Fluorine in PDB 6lwl: Crystal Structure of Human NEIL1(R242) Bound to Duplex Dna Containing 2'-Fluoro-2'-Deoxy-5,6-Dihydrouridine

All present enzymatic activity of Crystal Structure of Human NEIL1(R242) Bound to Duplex Dna Containing 2'-Fluoro-2'-Deoxy-5,6-Dihydrouridine:
4.2.99.18;

The structure of Crystal Structure of Human NEIL1(R242) Bound to Duplex Dna Containing 2'-Fluoro-2'-Deoxy-5,6-Dihydrouridine, PDB code: 6lwl was solved by M.H.Liu, J.Zhang, C.X.Zhu, X.X.Zhang, Y.Q.Gao, C.Q.Yi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.08 / 2.55
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	73.772, 108.653, 170.583, 90, 90, 90
R / Rfree (%)	20.9 / 25.3

The binding sites of Fluorine atom in the Crystal Structure of Human NEIL1(R242) Bound to Duplex Dna Containing 2'-Fluoro-2'-Deoxy-5,6-Dihydrouridine (pdb code 6lwl). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Structure of Human NEIL1(R242) Bound to Duplex Dna Containing 2'-Fluoro-2'-Deoxy-5,6-Dihydrouridine, PDB code: 6lwl:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Crystal Structure of Human NEIL1(R242) Bound to Duplex Dna Containing 2'-Fluoro-2'-Deoxy-5,6-Dihydrouridine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Human NEIL1(R242) Bound to Duplex Dna Containing 2'-Fluoro-2'-Deoxy-5,6-Dihydrouridine within 5.0Å range: probe atom residue distance (Å) B Occ B:F7 b:67.4 occ:1.00 F2 B:EW37 0.0 67.4 1.0 C2' B:EW37 1.3 67.8 1.0 C1' B:EW37 2.2 74.0 1.0 N A:PRO2 2.4 57.3 1.0 C3' B:EW37 2.4 66.2 1.0 O3' B:EW37 2.7 60.2 1.0 N1 B:EW37 2.9 78.0 1.0 CD A:PRO2 3.3 55.5 1.0 CA A:PRO2 3.4 55.1 1.0 O4' B:EW37 3.4 71.5 1.0 C4' B:EW37 3.5 66.2 1.0 C6 B:EW37 3.5 78.2 1.0 O A:MET81 3.6 53.5 1.0 C2 B:EW37 3.6 81.0 1.0 C5' B:DG8 3.8 58.1 1.0 CA A:MET81 3.9 57.9 1.0 O2 B:EW37 3.9 77.2 1.0 O A:GLY80 4.0 51.8 1.0 O5' B:DG8 4.0 55.2 1.0 SD A:MET81 4.0 66.9 1.0 P B:DG8 4.0 56.4 1.0 C A:PRO2 4.1 52.6 1.0 C A:MET81 4.1 57.8 1.0 O A:PRO2 4.1 47.5 1.0 C5' B:EW37 4.3 65.4 1.0 CE A:MET81 4.3 64.8 1.0 CG A:PRO2 4.6 55.8 1.0 N3 B:EW37 4.6 87.6 1.0 C5 B:EW37 4.6 81.6 1.0 CB A:PRO2 4.7 53.9 1.0 CB A:MET81 4.7 61.3 1.0 C A:GLY80 4.8 53.0 1.0 O5' B:EW37 4.8 61.2 1.0 O A:HOH305 4.8 47.0 1.0 N A:MET81 4.8 58.8 1.0 OP1 B:DG8 4.8 55.0 1.0 OP2 B:DG8 4.9 53.8 1.0 CG A:MET81 4.9 64.0 1.0

Fluorine binding site 2 out of 3 in the Crystal Structure of Human NEIL1(R242) Bound to Duplex Dna Containing 2'-Fluoro-2'-Deoxy-5,6-Dihydrouridine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Human NEIL1(R242) Bound to Duplex Dna Containing 2'-Fluoro-2'-Deoxy-5,6-Dihydrouridine within 5.0Å range: probe atom residue distance (Å) B Occ E:F7 b:71.4 occ:1.00 F2 E:EW37 0.0 71.4 1.0 C2' E:EW37 1.3 74.4 1.0 C1' E:EW37 2.2 81.7 1.0 N D:PRO2 2.2 55.3 1.0 C3' E:EW37 2.4 71.3 1.0 O3' E:EW37 2.7 66.8 1.0 N1 E:EW37 2.9 95.5 1.0 CD D:PRO2 3.1 56.1 1.0 O D:MET81 3.4 55.8 1.0 O4' E:EW37 3.4 78.4 1.0 CA D:PRO2 3.4 53.0 1.0 C4' E:EW37 3.5 73.9 1.0 C6 E:EW37 3.6 103.3 1.0 C2 E:EW37 3.6 104.2 1.0 C5' E:DG8 3.7 59.8 1.0 CA D:MET81 3.8 49.3 1.0 O2 E:EW37 3.9 98.0 1.0 O D:GLY80 3.9 47.4 1.0 SD D:MET81 3.9 60.9 1.0 C D:MET81 3.9 49.0 1.0 P E:DG8 4.0 57.6 1.0 O5' E:DG8 4.1 62.5 1.0 C D:PRO2 4.1 50.7 1.0 O D:PRO2 4.2 49.9 1.0 C5' E:EW37 4.3 72.8 1.0 CG D:PRO2 4.4 53.2 1.0 CB D:PRO2 4.6 52.9 1.0 C5 E:EW37 4.6 110.3 1.0 N3 E:EW37 4.7 111.4 1.0 C D:GLY80 4.7 44.4 1.0 CB D:MET81 4.7 53.6 1.0 N D:MET81 4.7 48.3 1.0 OP2 E:DG8 4.8 62.3 1.0 OP1 E:DG8 4.9 59.8 1.0 O5' E:EW37 4.9 69.9 1.0 CG D:MET81 4.9 57.0 1.0

Fluorine binding site 3 out of 3 in the Crystal Structure of Human NEIL1(R242) Bound to Duplex Dna Containing 2'-Fluoro-2'-Deoxy-5,6-Dihydrouridine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Human NEIL1(R242) Bound to Duplex Dna Containing 2'-Fluoro-2'-Deoxy-5,6-Dihydrouridine within 5.0Å range: probe atom residue distance (Å) B Occ H:F7 b:112.0 occ:1.00 F2 H:EW37 0.0 112.0 1.0 C2' H:EW37 1.3 111.2 1.0 N G:PRO2 2.1 101.3 1.0 C1' H:EW37 2.3 115.4 1.0 C3' H:EW37 2.4 108.1 1.0 O3' H:EW37 2.7 106.2 1.0 CD G:PRO2 2.9 101.8 1.0 N1 H:EW37 2.9 120.9 1.0 CA G:PRO2 3.2 100.6 1.0 O4' H:EW37 3.5 111.9 1.0 C4' H:EW37 3.5 107.5 1.0 C6 H:EW37 3.6 121.7 1.0 C2 H:EW37 3.6 126.8 1.0 O G:MET81 3.7 91.7 1.0 C5' H:DG8 3.8 103.7 1.0 O2 H:EW37 3.9 128.4 1.0 O G:GLY80 4.0 90.8 1.0 O5' H:DG8 4.0 102.6 1.0 C G:PRO2 4.0 96.7 1.0 P H:DG8 4.0 103.5 1.0 CA G:MET81 4.0 92.4 1.0 CG G:PRO2 4.0 102.6 1.0 CE G:MET81 4.1 99.0 1.0 O G:PRO2 4.1 92.9 1.0 SD G:MET81 4.1 100.4 1.0 C G:MET81 4.2 91.1 1.0 CB G:PRO2 4.3 103.4 1.0 C5' H:EW37 4.3 106.0 1.0 C5 H:EW37 4.4 125.2 1.0 N3 H:EW37 4.4 129.2 1.0 C4 H:EW37 4.8 129.2 1.0 OP1 H:DG8 4.8 105.7 1.0 C G:GLY80 4.8 90.8 1.0 O5' H:EW37 4.8 104.8 1.0 OP2 H:DG8 4.9 103.3 1.0 CB G:MET81 4.9 95.5 1.0 N G:MET81 4.9 92.5 1.0 N G:GLU3 5.0 93.3 1.0

M.Liu, J.Zhang, C.Zhu, X.Zhang, W.Xiao, Y.Yan, L.Liu, H.Zhang, Y.Q.Gao, C.Yi. Dna Repair Glycosylase HNEIL1 Triages Damaged Bases Via Competing Interaction Modes. To Be Published.