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Fluorine in PDB 4yn4: Structure of Human Dna Polymerase Beta Complexed with N7BG in the Template Opposite to Incoming Non-Hydrolyzable Dttp with Manganese in the Active Site

Enzymatic activity of Structure of Human Dna Polymerase Beta Complexed with N7BG in the Template Opposite to Incoming Non-Hydrolyzable Dttp with Manganese in the Active Site

All present enzymatic activity of Structure of Human Dna Polymerase Beta Complexed with N7BG in the Template Opposite to Incoming Non-Hydrolyzable Dttp with Manganese in the Active Site:
2.7.7.7;

Protein crystallography data

The structure of Structure of Human Dna Polymerase Beta Complexed with N7BG in the Template Opposite to Incoming Non-Hydrolyzable Dttp with Manganese in the Active Site, PDB code: 4yn4 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) 19.80 / 2.24
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.774, 79.179, 55.031, 90.00, 106.53, 90.00
R / Rfree (%) 20.3 / 25.5

Other elements in 4yn4:

The structure of Structure of Human Dna Polymerase Beta Complexed with N7BG in the Template Opposite to Incoming Non-Hydrolyzable Dttp 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 Beta Complexed with N7BG in the Template Opposite to Incoming Non-Hydrolyzable Dttp with Manganese in the Active Site (pdb code 4yn4). 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 Beta Complexed with N7BG in the Template Opposite to Incoming Non-Hydrolyzable Dttp with Manganese in the Active Site, PDB code: 4yn4:

Fluorine binding site 1 out of 1 in 4yn4

Go back to Fluorine Binding Sites List in 4yn4
Fluorine binding site 1 out of 1 in the Structure of Human Dna Polymerase Beta Complexed with N7BG in the Template Opposite to Incoming Non-Hydrolyzable Dttp 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 Beta Complexed with N7BG in the Template Opposite to Incoming Non-Hydrolyzable Dttp with Manganese in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
T:F6

b:59.6
occ:1.00
 F1' T:7BG6 0.0 59.6 1.0
C2' T:7BG6 1.1 70.2 1.0
C3' T:7BG6 2.1 73.8 1.0
C1' T:7BG6 2.2 79.3 1.0
C4' T:7BG6 2.6 69.1 1.0
C5' T:7BG6 2.6 60.7 1.0
O4' T:7BG6 2.6 80.3 1.0
N9 T:7BG6 2.8 83.4 1.0
C8 T:7BG6 3.1 81.0 1.0
O3' T:7BG6 3.2 73.7 1.0
O5' T:7BG6 3.4 47.8 1.0
C4 T:7BG6 4.1 80.0 1.0
OP2 T:DT7 4.2 63.3 1.0
C13 T:7BG6 4.2 83.6 1.0
O T:HOH110 4.3 59.4 1.0
C12 T:7BG6 4.3 77.4 1.0
P T:DT7 4.3 81.0 1.0
O3' T:DC5 4.3 38.3 1.0
P T:7BG6 4.4 46.8 1.0
N7 T:7BG6 4.4 75.8 1.0
C2' T:DC5 4.6 32.8 1.0
C3' T:DC5 4.6 31.6 1.0
OP1 T:7BG6 4.8 47.1 1.0
N3 T:7BG6 4.8 74.4 1.0
C14 T:7BG6 4.8 79.2 1.0
C5 T:7BG6 4.9 74.5 1.0
C7 T:DT7 4.9 53.9 1.0
C11 T:7BG6 4.9 76.9 1.0
OP1 T:DT7 5.0 69.2 1.0

Reference:

Y.Kou, M.C.Koag, S.Lee. Structural and Kinetic Studies of the Effect of Guanine-N7 Alkylation and Metal Cofactors on Dna Replication. Biochemistry 2018.
ISSN: ISSN 1520-4995
PubMed: 29957995
DOI: 10.1021/ACS.BIOCHEM.8B00331
Page generated: Thu Aug 1 07:04:19 2024

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