
CA A:ASP427 4.7 42.5 0.5
N A:ASP429 4.7 35.6 1.0
N A:ASP427 4.7 41.8 0.5
CA A:ASP427 4.7 38.5 0.5
N A:SER417 4.8 36.4 1.0
O12 A:PPV605 4.8 70.1 0.9
N A:VAL428 4.9 42.3 1.0
C A:VAL428 5.0 35.0 1.0

Reference:

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
Page generated: Wed Oct 2 23:42:12 2024

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