Fluorine in PDB 6lwm: Crystal Structure of Human NEIL1(K242) Bound to Duplex Dna Containing 2'-Fluoro-2'-Deoxy-5,6-Dihydrouridine

All present enzymatic activity of Crystal Structure of Human NEIL1(K242) Bound to Duplex Dna Containing 2'-Fluoro-2'-Deoxy-5,6-Dihydrouridine:
4.2.99.18;

The structure of Crystal Structure of Human NEIL1(K242) Bound to Duplex Dna Containing 2'-Fluoro-2'-Deoxy-5,6-Dihydrouridine, PDB code: 6lwm 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)	39.45 / 2.67
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	73.693, 109.246, 170.868, 90, 90, 90
R / Rfree (%)	20.5 / 25.8

The binding sites of Fluorine atom in the Crystal Structure of Human NEIL1(K242) Bound to Duplex Dna Containing 2'-Fluoro-2'-Deoxy-5,6-Dihydrouridine (pdb code 6lwm). 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(K242) Bound to Duplex Dna Containing 2'-Fluoro-2'-Deoxy-5,6-Dihydrouridine, PDB code: 6lwm:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Crystal Structure of Human NEIL1(K242) 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(K242) 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:80.5 occ:1.00 F2 B:EW37 0.0 80.5 1.0 C2' B:EW37 1.3 83.0 1.0 N A:PRO2 2.2 63.8 1.0 C1' B:EW37 2.4 91.9 1.0 C3' B:EW37 2.4 78.0 1.0 O3' B:EW37 2.8 72.8 1.0 CD A:PRO2 2.9 61.4 1.0 N1 B:EW37 3.2 101.5 1.0 CA A:PRO2 3.5 60.0 1.0 O A:HOH468 3.5 77.7 1.0 O4' B:EW37 3.5 86.3 1.0 C4' B:EW37 3.5 79.1 1.0 C6 B:EW37 3.7 102.9 1.0 O A:MET81 3.7 60.0 1.0 C5' B:DG8 3.8 64.3 1.0 SD A:MET81 3.9 69.8 1.0 CA A:MET81 4.0 63.6 1.0 O5' B:DG8 4.0 65.0 1.0 C A:PRO2 4.0 54.7 1.0 O A:PRO2 4.1 52.4 1.0 P B:DG8 4.1 63.7 1.0 O A:GLY80 4.1 56.8 1.0 C A:MET81 4.1 62.4 1.0 CG A:PRO2 4.1 59.1 1.0 C2 B:EW37 4.2 105.2 1.0 C5' B:EW37 4.3 77.1 1.0 O2 B:EW37 4.3 113.9 1.0 CB A:PRO2 4.5 56.8 1.0 CE A:MET81 4.6 73.2 1.0 CB A:MET81 4.8 67.0 1.0 O5' B:EW37 4.8 73.0 1.0 OP1 B:DG8 4.9 63.4 1.0 O A:HOH404 4.9 55.4 1.0 N A:MET81 4.9 65.3 1.0 C A:GLY80 4.9 57.9 1.0 N A:GLU3 5.0 50.0 1.0

Fluorine binding site 2 out of 3 in the Crystal Structure of Human NEIL1(K242) 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(K242) 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:82.9 occ:1.00 F2 E:EW37 0.0 82.9 1.0 C2' E:EW37 1.4 85.2 1.0 N D:PRO2 2.2 63.0 1.0 C3' E:EW37 2.4 79.3 1.0 C1' E:EW37 2.4 94.0 1.0 O3' E:EW37 2.8 70.7 1.0 CD D:PRO2 2.9 63.1 1.0 N1 E:EW37 3.2 103.2 1.0 O D:MET81 3.5 49.5 1.0 O4' E:EW37 3.5 89.3 1.0 C4' E:EW37 3.5 84.2 1.0 CA D:PRO2 3.6 60.1 1.0 C6 E:EW37 3.7 106.0 1.0 C5' E:DG8 3.8 62.4 1.0 SD D:MET81 3.8 71.5 1.0 CA D:MET81 3.9 49.7 1.0 C D:MET81 4.0 48.9 1.0 O5' E:DG8 4.0 62.1 1.0 O D:GLY80 4.0 46.8 1.0 P E:DG8 4.1 60.8 1.0 C D:PRO2 4.2 58.7 1.0 O D:PRO2 4.2 56.0 1.0 C2 E:EW37 4.3 107.4 1.0 CG D:PRO2 4.3 61.6 1.0 C5' E:EW37 4.3 83.7 1.0 O2 E:EW37 4.4 106.2 1.0 CB D:PRO2 4.6 58.2 1.0 O5' E:EW37 4.8 78.0 1.0 N D:MET81 4.8 49.4 1.0 CB D:MET81 4.8 56.6 1.0 C D:GLY80 4.8 44.8 1.0 OP1 E:DG8 4.9 61.7 1.0

Fluorine binding site 3 out of 3 in the Crystal Structure of Human NEIL1(K242) 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(K242) 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:119.3 occ:1.00 F2 H:EW37 0.0 119.3 1.0 C2' H:EW37 1.4 117.6 1.0 N G:PRO2 2.1 122.8 1.0 C3' H:EW37 2.4 114.7 1.0 C1' H:EW37 2.4 121.8 1.0 CD G:PRO2 2.8 124.5 1.0 O3' H:EW37 2.8 112.5 1.0 N1 H:EW37 3.2 125.5 1.0 CA G:PRO2 3.4 120.6 1.0 O4' H:EW37 3.5 118.8 1.0 C4' H:EW37 3.5 115.1 1.0 O G:MET81 3.6 92.0 1.0 C6 H:EW37 3.7 125.5 1.0 C5' H:DG8 3.8 108.6 1.0 CE G:MET81 3.9 106.9 1.0 CA G:MET81 4.0 95.7 1.0 O5' H:DG8 4.0 108.0 1.0 O G:GLY80 4.0 93.5 1.0 C G:MET81 4.0 93.3 1.0 C G:PRO2 4.1 115.4 1.0 O G:PRO2 4.1 110.4 1.0 P H:DG8 4.1 108.9 1.0 SD G:MET81 4.1 107.4 1.0 CG G:PRO2 4.1 124.1 1.0 C2 H:EW37 4.2 128.2 1.0 O2 H:EW37 4.3 127.7 1.0 C5' H:EW37 4.3 113.2 1.0 CB G:PRO2 4.4 124.1 1.0 O5' H:EW37 4.8 111.3 1.0 C G:GLY80 4.8 94.3 1.0 N G:MET81 4.9 97.3 1.0 OP1 H:DG8 4.9 110.8 1.0 CB G:MET81 4.9 99.5 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.