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Magnesium in PDB 7m4g: Dna Polymerase Lambda, Dctp:at MG2+ Product State Ternary Complex, 960 Min

Enzymatic activity of Dna Polymerase Lambda, Dctp:at MG2+ Product State Ternary Complex, 960 Min

All present enzymatic activity of Dna Polymerase Lambda, Dctp:at MG2+ Product State Ternary Complex, 960 Min:
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase Lambda, Dctp:at MG2+ Product State Ternary Complex, 960 Min, PDB code: 7m4g 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) 39.93 / 1.88
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 55.997, 62.235, 141.114, 90, 90, 90
R / Rfree (%) 21.2 / 24

Other elements in 7m4g:

The structure of Dna Polymerase Lambda, Dctp:at MG2+ Product State Ternary Complex, 960 Min also contains other interesting chemical elements:

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, 960 Min (pdb code 7m4g). 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, 960 Min, PDB code: 7m4g:

Magnesium binding site 1 out of 1 in 7m4g

Go back to Magnesium Binding Sites List in 7m4g
Magnesium binding site 1 out of 1 in the Dna Polymerase Lambda, Dctp:at MG2+ Product State Ternary Complex, 960 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, 960 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg604

b:70.3
occ:1.00
 OD2 A:ASP429 1.8 83.3 1.0
OD1 A:ASP427 2.1 61.9 1.0
OP1 P:DC7 2.2 57.7 1.0
O3 A:PO4609 2.7 67.6 0.9
CG A:ASP429 2.9 70.9 1.0
O1 A:PO4609 3.1 65.2 0.9
CG A:ASP427 3.2 66.1 1.0
OD1 A:ASP429 3.3 70.6 1.0
P A:PO4609 3.3 96.0 0.9
P P:DC7 3.6 51.4 1.0
O2 A:PO4609 3.7 50.5 0.9
OD2 A:ASP427 3.7 81.9 1.0
O A:ASP427 3.7 72.3 1.0
NA A:NA602 3.7 46.0 1.0
CA A:GLY416 3.9 48.6 1.0
C5' P:DC7 4.0 58.2 1.0
O5' P:DC7 4.1 54.4 1.0
CB A:ASP429 4.2 54.3 1.0
C A:ASP427 4.2 68.9 1.0
CB A:ASP427 4.4 46.8 1.0
O A:HOH726 4.4 40.2 1.0
OP2 P:DC7 4.5 55.0 1.0
N A:ASP429 4.6 35.6 1.0
O A:HOH764 4.6 41.1 1.0
N A:SER417 4.6 38.9 1.0
O3' P:DC6 4.6 55.0 1.0
N A:GLY416 4.7 38.8 1.0
CA A:ASP427 4.7 50.0 1.0
N A:ASP427 4.8 49.8 1.0
O4 A:PO4609 4.8 69.5 0.9
N A:VAL428 4.9 35.6 1.0
C A:GLY416 4.9 45.1 1.0
CA A:ASP429 5.0 35.5 1.0
C A:VAL428 5.0 36.9 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 23:42:14 2024

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