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Fluorine in PDB 4p2h: Structure of Human Dna Polymerase Complexed with N7MG in the Template Opposite to Incoming Non-Hydrolyzable Ttp with Manganese in the Active Site

Enzymatic activity of Structure of Human Dna Polymerase Complexed with N7MG in the Template Opposite to Incoming Non-Hydrolyzable Ttp with Manganese in the Active Site

All present enzymatic activity of Structure of Human Dna Polymerase Complexed with N7MG in the Template Opposite to Incoming Non-Hydrolyzable Ttp with Manganese in the Active Site:
2.7.7.7;

Protein crystallography data

The structure of Structure of Human Dna Polymerase Complexed with N7MG in the Template Opposite to Incoming Non-Hydrolyzable Ttp with Manganese in the Active Site, PDB code: 4p2h was solved by S.Lee, M.C.Koag, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.79 / 1.99
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.767, 79.167, 54.982, 90.00, 106.18, 90.00
R / Rfree (%) 20.4 / 25

Other elements in 4p2h:

The structure of Structure of Human Dna Polymerase Complexed with N7MG in the Template Opposite to Incoming Non-Hydrolyzable Ttp with Manganese in the Active Site also contains other interesting chemical elements:

Manganese (Mn) 2 atoms
Sodium (Na) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structure of Human Dna Polymerase Complexed with N7MG in the Template Opposite to Incoming Non-Hydrolyzable Ttp with Manganese in the Active Site (pdb code 4p2h). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total only one binding site of Fluorine was determined in the Structure of Human Dna Polymerase Complexed with N7MG in the Template Opposite to Incoming Non-Hydrolyzable Ttp with Manganese in the Active Site, PDB code: 4p2h:

Fluorine binding site 1 out of 1 in 4p2h

Go back to Fluorine Binding Sites List in 4p2h
Fluorine binding site 1 out of 1 in the Structure of Human Dna Polymerase Complexed with N7MG in the Template Opposite to Incoming Non-Hydrolyzable Ttp with Manganese in the Active Site


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of Human Dna Polymerase Complexed with N7MG in the Template Opposite to Incoming Non-Hydrolyzable Ttp with Manganese in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
T:F6

b:62.9
occ:1.00
 F1' T:FMG6 0.0 62.9 1.0
C2' T:FMG6 1.4 60.8 1.0
C3' T:FMG6 2.3 63.8 1.0
C1' T:FMG6 2.5 59.8 1.0
C8 T:FMG6 2.7 57.3 1.0
N9 T:FMG6 2.8 57.6 1.0
C4' T:FMG6 3.1 60.5 1.0
O4' T:FMG6 3.2 64.8 1.0
C5' T:FMG6 3.3 54.4 1.0
O5' T:FMG6 3.3 48.5 1.0
O3' T:FMG6 3.6 61.5 1.0
OP2 T:DT7 3.7 75.2 1.0
C7 T:DT7 3.7 46.8 1.0
C5 T:DT7 3.9 44.0 1.0
N7 T:FMG6 4.0 55.7 1.0
C6 T:DT7 4.1 46.2 1.0
C4 T:FMG6 4.1 52.3 1.0
P T:DT7 4.2 76.8 1.0
C5 T:FMG6 4.7 50.7 1.0
C4 T:DT7 4.7 40.3 1.0
P T:FMG6 4.9 49.2 1.0
CM7 T:FMG6 4.9 48.0 1.0
N1 T:DT7 5.0 45.1 1.0

Reference:

M.C.Koag, Y.Kou, H.Ouzon-Shubeita, S.Lee. Transition-State Destabilization Reveals How Human Dna Polymerase Beta Proceeds Across the Chemically Unstable Lesion N7-Methylguanine. Nucleic Acids Res. V. 42 8755 2014.
ISSN: ESSN 1362-4962
PubMed: 24966350
DOI: 10.1093/NAR/GKU554
Page generated: Sun Dec 13 12:10:12 2020

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